Fri May 17 21:05:57 UTC 2024 I: starting to build apbs/unstable/arm64 on jenkins on '2024-05-17 21:05' Fri May 17 21:05:57 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/43435/console.log Fri May 17 21:05:57 UTC 2024 I: Downloading source for unstable/apbs=3.4.1-5.1 --2024-05-17 21:05:58-- http://deb.debian.org/debian/pool/main/a/apbs/apbs_3.4.1-5.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2706 (2.6K) [text/prs.lines.tag] Saving to: ‘apbs_3.4.1-5.1.dsc’ 0K .. 100% 318M=0s 2024-05-17 21:05:58 (318 MB/s) - ‘apbs_3.4.1-5.1.dsc’ saved [2706/2706] Fri May 17 21:05:58 UTC 2024 I: apbs_3.4.1-5.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: apbs Binary: apbs, python3-apbslib, libapbs-dev, libapbs3t64, apbs-data, apbs-doc, libfetk-dev, libfetk1.9t64 Architecture: any all Version: 3.4.1-5.1 Maintainer: Debichem Team Uploaders: Michael Banck Homepage: http://www.poissonboltzmann.org/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debichem-team/apbs Vcs-Git: https://salsa.debian.org/debichem-team/apbs.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev Build-Depends-Indep: libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml Package-List: apbs deb science optional arch=any apbs-data deb science optional arch=all apbs-doc deb science optional arch=all libapbs-dev deb libdevel optional arch=any libapbs3t64 deb libs optional arch=any libfetk-dev deb libdevel optional arch=any libfetk1.9t64 deb libs optional arch=any python3-apbslib deb python optional arch=any Checksums-Sha1: 584fd36dc1424cb22fd8846f1cf2c7ead60ce0c6 85806314 apbs_3.4.1.orig.tar.gz 71c1bb5c7227576d6e46106c1c6829b7c9254aa5 20427140 apbs_3.4.1-5.1.debian.tar.xz Checksums-Sha256: 644e6246fd37c9dd4172fc7be1763337082ab8584dbcd53e738c831b62c89bb2 85806314 apbs_3.4.1.orig.tar.gz 7d7c55bec3615528afa07edac9ff2a1d532a7728c3aee91fcdca2a4d0316893b 20427140 apbs_3.4.1-5.1.debian.tar.xz Files: 5d2af7c3592f8c410a5df39887361520 85806314 apbs_3.4.1.orig.tar.gz 06812a5460841379cd5b22c7c81791fb 20427140 apbs_3.4.1-5.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEErEg/aN5yj0PyIC/KVo0w8yGyEz0FAmXeh+oSHHZvcmxvbkBk ZWJpYW4ub3JnAAoJEFaNMPMhshM99HMP/jo0ZeW/HEQGear3IyL7hIKGLn0Flxc0 qjLPfFwVky3/6hpQ1DqimqzqOgCWGrgO3SIqaSFwBmQrpXOz3BYz0z/XpsU/gNFt 4byQAWgOAp1o84DKviB/BorZQy9Q0YHawSZvK48b8AS4G6QwxWwqNTGS5fX7ljrO TyM+87AhWs7r4u6ubuwxaoe5eidcibkhnjCIy6CkO/gzFVjQugH4h1UeBWni2Mse YT1uR4hZ+a4tLBfjIvtZPU/kWkUt1MZBtGIGMH9UQC8N6D0JzrUMLAuzAVVDco/J HJDt6Ja2zkP6DRJG5foN3AfwSrBUQguJvxQGexq1HfYYMyAhI7H18Txn5ZWGCTM6 /rwnXH5ONzSH55lBQKut/SCw4xZw/HD9JG+RiBbX5iw25Lb0G1EvLqLSBHd+tnTi UetP5meoh1cKeEbBkmeebKyLOlj520DjF4NeoPItFMBvVSGiJy9eAwXlMqM3IzxM FVVHVubXmF+/XiPWlQv8qgcEaDHH6lX1+4nLeGgXF8dCAV0b/1fRTmkUcHm0YhbI goc+RFzfbPw0Gsi7u6CG5v30QEaDixT2ERZAZ9LQ3co5hmOaYhN1qVfhha0BmRSU sJdd5alspGg8CIHpOKTDL5oX0/tIZjbIXRpYwusDV5lgiVwI57JCBAVIr2tSorNY ITqetwnUeiXQ =Bm/7 -----END PGP SIGNATURE----- Fri May 17 21:05:58 UTC 2024 I: Checking whether the package is not for us Fri May 17 21:05:58 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Fri May 17 21:05:58 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Fri May 17 21:30:41 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 19 15:29:04 -12 2025 I: pbuilder-time-stamp: 1750390144 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [apbs_3.4.1-5.1.dsc] I: copying [./apbs_3.4.1.orig.tar.gz] I: copying [./apbs_3.4.1-5.1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Feb 28 01:10:02 2024 gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "vorlon@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-5.1.dsc: no acceptable signature found dpkg-source: info: extracting apbs in apbs-3.4.1 dpkg-source: info: unpacking apbs_3.4.1.orig.tar.gz dpkg-source: info: unpacking apbs_3.4.1-5.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying wrong-path-for-interpreter.patch dpkg-source: info: applying debian_testfiles.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying shared_library_soname.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying cmake.patch dpkg-source: info: applying docs.patch dpkg-source: info: applying open-U-obsolete.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2021122/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='36f187352bb44d5cb0b426b8d71800b6' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2021122' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/pbuilderrc_pU3P --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/b1 --logfile b1/build.log apbs_3.4.1-5.1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 19 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2021122/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19764 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libmaloc-dev; however: Package libmaloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libsuitesparse-dev; however: Package libsuitesparse-dev is not installed. pbuilder-satisfydepends-dummy depends on libsuperlu-dev; however: Package libsuperlu-dev is not installed. pbuilder-satisfydepends-dummy depends on libtirpc-dev; however: Package libtirpc-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx | sphinx; however: Package python3-sphinx is not installed. Package sphinx is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-aarch64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamd3{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbsd0{a} libbtf2{a} libcamd3{a} libcbor0.10{a} libccolamd3{a} libcholmod5{a} libcolamd3{a} libcom-err2{a} libcurl4t64{a} libcxsparse4{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libklu2{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldl3{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmaloc-dev{a} libmaloc1{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libparu0{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} librbio4{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libspex3{a} libspqr4{a} libssh2-1t64{a} libsub-override-perl{a} libsuitesparse-dev{a} libsuitesparse-mongoose3{a} libsuitesparseconfig7{a} libsuperlu-dev{a} libsuperlu6{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libumfpack6{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libyaml-0-2{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} pybind11-dev{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-installer{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pybind11{a} python3-pygments{a} python3-pyproject-hooks{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-toml{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} swig{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libgraphblas-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libsasl2-modules lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 218 newly installed, 0 to remove and 0 not upgraded. Need to get 157 MB of archives. After unpacking 708 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.1-1 [93.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-1.2 [27.2 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.14.0-1+b2 [73.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 38 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:9.7p1-5 [902 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.2-2 [321 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.7.1-5 [412 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-4 [142 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.29.3-1 [2167 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.29.3-1+b2 [9058 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 70 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240422 [107 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.1.0-1 [361 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libgfortran-13-dev arm64 13.2.0-25 [401 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-25 [8827 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 gfortran-13 arm64 13.2.0-25 [12.8 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.7.0-0.3 [56.5 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [165 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 50.0-2+b1 [58.2 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 50.0-2+b1 [315 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-12 [21.3 MB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b1 [12.1 MB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libsuitesparseconfig7 arm64 1:7.7.0+dfsg-2 [22.3 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libamd3 arm64 1:7.7.0+dfsg-2 [36.5 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 99 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1 [21.4 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libhsakmt1 arm64 5.7.0-1 [57.6 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 5.7.1-2 [276 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libamdhip64-5 arm64 5.7.1-3 [8698 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libarpack2t64 arm64 3.9.1-1.1+b1 [81.4 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.0-3 [98.2 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.0-3 [3584 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libarpack2-dev arm64 3.9.1-1.1+b1 [98.2 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libbtf2 arm64 1:7.7.0+dfsg-2 [23.0 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libcamd3 arm64 1:7.7.0+dfsg-2 [33.3 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libccolamd3 arm64 1:7.7.0+dfsg-2 [36.1 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libcolamd3 arm64 1:7.7.0+dfsg-2 [29.9 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libcholmod5 arm64 1:7.7.0+dfsg-2 [507 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libcxsparse4 arm64 1:7.7.0+dfsg-2 [73.7 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [169 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [125 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [102 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [54.3 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [60.3 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-8.1+b3 [303 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 50.0-2+b1 [66.6 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 1.17.0-3+b1 [479 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.10.0-1+b1 [140 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.18-1 [37.4 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.4.7-7+b1 [165 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.10.0-1+b1 [234 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b1 [51.1 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-1 [143 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1 [13.8 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b1 [39.3 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.10.0-1+b1 [18.0 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.7.0-0.3 [101 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.7.0-0.3 [197 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 50.0-2+b1 [626 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libklu2 arm64 1:7.7.0+dfsg-2 [76.3 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libldl3 arm64 1:7.7.0+dfsg-2 [22.7 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libmaloc1 arm64 1.5-1+b1 [76.9 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libmaloc-dev arm64 1.5-1+b1 [122 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.15-4 [19.2 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 5.0.2-3 [580 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.16.0+ds-5 [938 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libopenmpi3t64 arm64 4.1.6-13.3 [2170 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libpmix-dev arm64 5.0.2-3 [3921 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 4.1.6-13.3 [225 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 4.1.6-13.3 [972 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libumfpack6 arm64 1:7.7.0+dfsg-2 [214 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libparu0 arm64 1:7.7.0+dfsg-2 [56.5 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libpython3.11t64 arm64 3.11.9-1 [1814 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libpython3.11-dev arm64 3.11.9-1 [4358 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.11.8-1 [9564 B] Get: 169 http://deb.debian.org/debian unstable/main arm64 librbio4 arm64 1:7.7.0+dfsg-2 [36.5 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libspex3 arm64 1:7.7.0+dfsg-2 [51.7 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libspqr4 arm64 1:7.7.0+dfsg-2 [122 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libsuitesparse-mongoose3 arm64 1:7.7.0+dfsg-2 [42.1 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libsuitesparse-dev arm64 1:7.7.0+dfsg-2 [1253 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libsuperlu6 arm64 6.0.1+dfsg1-1+b1 [141 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libsuperlu-dev arm64 6.0.1+dfsg1-1+b1 [21.8 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [192 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 mpi-default-dev arm64 1.15 [3152 B] Get: 181 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 pybind11-dev all 2.11.1-2 [191 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.0.0-2 [10.6 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.1-1 [34.1 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 pybuild-plugin-pyproject all 6.20240422 [11.1 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.14.0-1 [111 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2023.11.17-1 [155 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3.11-dev arm64 3.11.9-1 [501 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.11.8-1 [26.1 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-roman all 3.3-3 [9880 B] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.6-2 [37.0 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1 [14.6 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.11.1-2 [201 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.16.0-6 [16.3 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.31.0+dfsg-2 [68.7 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.2.6-7 [702 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.2.6-7 [552 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 216 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.1-2 [153 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 swig arm64 4.2.1-1 [1350 kB] Fetched 157 MB in 2s (97.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19764 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. 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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc-dev:arm64. Preparing to unpack .../164-libtirpc-dev_1.3.4+ds-1.3_arm64.deb ... Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../165-libyaml-0-2_0.2.5-1+b1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1+b1) ... Selecting previously unselected package mpi-default-dev. Preparing to unpack .../166-mpi-default-dev_1.15_arm64.deb ... Unpacking mpi-default-dev (1.15) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../167-pkgconf-bin_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... 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Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libuv1t64:arm64 (1.48.0-4) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.61.0-1+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libcom-err2:arm64 (1.47.1~rc2-1) ... Setting up libldl3:arm64 (1:7.7.0+dfsg-2) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jun 20 03:30:37 UTC 2025. Universal Time is now: Fri Jun 20 03:30:37 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libbtf2:arm64 (1:7.7.0+dfsg-2) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1+b2) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up libmunge2:arm64 (0.5.15-4) ... Setting up libexpat1-dev:arm64 (2.6.2-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libproc2-0:arm64 (2:4.0.4-4) ... Setting up libhwloc15:arm64 (2.10.0-1+b1) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:arm64 (1.9.5-6+b2) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libltdl7:arm64 (2.4.7-7+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:arm64 (14.1.0-1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libnuma1:arm64 (2.0.18-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:arm64 (2.3.2-1+b1) ... Setting up librhash0:arm64 (1.4.3-3+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:arm64 (3.7.0-0.3) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up libsuitesparseconfig7:arm64 (1:7.7.0+dfsg-2) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.29.3-1) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:arm64 (1.14.0-1+b2) ... Setting up libgfortran-13-dev:arm64 (13.2.0-25) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up libblas-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libarpack2t64:arm64 (3.9.1-1.1+b1) ... Setting up libamd3:arm64 (1:7.7.0+dfsg-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:arm64 (1:7.7.0+dfsg-2) ... Setting up libspex3:arm64 (1:7.7.0+dfsg-2) ... Setting up libsuitesparse-mongoose3:arm64 (1:7.7.0+dfsg-2) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libedit2:arm64 (3.1-20230828-1+b1) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libcxsparse4:arm64 (1:7.7.0+dfsg-2) ... Setting up gfortran-13-aarch64-linux-gnu (13.2.0-25) ... Setting up libsuperlu6:arm64 (6.0.1+dfsg1-1+b1) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up libcamd3:arm64 (1:7.7.0+dfsg-2) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-7+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:arm64 (1:17.0.6-12) ... Setting up gfortran-13 (13.2.0-25) ... Setting up librbio4:arm64 (1:7.7.0+dfsg-2) ... Setting up liblapack-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up pkg-config:arm64 (1.8.1-1+b2) ... Setting up libjs-sphinxdoc (7.2.6-7) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libccolamd3:arm64 (1:7.7.0+dfsg-2) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:arm64 (2.4.120-2) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libhwloc-dev:arm64 (2.10.0-1+b1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libsuperlu-dev:arm64 (6.0.1+dfsg1-1+b1) ... Setting up libarchive13t64:arm64 (3.7.2-2) ... Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... Setting up libmaloc1 (1.5-1+b1) ... Setting up libibverbs1:arm64 (50.0-2+b1) ... Setting up libcholmod5:arm64 (1:7.7.0+dfsg-2) ... Setting up libarpack2-dev:arm64 (3.9.1-1.1+b1) ... Setting up libcurl4t64:arm64 (8.7.1-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up ibverbs-providers:arm64 (50.0-2+b1) ... Setting up libspqr4:arm64 (1:7.7.0+dfsg-2) ... Setting up openssh-client (1:9.7p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libpython3.11t64:arm64 (3.11.9-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:arm64 (535.171.04-1) ... Setting up libnl-route-3-dev:arm64 (3.7.0-0.3) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ... Setting up libklu2:arm64 (1:7.7.0+dfsg-2) ... Setting up libpython3.11-dev:arm64 (3.11.9-1) ... Setting up sphinx-common (7.2.6-7) ... Setting up libevent-dev (2.1.12-stable-8.1+b3) ... Setting up libumfpack6:arm64 (1:7.7.0+dfsg-2) ... Setting up cmake (3.29.3-1+b2) ... Setting up librdmacm1t64:arm64 (50.0-2+b1) ... Setting up libmaloc-dev (1.5-1+b1) ... Setting up libhsakmt1:arm64 (5.7.0-1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up libfabric1:arm64 (1.17.0-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libpython3-dev:arm64 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up libparu0:arm64 (1:7.7.0+dfsg-2) ... Setting up python3 (3.11.8-1) ... Setting up libibverbs-dev:arm64 (50.0-2+b1) ... Setting up libhwloc-plugins:arm64 (2.10.0-1+b1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-wheel (0.43.0-1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.6-2) ... Setting up libpmix2t64:arm64 (5.0.2-3) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up python3-build (1.2.1-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up libpmix-dev:arm64 (5.0.2-3) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up libsuitesparse-dev:arm64 (1:7.7.0+dfsg-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-requests (2.31.0+dfsg-2) ... Setting up dh-python (6.20240422) ... Setting up libucx0:arm64 (1.16.0+ds-5) ... Setting up pybuild-plugin-pyproject (6.20240422) ... Setting up libopenmpi3t64:arm64 (4.1.6-13.3) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:arm64 (4.1.6-13.3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up mpi-default-dev (1.15) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-7) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.34-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/apbs-3.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../apbs_3.4.1-5.1_source.changes dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 3.4.1-5.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steve Langasek dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules build dh build --with python3,sphinxdoc --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=None \ -DAPBS_STATIC_BUILD=Off \ -DBUILD_DOC=Off -DBUILD_TOOLS=On \ -DENABLE_OPENMP=On -DENABLE_MPI=On \ -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On \ -DENABLE_READLINE=Off -DENABLE_ZLIB=On \ -DFETCHCONTENT_SOURCE_DIR_FETK=/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk \ -DRPC_CFLAGS=-I/usr/include/tirpc \ -DBUILD_MALOC=Off cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_BUILD_TYPE=None -DAPBS_STATIC_BUILD=Off -DBUILD_DOC=Off -DBUILD_TOOLS=On -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On -DENABLE_READLINE=Off -DENABLE_ZLIB=On -DFETCHCONTENT_SOURCE_DIR_FETK=/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk -DRPC_CFLAGS=-I/usr/include/tirpc -DBUILD_MALOC=Off .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Install prefix: /usr -- -- APBS Static build: Off -- Building shared libs: ON -- Find-library suffixes: .so;.so;.a -- -- Building FETK from commit 57195e55351e04ce6ee0ef56a143c996a9aee7e2 -- FETK set_basic_vars_and_paths: FALSE, FETK -- Setting project paths -- Install prefix: /usr -- FETK static build: OFF -- Building shared libs: ON -- Find-library suffixes: .so;.so;.so;.a Configuring build for PUNC -- FETK set_basic_vars_and_paths: FALSE, punc -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of mode_t -- Check size of mode_t - done -- Check size of pid_t -- Check size of pid_t - done -- Check size of size_t -- Check size of size_t - done -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file sys/socket.h -- Looking for include file sys/socket.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file sys/un.h -- Looking for include file sys/un.h - found -- Looking for include file sys/wait.h -- Looking for include file sys/wait.h - found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Looking for include file arpa/inet.h -- Looking for include file arpa/inet.h - found -- Looking for include file netdb.h -- Looking for include file netdb.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file fcntl.h -- Looking for include file fcntl.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for O_NONBLOCK -- Looking for O_NONBLOCK - found -- Will build vf2c -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T - Success -- Performing Test SUPERLU_HAS_CLEAN_ENUMS -- Performing Test SUPERLU_HAS_CLEAN_ENUMS - Success -- Performing Test SUPERLU_HAS_GLOBALLU_T -- Performing Test SUPERLU_HAS_GLOBALLU_T - Success -- Found SuperLU: /usr/include/superlu (found version "5.0") -- Found ARPACK: libraries at /usr/lib/aarch64-linux-gnu/libarpack.so -- Will build CGCODE -- Building vf2c -- Type: EXTERNAL_HEADERS -- Items: punc/varpack.h;punc/vblas.h;punc/vcgcode.h;punc/vlapack.h;punc/vpmg.h;punc/vf2c.h -- Type: INTERNAL_HEADERS -- Items: f2c.h;fio.h;fmt.h;fp.h;lio.h;rawio.h;signal1.h;sysdep1.h -- Type: SOURCES -- Items: f77vers.c;i77vers.c;s_rnge.c;abort_.c;exit_.c;getarg_.c;iargc_.c;getenv_.c;signal_.c;s_stop.c;s_paus.c;system_.c;cabs.c;derf_.c;derfc_.c;erf_.c;erfc_.c;sig_die.c;uninit.c;pow_ci.c;pow_dd.c;pow_di.c;pow_hh.c;pow_ii.c;pow_ri.c;pow_zi.c;pow_zz.c;c_abs.c;c_cos.c;c_div.c;c_exp.c;c_log.c;c_sin.c;c_sqrt.c;z_abs.c;z_cos.c;z_div.c;z_exp.c;z_log.c;z_sin.c;z_sqrt.c;r_abs.c;r_acos.c;r_asin.c;r_atan.c;r_atn2.c;r_cnjg.c;r_cos.c;r_cosh.c;r_dim.c;r_exp.c;r_imag.c;r_int.c;r_lg10.c;r_log.c;r_mod.c;r_nint.c;r_sign.c;r_sin.c;r_sinh.c;r_sqrt.c;r_tan.c;r_tanh.c;d_abs.c;d_acos.c;d_asin.c;d_atan.c;d_atn2.c;d_cnjg.c;d_cos.c;d_cosh.c;d_dim.c;d_exp.c;d_imag.c;d_int.c;d_lg10.c;d_log.c;d_mod.c;d_nint.c;d_prod.c;d_sign.c;d_sin.c;d_sinh.c;d_sqrt.c;d_tan.c;d_tanh.c;i_abs.c;i_dim.c;i_dnnt.c;i_indx.c;i_len.c;i_mod.c;i_nint.c;i_sign.c;lbitbits.c;lbitshft.c;h_abs.c;h_dim.c;h_dnnt.c;h_indx.c;h_len.c;h_mod.c;h_nint.c;h_sign.c;l_ge.c;l_gt.c;l_le.c;l_lt.c;hl_ge.c;hl_gt.c;hl_le.c;hl_lt.c;ef1asc_.c;ef1cmc_.c;f77_aloc.c;s_cat.c;s_cmp.c;s_copy.c;dtime_.c;etime_.c;backspac.c;close.c;dfe.c;dolio.c;due.c;endfile.c;err.c;fmt.c;fmtlib.c;ftell_.c;iio.c;ilnw.c;inquire.c;lread.c;lwrite.c;open.c;rdfmt.c;rewind.c;rsfe.c;rsli.c;rsne.c;sfe.c;sue.c;typesize.c;uio.c;util.c;wref.c;wrtfmt.c;wsfe.c;wsle.c;wsne.c;xwsne.c;main.c -- Building cgcode -- Type: INTERNAL_HEADERS -- Items: vcgcode.h -- Type: SOURCES -- Items: scgdrv.c;scg.c;scr.c;scrind.c;spcg.c;scgnr.c;scgne.c;spcgnr.c;spcgne.c;sppcg.c;spcgca.c;sdpchb.c;scbfix.c;sckchb.c;scgchk.c;sonest.c;msstop.c;r1mach.c;sratqr.c;dcgdrv.c;dcg.c;dcr.c;dcrind.c;dpcg.c;dcgnr.c;dcgne.c;dpcgnr.c;dpcgne.c;dppcg.c;dpcgca.c;ddpchb.c;dcbfix.c;dckchb.c;dcgchk.c;donest.c;mdstop.c;d1mach.c;dratqr.c;depsln.c -- Type: INTERNAL_HEADERS -- Items: /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/punccf.h -- Type: SOURCES -- Items: punc_base.c -- Type: EXTERNAL_HEADERS -- Items: punc/punc.h;punc/punc_base.h -- Type: INTERNAL_HEADERS -- Items: punc_base_p.h Configuring build for GAMER -- FETK set_basic_vars_and_paths: FALSE, gamer -- Type: INTERNAL_HEADERS -- Items: /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src/gamercf.h -- Type: SOURCES -- Items: gamer_base.c -- Type: EXTERNAL_HEADERS -- Items: gamer/gamer.h;gamer/gamer_base.h -- Type: INTERNAL_HEADERS -- Items: gamer_base_p.h -- Type: SOURCES -- Items: triangle.c -- Type: EXTERNAL_HEADERS -- Items: gamer/triangle.h -- Type: INTERNAL_HEADERS -- Items: triangle_p.h -- Type: SOURCES -- Items: predicates.cpp;tetgen.cpp -- Type: EXTERNAL_HEADERS -- Items: gamer/tetgen.h -- Type: INTERNAL_HEADERS -- Items: tetgen_p.h -- Type: SOURCES -- Items: CorrectNormals.C;GenerateSphereMesh.C;MarchingCube.C;PDB2Mesh.C;PDB2Volume.C;ReadLattice.C;ReadPDB.C;ReadWriteMesh.C;RegionGrowing.C;SurfaceMesh.C;SurfExtract.C;SurfRefine.C;SurfSmooth.C -- Type: EXTERNAL_HEADERS -- Items: gamer/biom.h -- Type: INTERNAL_HEADERS -- Items: MarchingCube.h;PDB2Volume.h Configuring build for MC -- FETK set_basic_vars_and_paths: FALSE, mc -- Found UMFPACK: /usr/include/suitesparse -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/aarch64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/aarch64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/aarch64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/aarch64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/aarch64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/aarch64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/aarch64-linux-gnu/librt.a -- Adding librt: /usr/lib/aarch64-linux-gnu/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- Found SuiteSparse: TRUE (found version "..") -- Type: INTERNAL_HEADERS -- Items: /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src/mccf.h -- Type: SOURCES -- Items: mc_base.c -- Type: EXTERNAL_HEADERS -- Items: mc/mc_base.h;mc/mc.h -- Type: INTERNAL_HEADERS -- Items: mc_base_p.h -- Type: SOURCES -- Items: bmat.c;bsolv.c;bvec.c;mat.c;matcopy.c;matln.c;mtool.c;slu.c;vec.c;vec3.c;zslu.c -- Type: EXTERNAL_HEADERS -- Items: mc/bam.h;mc/bmat.h;mc/bvec.h;mc/mat.h;mc/mtool.h;mc/slu.h;mc/vec.h;mc/vec3.h;mc/zslu.h -- Type: INTERNAL_HEADERS -- Items: bam_p.h;bmat_p.h;bvec_p.h;mat_p.h;mtool_p.h;slu_p.h;vec_p.h;vec3_p.h;zslu_p.h -- Type: SOURCES -- Items: whb.c;bvechb.c;hbtools.c;rcmat.c;brcmat.c;subopt.c -- Type: EXTERNAL_HEADERS -- Items: mc/whb.h -- Type: INTERNAL_HEADERS -- Items: brcmat_p.h;bvechb_p.h;cholesky_p.h;hbtools_p.h;rcmat_p.h;subopt_p.h;whb_p.h -- Type: SOURCES -- Items: aprx.c;assem.c;bnode.c;estim.c;eval.c;io.c;node.c;parti.c;re.c -- Type: EXTERNAL_HEADERS -- Items: mc/aprx.h;mc/bnode.h;mc/node.h;mc/re.h -- Type: INTERNAL_HEADERS -- Items: aprx_p.h;bnode_p.h;node_p.h;re_p.h -- Type: SOURCES -- Items: vel.c;ves.c;gem.c;gemchk.c;gemdisp.c;gemg.c;gemgen.c;gemio.c;gemref.c;gemunref.c;gemcube.c -- Type: EXTERNAL_HEADERS -- Items: mc/gem.h;mc/vel.h;mc/ves.h -- Type: INTERNAL_HEADERS -- Items: gem_p.h;vel_p.h;ves_p.h -- Type: SOURCES -- Items: pde.c -- Type: EXTERNAL_HEADERS -- Items: mc/pde.h -- Type: INTERNAL_HEADERS -- Items: pde_p.h -- Type: SOURCES -- Items: am.c;lsolv.c;nsolv.c -- Type: EXTERNAL_HEADERS -- Items: mc/am.h;mc/nam.h -- Type: INTERNAL_HEADERS -- Items: am_p.h;nam_p.h -- Type: SOURCES -- Items: dyn.c;svio.c -- Type: EXTERNAL_HEADERS -- Items: mc/dyn.h -- Type: INTERNAL_HEADERS -- Items: dyn_p.h;svio_p.h -- Type: SOURCES -- Items: mcsh.c -- Type: EXTERNAL_HEADERS -- Items: mc/mcsh.h -- Type: INTERNAL_HEADERS -- Items: mcsh_p.h -- ############################################################# -- ** PROJECT NAME: APBS -- ** PROJECT DESC: Adaptive Poisson-Boltzmann Solver -- ** PROJECT URL: http://www.poissonboltzmann.org/ -- ** VERSION_DATA: 3.4.1 -- ** CURRENT_TIME: 2024-02-27T13:04:53 -- ** CURRENT_YEAR: 2024 -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Found Intl: built in to C library -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/aarch64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/aarch64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/aarch64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/aarch64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/aarch64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/aarch64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/aarch64-linux-gnu/librt.a -- Adding librt: /usr/lib/aarch64-linux-gnu/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- UMFPack libraries: /usr/lib/aarch64-linux-gnu/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a -- Checking for MPI -- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI support enabled -- Inline functions enabled -- Verbose debugging mode enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled -- Building of iAPBS interface disabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_fem -- With source files vcsm.c;vfetk.c;vpee.c -- With external header files vcsm.h;vfetk.h;vpee.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic -- Added apbs_fem -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem -- Added apbs_routines -- External Headers: -- -- APBS Libraries: mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- -- -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines CMake Deprecation Warning at tools/python/CMakeLists.txt:2 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig (found version "4.2.1") -- Found Python3: /usr/bin/python3 (found suitable version "3.11.9", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- ***** Python3 include path is: /usr/include/python3.11 -- ***** Python3 library path is: /usr/lib/aarch64-linux-gnu/libpython3.11.so -- ***** Python3 library dir is: /usr/lib/aarch64-linux-gnu CMake Warning at /usr/lib/cmake/pybind11/pybind11Tools.cmake:24 (message): Set PYBIND11_PYTHON_VERSION to search for a specific version, not PYTHON_VERSION (which is an output). Assuming that is what you meant to do and continuing anyway. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) CMake Warning (dev) at /usr/lib/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.11.9", minimum required is "3.6") -- Found PythonLibs: /usr/lib/aarch64-linux-gnu/libpython3.11.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.11.1") -- LIBS mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- INTERNAL_LIBS apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- ******* TESTING ADDED ***************** -- Found Python3: /usr/bin/python3 (found suitable exact version "3.11.9") found components: Interpreter -- ******* FOUND TEST CASE born, born -- TEST born_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t born -- ******* FOUND TEST CASE actin, actin-dimer-auto -- TEST actin-dimer-auto_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t actin-dimer-auto -- ******* FOUND TEST CASE alkanes, alkanes -- TEST alkanes_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t alkanes -- ******* FOUND TEST CASE FKBP, FKBP -- TEST FKBP_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t FKBP -- ******* FOUND TEST CASE hca, hca-bind -- TEST hca-bind_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t hca-bind -- ******* FOUND TEST CASE ionize, ionize -- TEST ionize_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t ionize -- ******* FOUND TEST CASE ion, ion-pmf -- TEST ion-pmf_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t ion-pmf -- ******* FOUND TEST CASE pka, pka-lig -- TEST pka-lig_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t pka-lig -- ******* FOUND TEST CASE point, point-pmf -- TEST point-pmf_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t point-pmf -- ******* FOUND TEST CASE solv, solv -- TEST solv_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t solv -- Configuring done (27.1s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY ENABLE_READLINE ENABLE_ZLIB -- Build files have been written to: /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' dh_auto_build -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/apbs-3.4.1 -B/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/DependInfo.cmake "--color=" make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c 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'/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build Dependee 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Scanning dependencies of target apbslib_swig_compilation make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build [ 0%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o -MF CMakeFiles/cgcode.dir/scgdrv.c.o.d -o CMakeFiles/cgcode.dir/scgdrv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgdrv.c [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o -MF CMakeFiles/cgcode.dir/scg.c.o.d -o CMakeFiles/cgcode.dir/scg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scg.c [ 1%] 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o -MF CMakeFiles/gamer.dir/triangle/triangle.c.o.d -o CMakeFiles/gamer.dir/triangle/triangle.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle/triangle.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o -MF CMakeFiles/cgcode.dir/scrind.c.o.d -o CMakeFiles/cgcode.dir/scrind.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scrind.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o -MF CMakeFiles/gamer.dir/base/gamer_base.c.o.d -o CMakeFiles/gamer.dir/base/gamer_base.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base/gamer_base.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o -MF CMakeFiles/cgcode.dir/spcg.c.o.d -o CMakeFiles/cgcode.dir/spcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcg.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o -MF CMakeFiles/vf2c.dir/i77vers.c.o.d -o CMakeFiles/vf2c.dir/i77vers.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i77vers.c [ 4%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o -MF CMakeFiles/cgcode.dir/scgnr.c.o.d -o CMakeFiles/cgcode.dir/scgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgnr.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -MF CMakeFiles/gamer.dir/tetgen/predicates.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E touch /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -python -outdir /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python -interface _apbslib -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/python3.11 -I/build/reproducible-path/apbs-3.4.1/tools/python -o /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /build/reproducible-path/apbs-3.4.1/tools/python/apbslib.i cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o -MF CMakeFiles/vf2c.dir/s_rnge.c.o.d -o CMakeFiles/vf2c.dir/s_rnge.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_rnge.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o -MF CMakeFiles/vf2c.dir/abort_.c.o.d -o CMakeFiles/vf2c.dir/abort_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/abort_.c [ 4%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -MF CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp [ 4%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o -MF CMakeFiles/cgcode.dir/scgne.c.o.d -o CMakeFiles/cgcode.dir/scgne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgne.c [ 4%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o -MF CMakeFiles/cgcode.dir/spcgnr.c.o.d -o CMakeFiles/cgcode.dir/spcgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgnr.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o -MF CMakeFiles/vf2c.dir/exit_.c.o.d -o CMakeFiles/vf2c.dir/exit_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/exit_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o -MF CMakeFiles/cgcode.dir/spcgne.c.o.d -o CMakeFiles/cgcode.dir/spcgne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgne.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o -MF CMakeFiles/vf2c.dir/getarg_.c.o.d -o CMakeFiles/vf2c.dir/getarg_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getarg_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o -MF CMakeFiles/cgcode.dir/sppcg.c.o.d -o CMakeFiles/cgcode.dir/sppcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sppcg.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o -MF CMakeFiles/cgcode.dir/spcgca.c.o.d -o CMakeFiles/cgcode.dir/spcgca.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgca.c [ 7%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -MF CMakeFiles/gamer.dir/biom/CorrectNormals.C.o.d -o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o -MF CMakeFiles/vf2c.dir/iargc_.c.o.d -o CMakeFiles/vf2c.dir/iargc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iargc_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o -MF CMakeFiles/vf2c.dir/getenv_.c.o.d -o CMakeFiles/vf2c.dir/getenv_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getenv_.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o -MF CMakeFiles/cgcode.dir/sdpchb.c.o.d -o CMakeFiles/cgcode.dir/sdpchb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o -MF CMakeFiles/cgcode.dir/scbfix.c.o.d -o CMakeFiles/cgcode.dir/scbfix.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scbfix.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o -MF CMakeFiles/vf2c.dir/signal_.c.o.d -o CMakeFiles/vf2c.dir/signal_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/signal_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o -MF CMakeFiles/cgcode.dir/sckchb.c.o.d -o CMakeFiles/cgcode.dir/sckchb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sckchb.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o -MF CMakeFiles/cgcode.dir/scgchk.c.o.d -o CMakeFiles/cgcode.dir/scgchk.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgchk.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o -MF CMakeFiles/vf2c.dir/s_stop.c.o.d -o CMakeFiles/vf2c.dir/s_stop.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_stop.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o -MF CMakeFiles/cgcode.dir/sonest.c.o.d -o CMakeFiles/cgcode.dir/sonest.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sonest.c [ 10%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -MF CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o.d -o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o -MF CMakeFiles/cgcode.dir/msstop.c.o.d -o CMakeFiles/cgcode.dir/msstop.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/msstop.c [ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o [ 10%] Built target apbslib_swig_compilation cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o -MF CMakeFiles/vf2c.dir/s_paus.c.o.d -o CMakeFiles/vf2c.dir/s_paus.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_paus.c [ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o -MF CMakeFiles/vf2c.dir/system_.c.o.d -o CMakeFiles/vf2c.dir/system_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/system_.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function 'void tetgenmesh::constrainedfacets()': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20804:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 20804 | equatptlist = new list("point *"); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20809:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 20809 | horizptlist = new list("point *"); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20810:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 20810 | belowptlist = new list("point *"); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20811:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 20811 | aboveptlist = new list("point *"); | ^~~~~~~~~ [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o -MF CMakeFiles/cgcode.dir/r1mach.c.o.d -o CMakeFiles/cgcode.dir/r1mach.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/r1mach.c [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o -MF CMakeFiles/cgcode.dir/sratqr.c.o.d -o CMakeFiles/cgcode.dir/sratqr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sratqr.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function 'long int tetgenmesh::reconstructmesh()': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:24383:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 24383 | markerlist = new list("int"); | ^~~~~ [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o -MF CMakeFiles/vf2c.dir/cabs.c.o.d -o CMakeFiles/vf2c.dir/cabs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/cabs.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o -MF CMakeFiles/cgcode.dir/dcgdrv.c.o.d -o CMakeFiles/cgcode.dir/dcgdrv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o -MF CMakeFiles/vf2c.dir/derf_.c.o.d -o CMakeFiles/vf2c.dir/derf_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derf_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o -MF CMakeFiles/cgcode.dir/dcg.c.o.d -o CMakeFiles/cgcode.dir/dcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcg.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o -MF CMakeFiles/cgcode.dir/dcr.c.o.d -o CMakeFiles/cgcode.dir/dcr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcr.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o -MF CMakeFiles/vf2c.dir/derfc_.c.o.d -o CMakeFiles/vf2c.dir/derfc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derfc_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o -MF CMakeFiles/vf2c.dir/erf_.c.o.d -o CMakeFiles/vf2c.dir/erf_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erf_.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o -MF CMakeFiles/cgcode.dir/dcrind.c.o.d -o CMakeFiles/cgcode.dir/dcrind.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcrind.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o -MF CMakeFiles/vf2c.dir/erfc_.c.o.d -o CMakeFiles/vf2c.dir/erfc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erfc_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o -MF CMakeFiles/cgcode.dir/dpcg.c.o.d -o CMakeFiles/cgcode.dir/dpcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcg.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o -MF CMakeFiles/vf2c.dir/sig_die.c.o.d -o CMakeFiles/vf2c.dir/sig_die.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sig_die.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o -MF CMakeFiles/cgcode.dir/dcgnr.c.o.d -o CMakeFiles/cgcode.dir/dcgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgnr.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o -MF CMakeFiles/cgcode.dir/dcgne.c.o.d -o CMakeFiles/cgcode.dir/dcgne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgne.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o -MF CMakeFiles/cgcode.dir/dpcgnr.c.o.d -o CMakeFiles/cgcode.dir/dpcgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgnr.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o -MF CMakeFiles/vf2c.dir/uninit.c.o.d -o CMakeFiles/vf2c.dir/uninit.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uninit.c [ 15%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o -MF CMakeFiles/gamer.dir/biom/MarchingCube.C.o.d -o CMakeFiles/gamer.dir/biom/MarchingCube.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o -MF CMakeFiles/cgcode.dir/dpcgne.c.o.d -o CMakeFiles/cgcode.dir/dpcgne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o -MF CMakeFiles/vf2c.dir/pow_ci.c.o.d -o CMakeFiles/vf2c.dir/pow_ci.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ci.c [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o -MF CMakeFiles/cgcode.dir/dppcg.c.o.d -o CMakeFiles/cgcode.dir/dppcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dppcg.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o -MF CMakeFiles/vf2c.dir/pow_dd.c.o.d -o CMakeFiles/vf2c.dir/pow_dd.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_dd.c [ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o -MF CMakeFiles/cgcode.dir/dpcgca.c.o.d -o CMakeFiles/cgcode.dir/dpcgca.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgca.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o -MF CMakeFiles/vf2c.dir/pow_di.c.o.d -o CMakeFiles/vf2c.dir/pow_di.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_di.c [ 18%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Mesh.C [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o -MF CMakeFiles/cgcode.dir/ddpchb.c.o.d -o CMakeFiles/cgcode.dir/ddpchb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o -MF CMakeFiles/cgcode.dir/dcbfix.c.o.d -o CMakeFiles/cgcode.dir/dcbfix.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o -MF CMakeFiles/vf2c.dir/pow_hh.c.o.d -o CMakeFiles/vf2c.dir/pow_hh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o -MF CMakeFiles/cgcode.dir/dckchb.c.o.d -o CMakeFiles/cgcode.dir/dckchb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dckchb.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o -MF CMakeFiles/vf2c.dir/pow_ii.c.o.d -o CMakeFiles/vf2c.dir/pow_ii.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC 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/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o -MF CMakeFiles/cgcode.dir/donest.c.o.d -o CMakeFiles/cgcode.dir/donest.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/donest.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o -MF CMakeFiles/cgcode.dir/mdstop.c.o.d -o CMakeFiles/cgcode.dir/mdstop.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/mdstop.c [ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o -MF CMakeFiles/cgcode.dir/d1mach.c.o.d -o CMakeFiles/cgcode.dir/d1mach.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/d1mach.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o -MF CMakeFiles/vf2c.dir/pow_zi.c.o.d -o CMakeFiles/vf2c.dir/pow_zi.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zi.c [ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o -MF CMakeFiles/cgcode.dir/dratqr.c.o.d -o CMakeFiles/cgcode.dir/dratqr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dratqr.c [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD 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_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o -MF CMakeFiles/vf2c.dir/c_abs.c.o.d -o CMakeFiles/vf2c.dir/c_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_abs.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o -MF CMakeFiles/vf2c.dir/c_cos.c.o.d -o CMakeFiles/vf2c.dir/c_cos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_cos.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o -MF CMakeFiles/vf2c.dir/c_div.c.o.d -o CMakeFiles/vf2c.dir/c_div.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_div.c [ 22%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Volume.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C [ 22%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o -MF CMakeFiles/gamer.dir/biom/ReadLattice.C.o.d -o CMakeFiles/gamer.dir/biom/ReadLattice.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o -MF CMakeFiles/vf2c.dir/c_exp.c.o.d -o CMakeFiles/vf2c.dir/c_exp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_exp.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o -MF CMakeFiles/vf2c.dir/c_log.c.o.d -o CMakeFiles/vf2c.dir/c_log.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_log.c [ 23%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o -MF CMakeFiles/gamer.dir/biom/ReadPDB.C.o.d -o CMakeFiles/gamer.dir/biom/ReadPDB.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o -MF CMakeFiles/vf2c.dir/c_sin.c.o.d -o CMakeFiles/vf2c.dir/c_sin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sin.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o -MF CMakeFiles/vf2c.dir/c_sqrt.c.o.d -o CMakeFiles/vf2c.dir/c_sqrt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c [ 25%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o -MF CMakeFiles/vf2c.dir/z_abs.c.o.d -o CMakeFiles/vf2c.dir/z_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_abs.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -MF CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o.d -o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C [ 25%] Linking C shared library libcgcode.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1 [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o -MF CMakeFiles/vf2c.dir/z_cos.c.o.d -o CMakeFiles/vf2c.dir/z_cos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_cos.c /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libcgcode.so.1.9 -o libcgcode.so.1.9.3 CMakeFiles/cgcode.dir/scgdrv.c.o CMakeFiles/cgcode.dir/scg.c.o CMakeFiles/cgcode.dir/scr.c.o CMakeFiles/cgcode.dir/scrind.c.o CMakeFiles/cgcode.dir/spcg.c.o CMakeFiles/cgcode.dir/scgnr.c.o CMakeFiles/cgcode.dir/scgne.c.o CMakeFiles/cgcode.dir/spcgnr.c.o CMakeFiles/cgcode.dir/spcgne.c.o CMakeFiles/cgcode.dir/sppcg.c.o CMakeFiles/cgcode.dir/spcgca.c.o CMakeFiles/cgcode.dir/sdpchb.c.o CMakeFiles/cgcode.dir/scbfix.c.o CMakeFiles/cgcode.dir/sckchb.c.o CMakeFiles/cgcode.dir/scgchk.c.o CMakeFiles/cgcode.dir/sonest.c.o CMakeFiles/cgcode.dir/msstop.c.o CMakeFiles/cgcode.dir/r1mach.c.o CMakeFiles/cgcode.dir/sratqr.c.o CMakeFiles/cgcode.dir/dcgdrv.c.o CMakeFiles/cgcode.dir/dcg.c.o CMakeFiles/cgcode.dir/dcr.c.o CMakeFiles/cgcode.dir/dcrind.c.o CMakeFiles/cgcode.dir/dpcg.c.o CMakeFiles/cgcode.dir/dcgnr.c.o CMakeFiles/cgcode.dir/dcgne.c.o CMakeFiles/cgcode.dir/dpcgnr.c.o CMakeFiles/cgcode.dir/dpcgne.c.o CMakeFiles/cgcode.dir/dppcg.c.o CMakeFiles/cgcode.dir/dpcgca.c.o CMakeFiles/cgcode.dir/ddpchb.c.o CMakeFiles/cgcode.dir/dcbfix.c.o CMakeFiles/cgcode.dir/dckchb.c.o CMakeFiles/cgcode.dir/dcgchk.c.o CMakeFiles/cgcode.dir/donest.c.o CMakeFiles/cgcode.dir/mdstop.c.o CMakeFiles/cgcode.dir/d1mach.c.o CMakeFiles/cgcode.dir/dratqr.c.o CMakeFiles/cgcode.dir/depsln.c.o [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o -MF CMakeFiles/vf2c.dir/z_div.c.o.d -o CMakeFiles/vf2c.dir/z_div.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_div.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_symlink_library libcgcode.so.1.9.3 libcgcode.so.1.9 libcgcode.so [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o -MF CMakeFiles/vf2c.dir/z_exp.c.o.d -o CMakeFiles/vf2c.dir/z_exp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_exp.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o -MF CMakeFiles/vf2c.dir/z_log.c.o.d -o CMakeFiles/vf2c.dir/z_log.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_log.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 26%] Built target cgcode /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C: In function 'float PDB2Volume(char*, float**, int*, int*, int*, float*, float*, ATOM**, int*, char)': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:85:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 85 | fscanf(fp,"%d\n",&m); | ~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:88:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fscanf(fp,"%f %f %f %f\n",&x,&y,&z,&radius); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 26%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function 'SurfaceMesh* SurfaceMesh_readOFF(char*)': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:401:14: warning: too many arguments for format [-Wformat-extra-args] 401 | printf("Read error. Expected 3 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -MF CMakeFiles/gamer.dir/biom/RegionGrowing.C.o.d -o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:494:14: warning: too many arguments for format [-Wformat-extra-args] 494 | printf("Read error. Expected 4 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function 'GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:754:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 754 | in.save_nodes("plc"); | ^~~~~ [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:755:16: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 755 | in.save_poly("plc"); | ^~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:761:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 761 | out.save_nodes("result"); | ^~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:762:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 762 | out.save_elements("result"); | ^~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:763:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 763 | out.save_faces("result"); | ^~~~~~~~ cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o -MF CMakeFiles/vf2c.dir/z_sin.c.o.d -o CMakeFiles/vf2c.dir/z_sin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sin.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o -MF CMakeFiles/vf2c.dir/z_sqrt.c.o.d -o CMakeFiles/vf2c.dir/z_sqrt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c [ 27%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -MF CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o.d -o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o -MF CMakeFiles/vf2c.dir/r_abs.c.o.d -o CMakeFiles/vf2c.dir/r_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_abs.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o -MF CMakeFiles/vf2c.dir/r_acos.c.o.d -o CMakeFiles/vf2c.dir/r_acos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_acos.c [ 28%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o -MF CMakeFiles/gamer.dir/biom/SurfExtract.C.o.d -o CMakeFiles/gamer.dir/biom/SurfExtract.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o -MF CMakeFiles/vf2c.dir/r_asin.c.o.d -o CMakeFiles/vf2c.dir/r_asin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_asin.c [ 28%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o -MF CMakeFiles/gamer.dir/biom/SurfRefine.C.o.d -o CMakeFiles/gamer.dir/biom/SurfRefine.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o -MF CMakeFiles/vf2c.dir/r_atan.c.o.d -o CMakeFiles/vf2c.dir/r_atan.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atan.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o -MF CMakeFiles/vf2c.dir/r_atn2.c.o.d -o CMakeFiles/vf2c.dir/r_atn2.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atn2.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o [ 29%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o -MF CMakeFiles/vf2c.dir/r_cnjg.c.o.d -o CMakeFiles/vf2c.dir/r_cnjg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -MF CMakeFiles/gamer.dir/biom/SurfSmooth.C.o.d -o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfSmooth.C [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o cd 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_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o -MF CMakeFiles/vf2c.dir/r_tanh.c.o.d -o CMakeFiles/vf2c.dir/r_tanh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o -MF CMakeFiles/vf2c.dir/d_abs.c.o.d -o CMakeFiles/vf2c.dir/d_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_abs.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o -MF CMakeFiles/vf2c.dir/d_acos.c.o.d -o CMakeFiles/vf2c.dir/d_acos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_acos.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o -MF CMakeFiles/vf2c.dir/d_asin.c.o.d -o CMakeFiles/vf2c.dir/d_asin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_asin.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o -MF CMakeFiles/vf2c.dir/d_atan.c.o.d -o CMakeFiles/vf2c.dir/d_atan.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atan.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o -MF CMakeFiles/vf2c.dir/d_atn2.c.o.d -o CMakeFiles/vf2c.dir/d_atn2.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o -MF CMakeFiles/vf2c.dir/d_cnjg.c.o.d -o CMakeFiles/vf2c.dir/d_cnjg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o -MF CMakeFiles/vf2c.dir/d_cos.c.o.d -o CMakeFiles/vf2c.dir/d_cos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cos.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o -MF CMakeFiles/vf2c.dir/d_cosh.c.o.d -o CMakeFiles/vf2c.dir/d_cosh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o -MF CMakeFiles/vf2c.dir/d_dim.c.o.d -o CMakeFiles/vf2c.dir/d_dim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_dim.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o -MF CMakeFiles/vf2c.dir/d_exp.c.o.d -o CMakeFiles/vf2c.dir/d_exp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_exp.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o -MF CMakeFiles/vf2c.dir/d_imag.c.o.d -o CMakeFiles/vf2c.dir/d_imag.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_imag.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o -MF CMakeFiles/vf2c.dir/d_int.c.o.d -o CMakeFiles/vf2c.dir/d_int.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_int.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o -MF CMakeFiles/vf2c.dir/d_lg10.c.o.d -o CMakeFiles/vf2c.dir/d_lg10.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o -MF CMakeFiles/vf2c.dir/d_log.c.o.d -o CMakeFiles/vf2c.dir/d_log.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_log.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o -MF CMakeFiles/vf2c.dir/d_mod.c.o.d -o CMakeFiles/vf2c.dir/d_mod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_mod.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o -MF CMakeFiles/vf2c.dir/d_nint.c.o.d -o CMakeFiles/vf2c.dir/d_nint.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_nint.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o -MF CMakeFiles/vf2c.dir/d_prod.c.o.d -o CMakeFiles/vf2c.dir/d_prod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_prod.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o -MF CMakeFiles/vf2c.dir/d_sign.c.o.d -o CMakeFiles/vf2c.dir/d_sign.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sign.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o -MF CMakeFiles/vf2c.dir/d_sin.c.o.d -o CMakeFiles/vf2c.dir/d_sin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sin.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o -MF CMakeFiles/vf2c.dir/d_sinh.c.o.d -o CMakeFiles/vf2c.dir/d_sinh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o -MF CMakeFiles/vf2c.dir/d_sqrt.c.o.d -o CMakeFiles/vf2c.dir/d_sqrt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o -MF CMakeFiles/vf2c.dir/d_tan.c.o.d -o CMakeFiles/vf2c.dir/d_tan.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tan.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o -MF CMakeFiles/vf2c.dir/d_tanh.c.o.d -o CMakeFiles/vf2c.dir/d_tanh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o -MF CMakeFiles/vf2c.dir/i_abs.c.o.d -o CMakeFiles/vf2c.dir/i_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_abs.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o -MF CMakeFiles/vf2c.dir/i_dim.c.o.d -o CMakeFiles/vf2c.dir/i_dim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dim.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o -MF CMakeFiles/vf2c.dir/i_dnnt.c.o.d -o CMakeFiles/vf2c.dir/i_dnnt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o -MF CMakeFiles/vf2c.dir/i_indx.c.o.d -o CMakeFiles/vf2c.dir/i_indx.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_indx.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o -MF CMakeFiles/vf2c.dir/i_len.c.o.d -o CMakeFiles/vf2c.dir/i_len.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_len.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o -MF CMakeFiles/vf2c.dir/i_mod.c.o.d -o CMakeFiles/vf2c.dir/i_mod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_mod.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o -MF CMakeFiles/vf2c.dir/i_sign.c.o.d -o CMakeFiles/vf2c.dir/i_sign.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_sign.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o -MF CMakeFiles/vf2c.dir/lbitbits.c.o.d -o CMakeFiles/vf2c.dir/lbitbits.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitbits.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o -MF CMakeFiles/vf2c.dir/lbitshft.c.o.d -o CMakeFiles/vf2c.dir/lbitshft.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitshft.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o -MF CMakeFiles/vf2c.dir/h_abs.c.o.d -o CMakeFiles/vf2c.dir/h_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_abs.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o -MF CMakeFiles/vf2c.dir/h_dim.c.o.d -o CMakeFiles/vf2c.dir/h_dim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dim.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o -MF CMakeFiles/vf2c.dir/h_dnnt.c.o.d -o CMakeFiles/vf2c.dir/h_dnnt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o -MF CMakeFiles/vf2c.dir/h_indx.c.o.d -o CMakeFiles/vf2c.dir/h_indx.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_indx.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o -MF CMakeFiles/vf2c.dir/h_len.c.o.d -o CMakeFiles/vf2c.dir/h_len.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_len.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o -MF CMakeFiles/vf2c.dir/h_mod.c.o.d -o CMakeFiles/vf2c.dir/h_mod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_mod.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o -MF CMakeFiles/vf2c.dir/h_nint.c.o.d -o CMakeFiles/vf2c.dir/h_nint.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_nint.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o -MF CMakeFiles/vf2c.dir/h_sign.c.o.d -o CMakeFiles/vf2c.dir/h_sign.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_sign.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o -MF CMakeFiles/vf2c.dir/l_ge.c.o.d -o CMakeFiles/vf2c.dir/l_ge.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_ge.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o -MF CMakeFiles/vf2c.dir/l_gt.c.o.d -o CMakeFiles/vf2c.dir/l_gt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_gt.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o -MF CMakeFiles/vf2c.dir/l_le.c.o.d -o CMakeFiles/vf2c.dir/l_le.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_le.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o -MF CMakeFiles/vf2c.dir/l_lt.c.o.d -o CMakeFiles/vf2c.dir/l_lt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_lt.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o -MF CMakeFiles/vf2c.dir/hl_ge.c.o.d -o CMakeFiles/vf2c.dir/hl_ge.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_ge.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o -MF CMakeFiles/vf2c.dir/hl_gt.c.o.d -o CMakeFiles/vf2c.dir/hl_gt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_gt.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o -MF CMakeFiles/vf2c.dir/hl_le.c.o.d -o CMakeFiles/vf2c.dir/hl_le.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_le.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o -MF CMakeFiles/vf2c.dir/hl_lt.c.o.d -o CMakeFiles/vf2c.dir/hl_lt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_lt.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o -MF CMakeFiles/vf2c.dir/ef1asc_.c.o.d -o CMakeFiles/vf2c.dir/ef1asc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1asc_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o -MF CMakeFiles/vf2c.dir/ef1cmc_.c.o.d -o CMakeFiles/vf2c.dir/ef1cmc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1cmc_.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o -MF CMakeFiles/vf2c.dir/f77_aloc.c.o.d -o CMakeFiles/vf2c.dir/f77_aloc.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77_aloc.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o -MF CMakeFiles/vf2c.dir/s_cat.c.o.d -o CMakeFiles/vf2c.dir/s_cat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_cat.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o -MF CMakeFiles/vf2c.dir/s_cmp.c.o.d -o CMakeFiles/vf2c.dir/s_cmp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_cmp.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o -MF CMakeFiles/vf2c.dir/s_copy.c.o.d -o CMakeFiles/vf2c.dir/s_copy.c.o -c 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CMakeFiles/vf2c.dir/dtime_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dtime_.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o -MF CMakeFiles/vf2c.dir/etime_.c.o.d -o CMakeFiles/vf2c.dir/etime_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/etime_.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o -MF CMakeFiles/vf2c.dir/backspac.c.o.d -o CMakeFiles/vf2c.dir/backspac.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o -MF CMakeFiles/vf2c.dir/close.c.o.d -o CMakeFiles/vf2c.dir/close.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/close.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o -MF CMakeFiles/vf2c.dir/dfe.c.o.d -o CMakeFiles/vf2c.dir/dfe.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dfe.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function 'f_back': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c:47:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 47 | fread((char *)&n,sizeof(uiolen),1,f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o -MF CMakeFiles/vf2c.dir/dolio.c.o.d -o CMakeFiles/vf2c.dir/dolio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dolio.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o -MF CMakeFiles/vf2c.dir/due.c.o.d -o CMakeFiles/vf2c.dir/due.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/due.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o -MF CMakeFiles/vf2c.dir/endfile.c.o.d -o CMakeFiles/vf2c.dir/endfile.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/endfile.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o -MF CMakeFiles/vf2c.dir/err.c.o.d -o CMakeFiles/vf2c.dir/err.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/err.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o -MF CMakeFiles/vf2c.dir/fmt.c.o.d -o CMakeFiles/vf2c.dir/fmt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmt.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o -MF CMakeFiles/vf2c.dir/fmtlib.c.o.d -o CMakeFiles/vf2c.dir/fmtlib.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmtlib.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o -MF CMakeFiles/vf2c.dir/ftell_.c.o.d -o CMakeFiles/vf2c.dir/ftell_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ftell_.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o -MF CMakeFiles/vf2c.dir/ilnw.c.o.d -o CMakeFiles/vf2c.dir/ilnw.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ilnw.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o -MF CMakeFiles/vf2c.dir/iio.c.o.d -o CMakeFiles/vf2c.dir/iio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iio.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o -MF CMakeFiles/vf2c.dir/inquire.c.o.d -o CMakeFiles/vf2c.dir/inquire.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/inquire.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o -MF CMakeFiles/vf2c.dir/lread.c.o.d -o CMakeFiles/vf2c.dir/lread.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lread.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o -MF CMakeFiles/vf2c.dir/lwrite.c.o.d -o CMakeFiles/vf2c.dir/lwrite.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lwrite.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o -MF CMakeFiles/vf2c.dir/open.c.o.d -o CMakeFiles/vf2c.dir/open.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/open.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o -MF CMakeFiles/vf2c.dir/rdfmt.c.o.d -o CMakeFiles/vf2c.dir/rdfmt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o -MF CMakeFiles/vf2c.dir/rewind.c.o.d -o CMakeFiles/vf2c.dir/rewind.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rewind.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o -MF CMakeFiles/vf2c.dir/rsfe.c.o.d -o CMakeFiles/vf2c.dir/rsfe.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o -MF CMakeFiles/vf2c.dir/sfe.c.o.d -o CMakeFiles/vf2c.dir/sfe.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sfe.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o -MF CMakeFiles/vf2c.dir/rsne.c.o.d -o CMakeFiles/vf2c.dir/rsne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsne.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o -MF CMakeFiles/vf2c.dir/sue.c.o.d -o CMakeFiles/vf2c.dir/sue.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sue.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o -MF CMakeFiles/vf2c.dir/typesize.c.o.d -o CMakeFiles/vf2c.dir/typesize.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/typesize.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o -MF CMakeFiles/vf2c.dir/uio.c.o.d -o CMakeFiles/vf2c.dir/uio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uio.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o -MF CMakeFiles/vf2c.dir/util.c.o.d -o CMakeFiles/vf2c.dir/util.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/util.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o -MF CMakeFiles/vf2c.dir/wref.c.o.d -o CMakeFiles/vf2c.dir/wref.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wref.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT 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CMakeFiles/vf2c.dir/wsfe.c.o.d -o CMakeFiles/vf2c.dir/wsfe.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsfe.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT 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/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o -MF CMakeFiles/vf2c.dir/xwsne.c.o.d -o CMakeFiles/vf2c.dir/xwsne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/xwsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o -MF CMakeFiles/vf2c.dir/main.c.o.d -o CMakeFiles/vf2c.dir/main.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c:115:1: warning: return type defaults to 'int' [-Wimplicit-int] 115 | main(int argc, char **argv) | ^~~~ [ 60%] Linking C shared library libvf2c.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_link_script CMakeFiles/vf2c.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libvf2c.so.1.9 -o libvf2c.so.1.9.3 CMakeFiles/vf2c.dir/f77vers.c.o CMakeFiles/vf2c.dir/i77vers.c.o CMakeFiles/vf2c.dir/s_rnge.c.o CMakeFiles/vf2c.dir/abort_.c.o CMakeFiles/vf2c.dir/exit_.c.o CMakeFiles/vf2c.dir/getarg_.c.o CMakeFiles/vf2c.dir/iargc_.c.o CMakeFiles/vf2c.dir/getenv_.c.o CMakeFiles/vf2c.dir/signal_.c.o CMakeFiles/vf2c.dir/s_stop.c.o CMakeFiles/vf2c.dir/s_paus.c.o CMakeFiles/vf2c.dir/system_.c.o CMakeFiles/vf2c.dir/cabs.c.o CMakeFiles/vf2c.dir/derf_.c.o CMakeFiles/vf2c.dir/derfc_.c.o CMakeFiles/vf2c.dir/erf_.c.o CMakeFiles/vf2c.dir/erfc_.c.o CMakeFiles/vf2c.dir/sig_die.c.o CMakeFiles/vf2c.dir/uninit.c.o CMakeFiles/vf2c.dir/pow_ci.c.o CMakeFiles/vf2c.dir/pow_dd.c.o CMakeFiles/vf2c.dir/pow_di.c.o CMakeFiles/vf2c.dir/pow_hh.c.o CMakeFiles/vf2c.dir/pow_ii.c.o CMakeFiles/vf2c.dir/pow_ri.c.o CMakeFiles/vf2c.dir/pow_zi.c.o CMakeFiles/vf2c.dir/pow_zz.c.o CMakeFiles/vf2c.dir/c_abs.c.o CMakeFiles/vf2c.dir/c_cos.c.o CMakeFiles/vf2c.dir/c_div.c.o CMakeFiles/vf2c.dir/c_exp.c.o CMakeFiles/vf2c.dir/c_log.c.o CMakeFiles/vf2c.dir/c_sin.c.o CMakeFiles/vf2c.dir/c_sqrt.c.o 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CMakeFiles/vf2c.dir/h_dnnt.c.o CMakeFiles/vf2c.dir/h_indx.c.o CMakeFiles/vf2c.dir/h_len.c.o CMakeFiles/vf2c.dir/h_mod.c.o CMakeFiles/vf2c.dir/h_nint.c.o CMakeFiles/vf2c.dir/h_sign.c.o CMakeFiles/vf2c.dir/l_ge.c.o CMakeFiles/vf2c.dir/l_gt.c.o CMakeFiles/vf2c.dir/l_le.c.o CMakeFiles/vf2c.dir/l_lt.c.o CMakeFiles/vf2c.dir/hl_ge.c.o CMakeFiles/vf2c.dir/hl_gt.c.o CMakeFiles/vf2c.dir/hl_le.c.o CMakeFiles/vf2c.dir/hl_lt.c.o CMakeFiles/vf2c.dir/ef1asc_.c.o CMakeFiles/vf2c.dir/ef1cmc_.c.o CMakeFiles/vf2c.dir/f77_aloc.c.o CMakeFiles/vf2c.dir/s_cat.c.o CMakeFiles/vf2c.dir/s_cmp.c.o CMakeFiles/vf2c.dir/s_copy.c.o CMakeFiles/vf2c.dir/dtime_.c.o CMakeFiles/vf2c.dir/etime_.c.o CMakeFiles/vf2c.dir/backspac.c.o CMakeFiles/vf2c.dir/close.c.o CMakeFiles/vf2c.dir/dfe.c.o CMakeFiles/vf2c.dir/dolio.c.o CMakeFiles/vf2c.dir/due.c.o CMakeFiles/vf2c.dir/endfile.c.o CMakeFiles/vf2c.dir/err.c.o CMakeFiles/vf2c.dir/fmt.c.o CMakeFiles/vf2c.dir/fmtlib.c.o CMakeFiles/vf2c.dir/ftell_.c.o CMakeFiles/vf2c.dir/iio.c.o CMakeFiles/vf2c.dir/ilnw.c.o CMakeFiles/vf2c.dir/inquire.c.o CMakeFiles/vf2c.dir/lread.c.o CMakeFiles/vf2c.dir/lwrite.c.o CMakeFiles/vf2c.dir/open.c.o CMakeFiles/vf2c.dir/rdfmt.c.o CMakeFiles/vf2c.dir/rewind.c.o CMakeFiles/vf2c.dir/rsfe.c.o CMakeFiles/vf2c.dir/rsli.c.o CMakeFiles/vf2c.dir/rsne.c.o CMakeFiles/vf2c.dir/sfe.c.o CMakeFiles/vf2c.dir/sue.c.o CMakeFiles/vf2c.dir/typesize.c.o CMakeFiles/vf2c.dir/uio.c.o CMakeFiles/vf2c.dir/util.c.o CMakeFiles/vf2c.dir/wref.c.o CMakeFiles/vf2c.dir/wrtfmt.c.o CMakeFiles/vf2c.dir/wsfe.c.o CMakeFiles/vf2c.dir/wsle.c.o CMakeFiles/vf2c.dir/wsne.c.o CMakeFiles/vf2c.dir/xwsne.c.o CMakeFiles/vf2c.dir/main.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_symlink_library libvf2c.so.1.9.3 libvf2c.so.1.9 libvf2c.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 60%] Built target vf2c make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o -MF CMakeFiles/punc.dir/base/punc_base.c.o.d -o CMakeFiles/punc.dir/base/punc_base.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base/punc_base.c [ 60%] Linking C shared library libpunc.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/punc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libpunc.so.1.9 -o libpunc.so.1.9.3 CMakeFiles/punc.dir/base/punc_base.c.o -lmaloc /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_symlink_library libpunc.so.1.9.3 libpunc.so.1.9 libpunc.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 60%] Built target punc make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o -MF CMakeFiles/mc.dir/base/mc_base.c.o.d -o CMakeFiles/mc.dir/base/mc_base.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc_base.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o -MF CMakeFiles/mc.dir/bam/bmat.c.o.d -o CMakeFiles/mc.dir/bam/bmat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o -MF CMakeFiles/mc.dir/bam/bsolv.c.o.d -o CMakeFiles/mc.dir/bam/bsolv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o -MF CMakeFiles/mc.dir/bam/mat.c.o.d -o CMakeFiles/mc.dir/bam/mat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mat.c [ 62%] Building C object 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o -MF 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_deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o -MF CMakeFiles/mc.dir/bam/matln.c.o.d -o CMakeFiles/mc.dir/bam/matln.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/matln.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o -MF CMakeFiles/mc.dir/bam/mtool.c.o.d -o CMakeFiles/mc.dir/bam/mtool.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mtool.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o -MF CMakeFiles/mc.dir/bam/slu.c.o.d -o CMakeFiles/mc.dir/bam/slu.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/slu.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o -MF CMakeFiles/mc.dir/bam/vec.c.o.d -o CMakeFiles/mc.dir/bam/vec.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o -MF CMakeFiles/mc.dir/bam/vec3.c.o.d -o CMakeFiles/mc.dir/bam/vec3.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec3.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o -MF CMakeFiles/mc.dir/bam/zslu.c.o.d -o CMakeFiles/mc.dir/bam/zslu.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/zslu.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function 'Bmat_ctor': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:36: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 2147483646] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 3] In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:34: In function 'sprintf', inlined from 'Bmat_ctor' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 22 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_bcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:29: warning: '%s' directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 922 | sprintf(rn,"Bvec_bcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: In function 'sprintf', inlined from 'Bvec_bcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_bcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:33: warning: '%s' directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 919 | sprintf(rn,"--->Bvec_bcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_bcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o -MF CMakeFiles/mc.dir/whb/whb.c.o.d -o CMakeFiles/mc.dir/whb/whb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/whb.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:28: warning: '%s' directive writing up to 79 bytes into a region of size 73 [-Wformat-overflow=] 631 | sprintf(rn,"Bvec_cg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_cg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 87 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:32: warning: '%s' directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 628 | sprintf(rn,"--->Bvec_cg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_cg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o -MF CMakeFiles/mc.dir/whb/bvechb.c.o.d -o CMakeFiles/mc.dir/whb/bvechb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o -MF CMakeFiles/mc.dir/whb/hbtools.c.o.d -o CMakeFiles/mc.dir/whb/hbtools.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function 'Bmat_galerkin': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:36: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] In function 'sprintf', inlined from 'Bmat_galerkin' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 31 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o -MF CMakeFiles/mc.dir/whb/rcmat.c.o.d -o CMakeFiles/mc.dir/whb/rcmat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/rcmat.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cgnr': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:30: warning: '%s' directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 1422 | sprintf(rn,"Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_cgnr' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cgnr': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:34: warning: '%s' directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 1419 | sprintf(rn,"--->Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_cgnr' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o -MF CMakeFiles/mc.dir/whb/brcmat.c.o.d -o CMakeFiles/mc.dir/whb/brcmat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/brcmat.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o -MF CMakeFiles/mc.dir/whb/subopt.c.o.d -o CMakeFiles/mc.dir/whb/subopt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function 'Bvec_ctorPoint': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:28: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 2147483646] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:34: In function 'sprintf', inlined from 'Bvec_ctorPoint' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 21 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o -MF CMakeFiles/mc.dir/aprx/aprx.c.o.d -o CMakeFiles/mc.dir/aprx/aprx.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o -MF CMakeFiles/mc.dir/aprx/assem.c.o.d -o CMakeFiles/mc.dir/aprx/assem.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/assem.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o -MF CMakeFiles/mc.dir/aprx/bnode.c.o.d -o CMakeFiles/mc.dir/aprx/bnode.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/bnode.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:29: warning: '%s' directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 267 | sprintf(rn,"Bvec_hcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: In function 'sprintf', inlined from 'Bvec_hcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:33: warning: '%s' directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 264 | sprintf(rn,"--->Bvec_hcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_hcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o -MF CMakeFiles/mc.dir/aprx/estim.c.o.d -o CMakeFiles/mc.dir/aprx/estim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/estim.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hbcg': [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:30: warning: '%s' directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 474 | sprintf(rn,"Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_hbcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hbcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:34: warning: '%s' directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 471 | sprintf(rn,"--->Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_hbcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:9: cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o -MF CMakeFiles/mc.dir/aprx/eval.c.o.d -o CMakeFiles/mc.dir/aprx/eval.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o -MF CMakeFiles/mc.dir/aprx/io.c.o.d -o CMakeFiles/mc.dir/aprx/io.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/io.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o -MF CMakeFiles/mc.dir/aprx/node.c.o.d -o CMakeFiles/mc.dir/aprx/node.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/node.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o -MF CMakeFiles/mc.dir/aprx/parti.c.o.d -o CMakeFiles/mc.dir/aprx/parti.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/parti.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o -MF CMakeFiles/mc.dir/aprx/re.c.o.d -o CMakeFiles/mc.dir/aprx/re.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/re.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o -MF CMakeFiles/mc.dir/gem/vel.c.o.d -o CMakeFiles/mc.dir/gem/vel.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/vel.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o -MF CMakeFiles/mc.dir/gem/ves.c.o.d -o CMakeFiles/mc.dir/gem/ves.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/ves.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o -MF CMakeFiles/mc.dir/gem/gem.c.o.d -o CMakeFiles/mc.dir/gem/gem.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:40: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 368 | sprintf(filename, "f%dz.dat", block); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:34: In function 'sprintf', inlined from 'Aprx_fe2fd' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:40: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 366 | sprintf(filename, "f%dy.dat", block); | ^ In function 'sprintf', inlined from 'Aprx_fe2fd' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:40: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 364 | sprintf(filename, "f%dx.dat", block); | ^ In function 'sprintf', inlined from 'Aprx_fe2fd' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o -MF CMakeFiles/mc.dir/gem/gemchk.c.o.d -o CMakeFiles/mc.dir/gem/gemchk.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemchk.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o -MF CMakeFiles/mc.dir/gem/gemdisp.c.o.d -o CMakeFiles/mc.dir/gem/gemdisp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o -MF CMakeFiles/mc.dir/gem/gemg.c.o.d -o CMakeFiles/mc.dir/gem/gemg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemg.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o -MF CMakeFiles/mc.dir/gem/gemgen.c.o.d -o CMakeFiles/mc.dir/gem/gemgen.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o -MF CMakeFiles/mc.dir/gem/gemio.c.o.d -o CMakeFiles/mc.dir/gem/gemio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemio.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o -MF CMakeFiles/mc.dir/gem/gemref.c.o.d -o CMakeFiles/mc.dir/gem/gemref.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemref.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function 'Gem_delaunay': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: warning: 'Gem_writeGV' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 522 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type 'double *[4]' In file included from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function 'Gem_writeGV' 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: warning: 'Gem_writeGV' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 659 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function 'Gem_writeGV' 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: warning: 'Gem_writeGV' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 743 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function 'Gem_writeGV' 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o -MF CMakeFiles/mc.dir/gem/gemunref.c.o.d -o CMakeFiles/mc.dir/gem/gemunref.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemunref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o -MF CMakeFiles/mc.dir/gem/gemcube.c.o.d -o CMakeFiles/mc.dir/gem/gemcube.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemcube.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:31: warning: '%s' directive writing up to 79 bytes into a region of size 70 [-Wformat-overflow=] 495 | sprintf(rn,"Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: In function 'sprintf', inlined from 'Bvec_sfpcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 11 and 90 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:35: warning: '%s' directive writing up to 79 bytes into a region of size 66 [-Wformat-overflow=] 492 | sprintf(rn,"--->Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_sfpcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 94 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:32: warning: '%s' directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 776 | sprintf(rn,"Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_sfpbcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:36: warning: '%s' directive writing up to 79 bytes into a region of size 65 [-Wformat-overflow=] 773 | sprintf(rn,"--->Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_sfpbcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 95 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o -MF CMakeFiles/mc.dir/pde/pde.c.o.d -o CMakeFiles/mc.dir/pde/pde.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde/pde.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o -MF CMakeFiles/mc.dir/nam/am.c.o.d -o CMakeFiles/mc.dir/nam/am.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/am.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o -MF CMakeFiles/mc.dir/nam/lsolv.c.o.d -o CMakeFiles/mc.dir/nam/lsolv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/lsolv.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o -MF CMakeFiles/mc.dir/nam/nsolv.c.o.d -o CMakeFiles/mc.dir/nam/nsolv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/nsolv.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o -MF CMakeFiles/mc.dir/dyn/dyn.c.o.d -o CMakeFiles/mc.dir/dyn/dyn.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/dyn.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o -MF CMakeFiles/mc.dir/dyn/svio.c.o.d -o CMakeFiles/mc.dir/dyn/svio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/svio.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o -MF CMakeFiles/mc.dir/mcsh/mcsh.c.o.d -o CMakeFiles/mc.dir/mcsh/mcsh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function 'MCsh_builtIn': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: warning: 'Gem_writeGEOM' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 765 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 766 | sock, | ~~~~~ 767 | defKey, | ~~~~~~~ 768 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 769 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 770 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 771 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 | defX, | ~~~~~ 773 | "GV"); | ~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type 'double *[4]' In file included from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function 'Gem_writeGEOM' 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: warning: 'Gem_writeGEOM' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 810 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 811 | sock, | ~~~~~ 812 | defKey, | ~~~~~~~ 813 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 814 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 815 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 816 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 817 | defX, | ~~~~~ 818 | "MATH"); | ~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function 'Gem_writeGEOM' 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function 'Gem_writeTEC': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:33: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 1656 | sprintf(str1,"TETRAHEDRA"); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: In function 'sprintf', inlined from 'Gem_writeTEC' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function 'Gem_writeTEC': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:33: warning: 'TETRAHEDRON' directive writing 11 bytes into a region of size 10 [-Wformat-overflow=] 1657 | sprintf(str2,"TETRAHEDRON"); | ~~~~~~~~~~^ In function 'sprintf', inlined from 'Gem_writeTEC' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 73%] Linking C shared library libmc.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/mc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libmc.so.1.9 -o libmc.so.1.9.3 CMakeFiles/mc.dir/base/mc_base.c.o CMakeFiles/mc.dir/bam/bmat.c.o CMakeFiles/mc.dir/bam/bsolv.c.o CMakeFiles/mc.dir/bam/bvec.c.o CMakeFiles/mc.dir/bam/mat.c.o CMakeFiles/mc.dir/bam/matcopy.c.o CMakeFiles/mc.dir/bam/matln.c.o CMakeFiles/mc.dir/bam/mtool.c.o CMakeFiles/mc.dir/bam/slu.c.o CMakeFiles/mc.dir/bam/vec.c.o CMakeFiles/mc.dir/bam/vec3.c.o CMakeFiles/mc.dir/bam/zslu.c.o CMakeFiles/mc.dir/whb/whb.c.o CMakeFiles/mc.dir/whb/bvechb.c.o CMakeFiles/mc.dir/whb/hbtools.c.o CMakeFiles/mc.dir/whb/rcmat.c.o CMakeFiles/mc.dir/whb/brcmat.c.o CMakeFiles/mc.dir/whb/subopt.c.o CMakeFiles/mc.dir/aprx/aprx.c.o CMakeFiles/mc.dir/aprx/assem.c.o CMakeFiles/mc.dir/aprx/bnode.c.o CMakeFiles/mc.dir/aprx/estim.c.o CMakeFiles/mc.dir/aprx/eval.c.o CMakeFiles/mc.dir/aprx/io.c.o CMakeFiles/mc.dir/aprx/node.c.o CMakeFiles/mc.dir/aprx/parti.c.o CMakeFiles/mc.dir/aprx/re.c.o CMakeFiles/mc.dir/gem/vel.c.o CMakeFiles/mc.dir/gem/ves.c.o CMakeFiles/mc.dir/gem/gem.c.o CMakeFiles/mc.dir/gem/gemchk.c.o CMakeFiles/mc.dir/gem/gemdisp.c.o CMakeFiles/mc.dir/gem/gemg.c.o CMakeFiles/mc.dir/gem/gemgen.c.o CMakeFiles/mc.dir/gem/gemio.c.o CMakeFiles/mc.dir/gem/gemref.c.o CMakeFiles/mc.dir/gem/gemunref.c.o CMakeFiles/mc.dir/gem/gemcube.c.o CMakeFiles/mc.dir/pde/pde.c.o CMakeFiles/mc.dir/nam/am.c.o CMakeFiles/mc.dir/nam/lsolv.c.o CMakeFiles/mc.dir/nam/nsolv.c.o CMakeFiles/mc.dir/dyn/dyn.c.o CMakeFiles/mc.dir/dyn/svio.c.o CMakeFiles/mc.dir/mcsh/mcsh.c.o /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/aarch64-linux-gnu/libblas.so -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3 cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_symlink_library libmc.so.1.9.3 libmc.so.1.9 libmc.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 73%] Built target mc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/generic /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/pmgc /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o -MF CMakeFiles/apbs_generic.dir/nosh.c.o.d -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/nosh.c [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o -MF CMakeFiles/apbs_generic.dir/mgparm.c.o.d -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/mgparm.c [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o -MF CMakeFiles/apbs_generic.dir/femparm.c.o.d -o CMakeFiles/apbs_generic.dir/femparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/femparm.c [ 74%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildBd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/buildBd.c [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/pbamparm.c [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildAd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/buildAd.c [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildGd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/buildGd.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbsamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/pbsamparm.c [ 77%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o -MF CMakeFiles/apbs_pmgc.dir/cgd.c.o.d -o CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/cgd.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o -MF CMakeFiles/apbs_generic.dir/pbeparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/pbeparm.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildPd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/buildPd.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o -MF CMakeFiles/apbs_generic.dir/bemparm.c.o.d -o CMakeFiles/apbs_generic.dir/bemparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/bemparm.c [ 77%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o -MF CMakeFiles/apbs_pmgc.dir/gsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/gsd.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o -MF CMakeFiles/apbs_generic.dir/geoflowparm.c.o.d -o CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/geoflowparm.c [ 78%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o -MF CMakeFiles/apbs_pmgc.dir/matvecd.c.o.d -o CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/matvecd.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o -MF CMakeFiles/apbs_generic.dir/apolparm.c.o.d -o CMakeFiles/apbs_generic.dir/apolparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/apolparm.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o -MF CMakeFiles/apbs_generic.dir/vacc.c.o.d -o CMakeFiles/apbs_generic.dir/vacc.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vacc.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/valist.c.o -MF CMakeFiles/apbs_generic.dir/valist.c.o.d -o CMakeFiles/apbs_generic.dir/valist.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/valist.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o -MF CMakeFiles/apbs_generic.dir/vatom.c.o.d -o CMakeFiles/apbs_generic.dir/vatom.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vatom.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o -MF CMakeFiles/apbs_generic.dir/vpbe.c.o.d -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vpbe.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o -MF CMakeFiles/apbs_generic.dir/vcap.c.o.d -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vcap.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o -MF CMakeFiles/apbs_generic.dir/vclist.c.o.d -o CMakeFiles/apbs_generic.dir/vclist.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vclist.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o -MF CMakeFiles/apbs_generic.dir/vstring.c.o.d -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vstring.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgcsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mgcsd.c [ 81%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o -MF CMakeFiles/apbs_generic.dir/vparam.c.o.d -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vparam.c [ 81%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o -MF CMakeFiles/apbs_generic.dir/vgreen.c.o.d -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vgreen.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mgdrvd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgsubd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mgsubd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mikpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mikpckd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o -MF CMakeFiles/apbs_pmgc.dir/mypdec.c.o.d -o CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mypdec.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mlinpckd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o -MF CMakeFiles/apbs_pmgc.dir/newtond.c.o.d -o CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/newtond.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/newdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/newdrvd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o -MF CMakeFiles/apbs_pmgc.dir/powerd.c.o.d -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/powerd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o -MF CMakeFiles/apbs_pmgc.dir/smoothd.c.o.d -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/smoothd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgfasd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mgfasd.c [ 84%] Linking C shared library libapbs_generic.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.3 -o libapbs_generic.so.3 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/aarch64-linux-gnu/libblas.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_symlink_library libapbs_generic.so.3 libapbs_generic.so.3 libapbs_generic.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 84%] Built target apbs_generic make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/fem /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 84%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o -MF CMakeFiles/apbs_fem.dir/vcsm.c.o.d -o CMakeFiles/apbs_fem.dir/vcsm.c.o -c /build/reproducible-path/apbs-3.4.1/src/fem/vcsm.c [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o -MF CMakeFiles/apbs_fem.dir/vfetk.c.o.d -o CMakeFiles/apbs_fem.dir/vfetk.c.o -c /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o -MF CMakeFiles/apbs_fem.dir/vpee.c.o.d -o CMakeFiles/apbs_fem.dir/vpee.c.o -c /build/reproducible-path/apbs-3.4.1/src/fem/vpee.c /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Vfetk_PDE_ctor2': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1211:24: warning: assignment to 'void (*)(struct sPDE *, int, int, double *, double *, double (*)[3])' from incompatible pointer type 'void (*)(PDE *, int, int, double *, double *)' {aka 'void (*)(struct sPDE *, int, int, double *, double *)'} [-Wincompatible-pointer-types] 1211 | thee->u_T = Vfetk_PDE_u_T; | ^ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1073:28: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 1073 | sprintf(ptrfmt,"(%dI%d)",nptrline,numZdigits+1); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.h:67, from /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:57: In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1073:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1074:26: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1074:23: note: directive argument in the range [-2147483646, 2147483647] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~~~~~~ In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1074:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1075:28: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 1075 | sprintf(indfmt,"(%dI%d)",nindline,nrowdigits+1); | ^ In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1075:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1076:26: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1076:23: note: directive argument in the range [-2147483646, 2147483647] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~~~~~~ In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1076:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 85%] Linking C shared library libapbs_fem.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_fem.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_fem.so.3 -o libapbs_fem.so.3 CMakeFiles/apbs_fem.dir/vcsm.c.o CMakeFiles/apbs_fem.dir/vfetk.c.o CMakeFiles/apbs_fem.dir/vpee.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_symlink_library libapbs_fem.so.3 libapbs_fem.so.3 libapbs_fem.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 85%] Built target apbs_fem [ 86%] Linking C shared library libapbs_pmgc.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.3 -o libapbs_pmgc.so.3 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/aarch64-linux-gnu/libblas.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_symlink_library libapbs_pmgc.so.3 libapbs_pmgc.so.3 libapbs_pmgc.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 86%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/mg /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -MF CMakeFiles/apbs_mg.dir/vgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o -MF CMakeFiles/apbs_mg.dir/vmgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vmgrid.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o -MF CMakeFiles/apbs_mg.dir/vopot.c.o.d -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vopot.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o -MF CMakeFiles/apbs_mg.dir/vpmg.c.o.d -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vpmg.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -MF CMakeFiles/apbs_mg.dir/vpmgp.c.o.d -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vpmgp.c /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c: In function 'Vgrid_readDXBIN': /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c:853:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c:831:7: warning: argument 1 null where non-null expected [-Wnonnull] 831 | fclose(fd); | ^~~~~~~~~~ In file included from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.h:67, from /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c:57: /usr/include/stdio.h:183:12: note: in a call to function 'fclose' declared 'nonnull' 183 | extern int fclose (FILE *__stream) __nonnull ((1)); | ^~~~~~ [ 87%] Linking C shared library libapbs_mg.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.3 -o libapbs_mg.so.3 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../pmgc/libapbs_pmgc.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_symlink_library libapbs_mg.so.3 libapbs_mg.so.3 libapbs_mg.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 87%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/CMakeFiles/apbs_routines.dir/routines.c.o -MF CMakeFiles/apbs_routines.dir/routines.c.o.d -o CMakeFiles/apbs_routines.dir/routines.c.o -c /build/reproducible-path/apbs-3.4.1/src/routines.c /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'initAPOL': /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5046 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 2 of type 'char[1024]' /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 3 of type 'char[1024]' In file included from /build/reproducible-path/apbs-3.4.1/src/generic/apolparm.h:73, from /build/reproducible-path/apbs-3.4.1/src/generic/nosh.h:73, from /build/reproducible-path/apbs-3.4.1/src/apbs.h:70, from /build/reproducible-path/apbs-3.4.1/src/routines.h:64, from /build/reproducible-path/apbs-3.4.1/src/routines.c:54: /build/reproducible-path/apbs-3.4.1/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5048 | atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 2 of type 'char[1024]' /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 3 of type 'char[1024]' /build/reproducible-path/apbs-3.4.1/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ [ 87%] Linking CXX shared library libgamer.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgamer.so.1.9 -o libgamer.so.1.9.3 CMakeFiles/gamer.dir/base/gamer_base.c.o CMakeFiles/gamer.dir/triangle/triangle.c.o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o CMakeFiles/gamer.dir/biom/MarchingCube.C.o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o CMakeFiles/gamer.dir/biom/ReadLattice.C.o CMakeFiles/gamer.dir/biom/ReadPDB.C.o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o CMakeFiles/gamer.dir/biom/SurfExtract.C.o CMakeFiles/gamer.dir/biom/SurfRefine.C.o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -lmaloc /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writematMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2020:30: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2020 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/src/apbs.h:67: In function 'sprintf', inlined from 'writematMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2020:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_symlink_library libgamer.so.1.9.3 libgamer.so.1.9 libgamer.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 87%] Built target gamer /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2937:34: warning: '%s' directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2937 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2937:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2963:34: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2963 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2963:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2919:34: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2919 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2919:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2954:34: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2954 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2954:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2944:34: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2944 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2944:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2930:34: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2930 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2930:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2909:34: warning: '%s' directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2909 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2909:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/apbs-3.4.1/src/routines.c:4893:34: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4893 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataFE' at /build/reproducible-path/apbs-3.4.1/src/routines.c:4893:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/apbs-3.4.1/src/routines.c:4887:34: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4887 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataFE' at /build/reproducible-path/apbs-3.4.1/src/routines.c:4887:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/apbs-3.4.1/src/routines.c:4880:34: warning: '%s' directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4880 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function 'sprintf', inlined from 'writedataFE' at /build/reproducible-path/apbs-3.4.1/src/routines.c:4880:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 88%] Linking C shared library libapbs_routines.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.3 -o libapbs_routines.so.3 CMakeFiles/apbs_routines.dir/routines.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp mg/libapbs_mg.so.3 fem/libapbs_fem.so.3 pmgc/libapbs_pmgc.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libapbs_routines.so.3 libapbs_routines.so.3 libapbs_routines.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 88%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake "--color=" make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh 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/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 88%] Building C object src/CMakeFiles/apbs.dir/main.c.o make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs.dir/main.c.o -MF CMakeFiles/apbs.dir/main.c.o.d -o CMakeFiles/apbs.dir/main.c.o -c /build/reproducible-path/apbs-3.4.1/src/main.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o -MF CMakeFiles/mgmesh.dir/mgmesh.c.o.d -o CMakeFiles/mgmesh.dir/mgmesh.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/mgmesh.c make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend [ 89%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o [ 90%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/multivalue.dir/DependInfo.cmake "--color=" [ 90%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o -MF CMakeFiles/dxmath.dir/dxmath.c.o.d -o CMakeFiles/dxmath.dir/dxmath.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/dxmath.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/smooth.dir/smooth.c.o -MF CMakeFiles/smooth.dir/smooth.c.o.d -o CMakeFiles/smooth.dir/smooth.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/smooth.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o -MF CMakeFiles/mergedx.dir/mergedx.c.o.d -o CMakeFiles/mergedx.dir/mergedx.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/mergedx.c make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/benchmark.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/depend make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/similarity.dir/DependInfo.cmake "--color=" [ 90%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o -MF CMakeFiles/mergedx2.dir/mergedx2.c.o.d -o CMakeFiles/mergedx2.dir/mergedx2.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/mergedx2.c make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 91%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/build cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/dx2mol.dir/DependInfo.cmake "--color=" [ 91%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o /build/reproducible-path/apbs-3.4.1/src/main.c: In function 'main': cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src 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-I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc 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builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/main.c:319:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o -MF CMakeFiles/benchmark.dir/benchmark.c.o.d -o CMakeFiles/benchmark.dir/benchmark.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/benchmark.c [ 91%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/similarity.dir/similarity.c.o -MF CMakeFiles/similarity.dir/similarity.c.o.d -o CMakeFiles/similarity.dir/similarity.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/similarity.c [ 91%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/build cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/analysis.dir/analysis.c.o -MF CMakeFiles/analysis.dir/analysis.c.o.d -o CMakeFiles/analysis.dir/analysis.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/analysis.c make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 91%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o -MF CMakeFiles/dx2mol.dir/dx2mol.c.o.d -o CMakeFiles/dx2mol.dir/dx2mol.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/dx2mol.c [ 91%] Linking C executable ../bin/mgmesh cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mgmesh.dir/mgmesh.c.o -o ../bin/mgmesh ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Linking C executable ../bin/multivalue cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/multivalue.dir/link.txt --verbose=1 [ 92%] Linking C executable ../bin/value cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/value.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/multivalue.dir/multivalue.c.o -o ../bin/multivalue ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Linking C executable ../bin/smooth [ 93%] Linking C executable ../bin/benchmark cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/value.dir/value.c.o -o ../bin/value ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 93%] Linking C executable ../bin/dx2mol cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/smooth.dir/smooth.c.o -o ../bin/smooth ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/benchmark.dir/benchmark.c.o -o ../bin/benchmark ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 93%] Linking C executable ../bin/dxmath /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2mol.dir/dx2mol.c.o -o ../bin/dx2mol ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so 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/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dxmath.dir/dxmath.c.o -o ../bin/dxmath ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so 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../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 94%] Linking C executable apbs cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp libapbs_routines.so.3 mg/libapbs_mg.so.3 pmgc/libapbs_pmgc.so.3 fem/libapbs_fem.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 94%] Built target mgmesh [ 94%] Linking C executable ../bin/mergedx make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/dx2uhbd.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 94%] Linking C executable ../bin/mergedx2 cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 [ 94%] Built target multivalue make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx2.dir/mergedx2.c.o -o ../bin/mergedx2 ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -MF CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o.d -o CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/dx2uhbd.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake "--color=" [ 94%] Built target dx2mol make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend [ 94%] Built target benchmark make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o -MF CMakeFiles/del2dx.dir/del2dx.c.o.d -o CMakeFiles/del2dx.dir/del2dx.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/similarity.dir/similarity.c.o -o ../bin/similarity ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend [ 96%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o -MF CMakeFiles/tensor2dx.dir/tensor2dx.c.o.d -o CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c [ 96%] Built target dxmath [ 96%] Built target analysis make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/manip /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake "--color=" make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python-pybind /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o -MF CMakeFiles/coulomb.dir/coulomb.c.o.d -o CMakeFiles/coulomb.dir/coulomb.c.o -c /build/reproducible-path/apbs-3.4.1/tools/manip/coulomb.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/born.dir/born.c.o -MF CMakeFiles/born.dir/born.c.o.d -o CMakeFiles/born.dir/born.c.o -c /build/reproducible-path/apbs-3.4.1/tools/manip/born.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 97%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o [ 97%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cc -D_apbslib_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/python3.11 -I/build/reproducible-path/apbs-3.4.1/tools/python -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -MF CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o.d -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o -MF CMakeFiles/apbs_pybind.dir/module.cpp.o.d -o CMakeFiles/apbs_pybind.dir/module.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/module.cpp [ 97%] Built target apbs make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c: In function 'main': /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:76:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:89:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:97:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:103:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:106:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 97%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_nosh.cpp [ 97%] Built target mergedx [ 98%] Linking C executable ../bin/dx2uhbd /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c: In function 'main': /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2uhbd.dir/link.txt --verbose=1 /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c: In function 'main': /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_vatom.cpp [ 99%] Built target mergedx2 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o [ 99%] Linking C executable ../bin/uhbd_asc2bin [100%] Linking C executable ../bin/del2dx cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_valist.cpp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 [100%] Linking C executable ../bin/coulomb cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/coulomb.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/del2dx.dir/del2dx.c.o -o ../bin/del2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [100%] Linking C executable ../bin/tensor2dx [100%] Built target similarity cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -o ../bin/uhbd_asc2bin ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/coulomb.dir/coulomb.c.o -o ../bin/coulomb ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Linking C executable ../bin/born cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 [100%] Built target dx2uhbd /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/born.dir/born.c.o -o ../bin/born ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target uhbd_asc2bin [100%] Built target tensor2dx [100%] Built target del2dx [100%] Built target coulomb make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target born [100%] Linking C shared library _apbslib.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,_apbslib.so -o _apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target _apbslib [100%] Linking CXX shared module apbs.cpython-311-aarch64-linux-gnu.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pybind.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o apbs.cpython-311-aarch64-linux-gnu.so CMakeFiles/apbs_pybind.dir/module.cpp.o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target apbs_pybind make[2]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' PYTHONPATH=/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python sphinx-build -b html docs /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/docs/_build/html # HTML generator Running Sphinx v7.2.6 WARNING: html_static_path entry '_static' does not exist [autosummary] generating autosummary for: api/index.rst, background.rst, formats/apbs-xml-parm.rst, formats/flat-parm.rst, formats/harwell.rst, formats/index.rst, formats/mcsf.rst, formats/opendx.rst, formats/pdb.rst, formats/pqr.rst, ..., using/input/old/generic/sdens.rst, using/input/old/generic/srad.rst, using/input/old/generic/swin.rst, using/input/old/generic/temp.rst, using/input/old/index.rst, using/input/old/print.rst, using/input/old/read.rst, using/tests.rst, using/tools.rst, using/units.rst WARNING: Failed to import apbs.input_file.read. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' WARNING: Failed to import apbs.input_file.calculate.boundary_element. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' WARNING: Failed to import apbs.input_file.calculate. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' WARNING: Failed to import apbs.input_file.calculate.generic. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' WARNING: Failed to import apbs.input_file.calculate.finite_element. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' WARNING: Failed to import apbs.input_file.calculate.nonpolar.Nonpolar. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' WARNING: Failed to import apbs.input_file.process. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' WARNING: Failed to import apbs.input_file.calculate.finite_difference. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' WARNING: Failed to import apbs.input_file. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' loading intersphinx inventory from https://docs.python.org/3/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 127 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 1%] api/index reading sources... [ 2%] background reading sources... [ 2%] formats/apbs-xml-parm reading sources... [ 3%] formats/flat-parm reading sources... [ 4%] formats/harwell reading sources... [ 5%] formats/index reading sources... [ 6%] formats/mcsf reading sources... [ 6%] formats/opendx reading sources... [ 7%] formats/pdb reading sources... [ 8%] formats/pqr reading sources... [ 9%] formats/uhbd reading sources... [ 9%] formats/xml-struct reading sources... [ 10%] getting/index reading sources... [ 11%] getting/source reading sources... [ 12%] help reading sources... [ 13%] index reading sources... [ 13%] reading reading sources... [ 14%] releases reading sources... [ 15%] supporting reading sources... [ 16%] todo reading sources... [ 17%] using/examples/binding-energies reading sources... [ 17%] using/examples/salt-linkage reading sources... [ 18%] using/examples/solvation-energies reading sources... [ 19%] using/examples/visualization-pymol reading sources... [ 20%] using/examples/visualization-unitymol reading sources... [ 20%] using/index reading sources... [ 21%] using/input/new/calculate/boundary_element reading sources... [ 22%] using/input/new/calculate/finite_difference reading sources... [ 23%] using/input/new/calculate/finite_element reading sources... [ 24%] using/input/new/calculate/index reading sources... [ 24%] using/input/new/calculate/nonpolar reading sources... [ 25%] using/input/new/index reading sources... [ 26%] using/input/new/process reading sources... [ 27%] using/input/new/process_api reading sources... [ 28%] using/input/new/read reading sources... [ 28%] using/input/old/apolar/dpos reading sources... [ 29%] using/input/old/apolar/gamma reading sources... [ 30%] using/input/old/apolar/index reading sources... [ 31%] using/input/old/apolar/press reading sources... [ 31%] using/input/old/apolar/srfm reading sources... [ 32%] using/input/old/elec/3dmap reading sources... [ 33%] using/input/old/elec/akeyPRE reading sources... [ 34%] using/input/old/elec/akeySOLVE reading sources... [ 35%] using/input/old/elec/async reading sources... [ 35%] using/input/old/elec/bcfl reading sources... [ 36%] using/input/old/elec/cgcent reading sources... [ 37%] using/input/old/elec/cglen reading sources... [ 38%] using/input/old/elec/chgm reading sources... [ 39%] using/input/old/elec/diff reading sources... [ 39%] using/input/old/elec/dime reading sources... [ 40%] using/input/old/elec/domainLength reading sources... [ 41%] using/input/old/elec/dx reading sources... [ 42%] using/input/old/elec/ekey reading sources... [ 43%] using/input/old/elec/etol reading sources... [ 43%] using/input/old/elec/exp reading sources... [ 44%] using/input/old/elec/fe-manual reading sources... [ 45%] using/input/old/elec/fgcent reading sources... [ 46%] using/input/old/elec/fglen reading sources... [ 46%] using/input/old/elec/gamma-geoflow reading sources... [ 47%] using/input/old/elec/gcent reading sources... [ 48%] using/input/old/elec/geoflow-auto reading sources... [ 49%] using/input/old/elec/glen reading sources... [ 50%] using/input/old/elec/grid2d reading sources... [ 50%] using/input/old/elec/gridpts reading sources... [ 51%] using/input/old/elec/imat reading sources... [ 52%] using/input/old/elec/index reading sources... [ 53%] using/input/old/elec/ion reading sources... [ 54%] using/input/old/elec/lpbe reading sources... [ 54%] using/input/old/elec/lrpbe reading sources... [ 55%] using/input/old/elec/mac reading sources... [ 56%] using/input/old/elec/maxsolve reading sources... [ 57%] using/input/old/elec/maxvert reading sources... [ 57%] using/input/old/elec/mesh reading sources... [ 58%] using/input/old/elec/mg-auto reading sources... [ 59%] using/input/old/elec/mg-dummy reading sources... [ 60%] using/input/old/elec/mg-manual reading sources... [ 61%] using/input/old/elec/mg-para reading sources... [ 61%] using/input/old/elec/nlev reading sources... [ 62%] using/input/old/elec/npbe reading sources... [ 63%] using/input/old/elec/nrpbe reading sources... [ 64%] using/input/old/elec/ntraj reading sources... [ 65%] using/input/old/elec/ofrac reading sources... [ 65%] using/input/old/elec/outdata reading sources... [ 66%] using/input/old/elec/pbam-auto reading sources... [ 67%] using/input/old/elec/pbc reading sources... [ 68%] using/input/old/elec/pbsam-auto reading sources... [ 69%] using/input/old/elec/pdie reading sources... [ 69%] using/input/old/elec/pdime reading sources... [ 70%] using/input/old/elec/press-geoflow reading sources... [ 71%] using/input/old/elec/pygbe reading sources... [ 72%] using/input/old/elec/randorient reading sources... [ 72%] using/input/old/elec/runname reading sources... [ 73%] using/input/old/elec/runtype reading sources... [ 74%] using/input/old/elec/salt reading sources... [ 75%] using/input/old/elec/sdie reading sources... [ 76%] using/input/old/elec/srfm reading sources... [ 76%] using/input/old/elec/surf reading sources... [ 77%] using/input/old/elec/tabi reading sources... [ 78%] using/input/old/elec/targetNum reading sources... [ 79%] using/input/old/elec/targetRes reading sources... [ 80%] using/input/old/elec/term reading sources... [ 80%] using/input/old/elec/termcombine reading sources... [ 81%] using/input/old/elec/tolsp reading sources... [ 82%] using/input/old/elec/tree_n0 reading sources... [ 83%] using/input/old/elec/tree_order reading sources... [ 83%] using/input/old/elec/units reading sources... [ 84%] using/input/old/elec/usemap reading sources... [ 85%] using/input/old/elec/usemesh reading sources... [ 86%] using/input/old/elec/vdwdisp reading sources... [ 87%] using/input/old/elec/write reading sources... [ 87%] using/input/old/elec/writemat reading sources... [ 88%] using/input/old/elec/xyz reading sources... [ 89%] using/input/old/generic/bconc reading sources... [ 90%] using/input/old/generic/calcenergy reading sources... [ 91%] using/input/old/generic/calcforce reading sources... [ 91%] using/input/old/generic/grid reading sources... [ 92%] using/input/old/generic/mol reading sources... [ 93%] using/input/old/generic/sdens reading sources... [ 94%] using/input/old/generic/srad reading sources... [ 94%] using/input/old/generic/swin reading sources... [ 95%] using/input/old/generic/temp reading sources... [ 96%] using/input/old/index reading sources... [ 97%] using/input/old/print reading sources... [ 98%] using/input/old/read reading sources... [ 98%] using/tests reading sources... [ 99%] using/tools reading sources... [100%] using/units /build/reproducible-path/apbs-3.4.1/docs/getting/index.rst:41: ERROR: Unexpected indentation. /build/reproducible-path/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "geometric flow". /build/reproducible-path/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "fetk". /build/reproducible-path/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "pbam/pbsam". /build/reproducible-path/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "tabi-pb". WARNING: autodoc: failed to import module 'input_file.calculate.boundary_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_difference' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.generic' from module 'apbs'; the following exception was raised: No module named 'pyparsing' /build/reproducible-path/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document or section may not begin with a transition. /build/reproducible-path/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document may not end with a transition. WARNING: autodoc: failed to import module 'input_file.calculate.nonpolar.Nonpolar' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.process' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.read' from module 'apbs'; the following exception was raised: No module named 'pyparsing' looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/apbs-3.4.1/docs/using/input/old/elec/pygbe.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [ 1%] api/index writing output... [ 2%] background writing output... [ 2%] formats/apbs-xml-parm writing output... [ 3%] formats/flat-parm writing output... [ 4%] formats/harwell writing output... [ 5%] formats/index writing output... [ 6%] formats/mcsf writing output... [ 6%] formats/opendx writing output... [ 7%] formats/pdb writing output... [ 8%] formats/pqr writing output... [ 9%] formats/uhbd writing output... [ 9%] formats/xml-struct writing output... [ 10%] getting/index writing output... [ 11%] getting/source writing output... [ 12%] help writing output... [ 13%] index writing output... [ 13%] reading writing output... [ 14%] releases writing output... [ 15%] supporting writing output... [ 16%] todo writing output... [ 17%] using/examples/binding-energies writing output... [ 17%] using/examples/salt-linkage writing output... [ 18%] using/examples/solvation-energies writing output... [ 19%] using/examples/visualization-pymol writing output... [ 20%] using/examples/visualization-unitymol writing output... 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[ 80%] media/1fas_VR.png copying images... [ 90%] media/UI.png copying images... [100%] media/AChE.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 28 warnings. The HTML pages are in obj-aarch64-linux-gnu/docs/_build/html. make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=cmake dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_installdirs -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/apbs-3.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/apbs-3.4.1 -B/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RELWITHDEBINFO" -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindUMFPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuperLU.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuiteSparse.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindLAPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindARPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindAMD.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/punc.h -- Installing: 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/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/parm.dat -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.pdb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.in -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/complex.in -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/apolarforces -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/ion-pmf/README.md -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Run_membrane-helix.sh -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy.in -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/hca-bind -- Installing: 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/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/isobutane.pdb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/force.result -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/ethane.pdb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/cyclopentane.pdb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/cyclohexane.pdb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/butane.pdb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/apbs-forces.in -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in -- Installing: 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/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/value -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mgmesh make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' (cd tests; PATH=/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/build/reproducible-path/apbs-3.4.1/tools/manip python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__) TESTING WITH BINARY_NAME:apbs START_DIR:/build/reproducible-path/apbs-3.4.1/build -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.001006 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in CHECKING:/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs NOTE: Using apbs binary:/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs Testing all sections The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv ================================================================================ Running tests for born section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential-PE0.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) *** PASSED *** Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) *** PASSED *** Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) *** PASSED *** Elapsed time: 14.529334 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] COMPUTED RESULT 960.7073836227 COMPUTED RESULT 2200.266567971 COMPUTED RESULT 4732.245131587 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.7735526282 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) *** PASSED *** Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) *** PASSED *** Elapsed time: 13.395385 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 2201.243880085 COMPUTED RESULT 4733.006258977 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.0124252387 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE0.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.401768459022e+02 8.142935592471e+02 1.485255308186e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.761864094552e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE0.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE1.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.401768459022e+02 8.142778312125e+02 1.485246667424e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.762728170718e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE1.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE2.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605695E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.401768459091e+02 8.142935605695e+02 1.485255306569e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.761864257239e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE2.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE3.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344953E+01 kJ/mol Global net ELEC energy = -5.762728344953E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.401768459091e+02 8.142778325440e+02 1.485246665692e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.762728344953e+01 Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) *** PASSED *** Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) *** PASSED *** Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) *** PASSED *** Elapsed time: 68.942458 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-mol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] COMPUTED RESULT 960.7073836226 COMPUTED RESULT 3257.1427835730997 COMPUTED RESULT 5941.0039478710005 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867462003 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE0.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.383232191816e+02 8.145369591602e+02 1.485524998001e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734895113069e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE0.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE1.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.383232191816e+02 8.145419898332e+02 1.485529328612e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734462051928e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE1.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE2.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.383232191909e+02 8.145369593489e+02 1.485524997676e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734895146550e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE2.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE3.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.383232191909e+02 8.145419900310e+02 1.485529328301e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734462084052e+01 Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) *** PASSED *** Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) *** PASSED *** Elapsed time: 60.712687 seconds -------------------------------------------------------------------------------- Total elapsed time: 157.58087 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in Checking for intermediate energies in input file apbs-smol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 3258.1578983732998 COMPUTED RESULT 5942.108652589999 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -229.38714395599 Running tests for actin-dimer-auto section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058621E+02 kJ/mol Global net ELEC energy = 1.048683058621E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) *** PASSED *** Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) *** PASSED *** Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) *** PASSED *** Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) *** PASSED *** Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) *** PASSED *** Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) *** PASSED *** Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02) *** PASSED *** Elapsed time: 232.533018 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058621] EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] COMPUTED RESULT 152761.7850342 COMPUTED RESULT 291951.0754196 COMPUTED RESULT 152767.184488 COMPUTED RESULT 291546.8859278 COMPUTED RESULT 305631.7807611 COMPUTED RESULT 583602.8296532 COMPUTED RESULT 104.8683058621 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077688E+02 kJ/mol Global net ELEC energy = 1.095841077688E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) *** PASSED *** Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) *** PASSED *** Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) *** PASSED *** Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) *** PASSED *** Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) *** PASSED *** Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) *** PASSED *** Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 166.971375 seconds -------------------------------------------------------------------------------- Total elapsed time: 399.504393 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file alkanes.in Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077688] EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] COMPUTED RESULT 152863.2421825 COMPUTED RESULT 292061.866232 COMPUTED RESULT 152929.7900572 COMPUTED RESULT 291659.2202835 COMPUTED RESULT 305924.4262535 COMPUTED RESULT 583830.6706232 COMPUTED RESULT 109.5841077688 Running tests for alkanes section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: alkanes.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'alkanes.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) *** PASSED *** Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) *** PASSED *** Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) *** PASSED *** Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) *** PASSED *** Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) *** PASSED *** Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) *** PASSED *** Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) *** PASSED *** Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) *** PASSED *** Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) *** PASSED *** Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) *** PASSED *** Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) *** PASSED *** Elapsed time: 18.884722 seconds -------------------------------------------------------------------------------- Total elapsed time: 18.884722 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in Checking for intermediate energies in input file alkanes.out EXPECTED COMPUTED: 11 EXPECTED EXPECTED: 11 COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] EXPECTED: ['1.439739455792E+01', '1.208346456826E+01', '1.354016672221E+01', '9.363673200142E+00', '9.422717598546E+00', '1.640068943201E+01', '1.323144287435E+01', '7.894367190329E+00', '1.449633815052E+01', '1.447900211546E+01', '1.192358496286E+01'] COMPUTED RESULT 14.39739455792 COMPUTED RESULT 12.08346456826 COMPUTED RESULT 13.54016672221 COMPUTED RESULT 9.363673200142 COMPUTED RESULT 9.422717598546 COMPUTED RESULT 16.40068943201 COMPUTED RESULT 13.23144287435 COMPUTED RESULT 7.894367190329 COMPUTED RESULT 14.49633815052 COMPUTED RESULT 14.47900211546 COMPUTED RESULT 11.92358496286 Running tests for FKBP section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7h-dmso-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086373E+01 kJ/mol Global net ELEC energy = 1.500810086373E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) *** PASSED *** Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) *** PASSED *** Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) *** PASSED *** Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 44.335959 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in Checking for intermediate energies in input file 1d7h-dmso-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086373] EXPECTED: ['1.060899690259E+04', '4.276523673491E+04', '1.399234956777E+04', '4.610066575192E+04', '3.961107503213E+01', '7.121048606059E+02', '6.751571424823E+01', '7.339101343121E+02', '1.058410584089E+04', '4.205385249581E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.500810086371E+01'] COMPUTED RESULT 10608.99690259 COMPUTED RESULT 42765.23673491 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 39.61107503213 COMPUTED RESULT 712.1048606059 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10584.10584089 COMPUTED RESULT 42053.85249581 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3335.429017008 COMPUTED RESULT -21.80527370616 COMPUTED RESULT -3328.631844166 COMPUTED RESULT 15.00810086373 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7h-dmso-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192074E+01 kJ/mol Global net ELEC energy = 1.624454192074E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) *** PASSED *** Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) *** PASSED *** Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) *** PASSED *** Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 32.61131 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in Checking for intermediate energies in input file 1d7h-dmso-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192074] EXPECTED: ['1.074948704824E+04', '4.289487256481E+04', '1.399234956777E+04', '4.610066575192E+04', '3.719709905887E+01', '7.125747080979E+02', '6.751571424823E+01', '7.339101343121E+02', '1.071654753674E+04', '4.218178203716E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.624454192072E+01'] COMPUTED RESULT 10749.48704824 COMPUTED RESULT 42894.87256481 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 37.19709905887 COMPUTED RESULT 712.5747080979 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10716.54753674 COMPUTED RESULT 42181.78203716 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3205.793187109 COMPUTED RESULT -21.33542621421 COMPUTED RESULT -3200.702302816 COMPUTED RESULT 16.24454192074 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7i-dss-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933664E+01 kJ/mol Global net ELEC energy = 1.442499933664E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) *** PASSED *** Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) *** PASSED *** Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) *** PASSED *** Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 44.837336 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in Checking for intermediate energies in input file 1d7i-dss-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933664] EXPECTED: ['9.160578033846E+03', '3.955701871716E+04', '1.264965939588E+04', '4.301801664829E+04', '9.431133325426E+01', '1.677348113184E+03', '1.171079106781E+02', '1.697869784185E+03', '9.040108332204E+03', '3.787747796627E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.442500529301E+01'] COMPUTED RESULT 9160.578033846 COMPUTED RESULT 39557.01871716 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 94.31133325426 COMPUTED RESULT 1677.348113184 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9040.108332204 COMPUTED RESULT 37877.47796627 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -3460.997931137 COMPUTED RESULT -20.52167100108 COMPUTED RESULT -3454.901259473 COMPUTED RESULT 14.42499933664 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7i-dss-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742843E+01 kJ/mol Global net ELEC energy = 1.545150742843E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) *** PASSED *** Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) *** PASSED *** Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) *** PASSED *** Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 32.759785 seconds -------------------------------------------------------------------------------- Total elapsed time: 154.54439 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file 1d7i-dss-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742843] EXPECTED: ['9.634884642408E+03', '4.003177540425E+04', '1.264965939588E+04', '4.301801664829E+04', '7.942232645345E+01', '1.677798535473E+03', '1.171079106781E+02', '1.697869784185E+03', '9.507068451372E+03', '3.835075772299E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.545150009785E+01'] COMPUTED RESULT 9634.884642408 COMPUTED RESULT 40031.77540425 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 79.42232645345 COMPUTED RESULT 1677.798535473 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9507.068451372 COMPUTED RESULT 38350.75772299 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -2986.24124404 COMPUTED RESULT -20.07124871262 COMPUTED RESULT -2981.621502756 COMPUTED RESULT 15.45150742843 Running tests for hca-bind section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812684E+01 kJ/mol Global net ELEC energy = -5.246475812684E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) *** PASSED *** Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) *** PASSED *** Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) *** PASSED *** Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) *** PASSED *** Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) *** PASSED *** Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) *** PASSED *** Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) *** PASSED *** Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) *** PASSED *** Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) *** PASSED *** Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 39.423452 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812684] EXPECTED: ['2.213600726771E+02', '1.825764811255E+03', '6.458471211905E+03', '2.093606095527E+04', '1.515433544464E+05', '1.786369323561E+05', '2.105322784838E+04', '1.533304996252E+05', '1.850429388099E+05', '-5.246475812665E+01'] COMPUTED RESULT 221.3600726771 COMPUTED RESULT 1825.764811255 COMPUTED RESULT 6458.471211905 COMPUTED RESULT 20936.06095527 COMPUTED RESULT 151543.3544464 COMPUTED RESULT 178636.9323561 COMPUTED RESULT 21053.22784838 COMPUTED RESULT 153330.4996252 COMPUTED RESULT 185042.9388099 COMPUTED RESULT -52.46475812684 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017059E+01 kJ/mol Global net ELEC energy = -5.405979017059E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) *** PASSED *** Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) *** PASSED *** Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) *** PASSED *** Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) *** PASSED *** Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) *** PASSED *** Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) *** PASSED *** Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) *** PASSED *** Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) *** PASSED *** Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) *** PASSED *** Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 27.900462 seconds -------------------------------------------------------------------------------- Total elapsed time: 67.323914 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017059] EXPECTED: ['1.884888131017E+02', '1.820045922544E+03', '6.460002606908E+03', '2.189161497021E+04', '1.520000494925E+05', '1.790436191580E+05', '2.195842512312E+04', '1.537771604355E+05', '1.854495619747E+05', '-5.405977880082E+01'] COMPUTED RESULT 188.4888131017 COMPUTED RESULT 1820.045922544 COMPUTED RESULT 6460.002606908 COMPUTED RESULT 21891.61497021 COMPUTED RESULT 152000.0494925 COMPUTED RESULT 179043.619158 COMPUTED RESULT 21958.42512312 COMPUTED RESULT 153777.1604355 COMPUTED RESULT 185449.5619747 COMPUTED RESULT -54.05979017059 Running tests for ionize section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) *** PASSED *** Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) *** PASSED *** Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) *** PASSED *** Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) *** PASSED *** Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) *** PASSED *** Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) *** PASSED *** Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) *** PASSED *** Elapsed time: 29.346041 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5823.898055191, 9793.274462353, 5846.917564309, 9815.953282539, 8219.846763777, 13927.41988698, 8420.373979905, 14127.16615065, 3862.359524598, 6288.15625161, 4162.533113906, 6585.616091973, -22.67882018629, -199.7462636633, -297.4598403628, -474.5272838398] EXPECTED: ['5.823898055191E+03', '9.793274462353E+03', '5.846917564309E+03', '9.815953282539E+03', '8.219846763777E+03', '1.392741988698E+04', '8.420373979905E+03', '1.412716615065E+04', '3.862359524598E+03', '6.288156251610E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.267881997628E+01', '-1.997462580204E+02', '-2.974598331751E+02', '-4.745272868358E+02'] COMPUTED RESULT 5823.898055191 COMPUTED RESULT 9793.274462353 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8219.846763777 COMPUTED RESULT 13927.41988698 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3862.359524598 COMPUTED RESULT 6288.15625161 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.67882018629 COMPUTED RESULT -199.7462636633 COMPUTED RESULT -297.4598403628 COMPUTED RESULT -474.5272838398 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) *** PASSED *** Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) *** PASSED *** Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) *** PASSED *** Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) *** PASSED *** Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) *** PASSED *** Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) *** PASSED *** Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) *** PASSED *** Elapsed time: 21.833455999999998 seconds -------------------------------------------------------------------------------- Total elapsed time: 51.179497 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file ion-pmf.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5824.172730822, 9793.622759239, 5846.917564309, 9815.953282539, 8221.328580569, 13928.67783119, 8420.373979905, 14127.16615065, 3863.066835285, 6289.649216644, 4162.533113906, 6585.616091973, -22.33052329981, -198.4883194538, -295.9668753288, -472.1246714828] EXPECTED: ['5.824172730822E+03', '9.793622759239E+03', '5.846917564309E+03', '9.815953282539E+03', '8.221328580569E+03', '1.392867783119E+04', '8.420373979905E+03', '1.412716615065E+04', '3.863066835285E+03', '6.289649216644E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.233050451129E+01', '-1.984883191396E+02', '-2.959668653531E+02', '-4.721247084138E+02'] COMPUTED RESULT 5824.172730822 COMPUTED RESULT 9793.622759239 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8221.328580569 COMPUTED RESULT 13928.67783119 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3863.066835285 COMPUTED RESULT 6289.649216644 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.33052329981 COMPUTED RESULT -198.4883194538 COMPUTED RESULT -295.9668753288 COMPUTED RESULT -472.1246714828 Running tests for ion-pmf section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: ion-pmf.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'ion-pmf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.128e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.766e-05 tot 1 -2.723e-02 9.131e-07 9.134e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.768e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718345777E+00 WCA energy for atom 1: -6.909411348230E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365306965532E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365306965532E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) *** PASSED *** Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) *** PASSED *** Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) *** PASSED *** Elapsed time: 17.416918 seconds -------------------------------------------------------------------------------- Total elapsed time: 17.416918 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in Checking for intermediate energies in input file ion-pmf.out EXPECTED COMPUTED: 4 EXPECTED EXPECTED: 4 COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65306965532 Running tests for pka-lig section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-vdw.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648803E+00 kJ/mol Global net ELEC energy = 8.083515648803E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) *** PASSED *** Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) *** PASSED *** Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) *** PASSED *** Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) *** PASSED *** Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) *** PASSED *** Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) *** PASSED *** Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 41.129485 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in Checking for intermediate energies in input file apbs-mol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.083515648803] EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] COMPUTED RESULT 2224.988750664 COMPUTED RESULT 10496.95084686 COMPUTED RESULT 181845.0789522 COMPUTED RESULT 300825.4338259 COMPUTED RESULT 184091.8409896 COMPUTED RESULT 311330.4681884 COMPUTED RESULT 8.083515648803 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255720E+01 kJ/mol Global net ELEC energy = 2.096300255720E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) *** PASSED *** Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) *** PASSED *** Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) *** PASSED *** Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) *** PASSED *** Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) *** PASSED *** Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) *** PASSED *** Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 30.842386 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in Checking for intermediate energies in input file apbs-smol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.9630025572] EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] COMPUTED RESULT 2226.793167046 COMPUTED RESULT 10505.04485887 COMPUTED RESULT 182797.6621645 COMPUTED RESULT 301722.8546773 COMPUTED RESULT 185081.9075387 COMPUTED RESULT 312248.8625388 COMPUTED RESULT 20.9630025572 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-surf.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686582E+02 kJ/mol Global net ELEC energy = 1.192607686582E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) *** PASSED *** Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) *** PASSED *** Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) *** PASSED *** Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) *** PASSED *** Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) *** PASSED *** Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) *** PASSED *** Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 32.838168 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in Checking for intermediate energies in input file apbs-mol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686582] EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] COMPUTED RESULT 2244.350164274 COMPUTED RESULT 10521.49475373 COMPUTED RESULT 186261.5690066 COMPUTED RESULT 305181.0884053 COMPUTED RESULT 188662.5455219 COMPUTED RESULT 315821.8439277 COMPUTED RESULT 119.2607686582 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-surf.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) *** PASSED *** Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) *** PASSED *** Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) *** PASSED *** Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) *** PASSED *** Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) *** PASSED *** Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) *** PASSED *** Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) *** PASSED *** Elapsed time: 25.904317 seconds -------------------------------------------------------------------------------- Total elapsed time: 130.714356 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_1.in Checking for intermediate energies in input file apbs-smol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] COMPUTED RESULT 2251.46678942 COMPUTED RESULT 10528.14502873 COMPUTED RESULT 186407.1689626 COMPUTED RESULT 305331.9953673 COMPUTED RESULT 188802.7142979 COMPUTED RESULT 315969.0177241 COMPUTED RESULT 108.8773280806 Running tests for point-pmf section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_1.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) *** PASSED *** Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) *** PASSED *** Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) *** PASSED *** Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) *** PASSED *** Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) *** PASSED *** Elapsed time: 5.796174 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in Checking for intermediate energies in input file complex-0_1.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 89.75920687031, 205.8277719334, 0.0, 0.0, 0.0, 97.7604, 89.7592, 205.828, 96.5336, 88.6151, 201.106, 18.30820799027] EXPECTED: ['9.776035707281E+01', '8.975920687031E+01', '2.058277719334E+02', '*', '*', '*', '97.7604', '89.7592', '205.828', '96.5336', '88.6151', '201.106', '1.830820799027E+01'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 89.75920687031 COMPUTED RESULT 205.8277719334 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 89.7592 COMPUTED RESULT 205.828 COMPUTED RESULT 96.5336 COMPUTED RESULT 88.6151 COMPUTED RESULT 201.106 COMPUTED RESULT 18.30820799027 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_2.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086751E+00 kJ/mol Global net ELEC energy = 8.906694086751E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) *** PASSED *** Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) *** PASSED *** Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00) *** PASSED *** Elapsed time: 5.809542 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in Checking for intermediate energies in input file complex-0_2.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.906694086751] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.084282010393E+02', '*', '*', '*', '97.7604', '101.761', '208.428', '96.5336', '100.656', '203.83', '8.906694086750E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 208.4282010393 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 208.428 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.656 COMPUTED RESULT 203.83 COMPUTED RESULT 8.906694086751 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_3.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) *** PASSED *** Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) *** PASSED *** Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) *** PASSED *** Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) *** PASSED *** Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) *** PASSED *** Elapsed time: 5.610425 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in Checking for intermediate energies in input file complex-0_3.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 133.7661883222, 237.436145212, 0.0, 0.0, 0.0, 97.7604, 133.766, 237.436, 96.5336, 132.672, 232.924, 5.909599816984] EXPECTED: ['9.776035707281E+01', '1.337661883222E+02', '2.374361452120E+02', '*', '*', '*', '97.7604', '133.766', '237.436', '96.5336', '132.672', '232.924', '5.909599816984E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 133.7661883222 COMPUTED RESULT 237.436145212 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 133.766 COMPUTED RESULT 237.436 COMPUTED RESULT 96.5336 COMPUTED RESULT 132.672 COMPUTED RESULT 232.924 COMPUTED RESULT 5.909599816984 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_4.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_4.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) *** PASSED *** Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) *** PASSED *** Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) *** PASSED *** Elapsed time: 5.793522 seconds -------------------------------------------------------------------------------- Total elapsed time: 23.009663 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file complex-0_4.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 203.9516519, 0.0, 0.0, 0.0, 97.7604, 101.761, 203.952, 96.5336, 100.654, 199.493, 4.430144947418] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.039516519000E+02', '*', '*', '*', '97.7604', '101.761', '203.952', '96.5336', '100.654', '199.493', '4.430144947418E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 203.9516519 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 203.952 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.654 COMPUTED RESULT 199.493 COMPUTED RESULT 4.430144947418 Running tests for solv section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488075E+01 kJ/mol Global net ELEC energy = -3.624863488075E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) *** PASSED *** Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) *** PASSED *** Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) *** PASSED *** Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) *** PASSED *** Testing computed result against expected result (-3.624863488075e+01, -3.624863445503e+01) *** PASSED *** Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) *** PASSED *** Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) *** PASSED *** Elapsed time: 8.903639 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488075, -390.4121708125, -354.1635359318] EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] COMPUTED RESULT 1847.663548071 COMPUTED RESULT 1883.912182952 COMPUTED RESULT 2732.623683321 COMPUTED RESULT 3123.035854133 COMPUTED RESULT -36.24863488075 COMPUTED RESULT -390.4121708125 COMPUTED RESULT -354.1635359318 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772492E+01 kJ/mol Global net ELEC energy = -3.757593772492E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) *** PASSED *** Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) *** PASSED *** Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) *** PASSED *** Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) *** PASSED *** Testing computed result against expected result (-3.757593772492e+01, -3.757593797629e+01) *** PASSED *** Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) *** PASSED *** Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) *** PASSED *** Elapsed time: 8.170547 seconds -------------------------------------------------------------------------------- Total elapsed time: 17.074186 seconds Test results have been logged -------------------------------------------------------------------------------- Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772492, -391.2388603848, -353.6629226599] EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] COMPUTED RESULT 1847.86044002 COMPUTED RESULT 1885.436377745 COMPUTED RESULT 2734.040568569 COMPUTED RESULT 3125.279428954 COMPUTED RESULT -37.57593772492 COMPUTED RESULT -391.2388603848 COMPUTED RESULT -353.6629226599 make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_sphinxdoc -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_python3 -O--buildsystem=cmake I: dh_python3 fs:418: renaming _apbslib.so to _apbslib.cpython-311-aarch64-linux-gnu.so dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' dh_fixperms for example in FKBP/1d7h-dmso/UHBD/pqr2qcd \ ion-pmf/runme.sh \ point-pmf/runme.sh \ protein-rna/postprocess.sh \ protein-rna/test.sh \ helix/Run_membrane-helix.sh \ protein-rna/run_apdx_files.sh; \ do \ chmod +x debian/apbs-data/usr/share/apbs/examples/${example}; \ done for script in amber2charmm.sh \ param/pdb2pqr/amber2uhbd.sh \ qcd2pqr.awk; \ do \ chmod a+x debian/apbs-data/usr/share/apbs/tools/conversion/${script}; \ done for example in bem-pKa/test_proteins \ pbsam-barn_bars; \ do \ chmod a-x debian/apbs-data/usr/share/apbs/examples/${example}/*.pqr; \ done make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' dh_fixperms -O--buildsystem=cmake -Napbs-data -Napbs-doc dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/libapbs3t64/usr/lib/aarch64-linux-gnu/libapbs_pmgc.so.3: DWARF compression not beneficial - old size 156081 new size 156709 dwz: debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3: DWARF compression not beneficial - old size 90449 new size 92959 dwz: debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libmc.so.1.9.3: DWARF compression not beneficial - old size 454851 new size 461553 dwz: debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libgamer.so.1.9.3: DWARF compression not beneficial - old size 918211 new size 921070 dwz: debian/python3-apbslib/usr/lib/python3/dist-packages/apbs.cpython-311-aarch64-linux-gnu.so: DWARF compression not beneficial - old size 6193169 new size 6205875 dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol atan2 used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sinh used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cos used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol acos used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol erfc used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sin used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cosh used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol asin used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol e_wsfe used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol do_fio used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sqrtf used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol daxpy_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol ddot_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dnrm2_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cosh used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dcopy_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_ri used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libcolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libapbs_pmgc.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libarpack.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libapbs_fem.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libvf2c.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libsuperlu.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libcamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libspqr.so.4 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libumfpack.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libgomp.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libblas.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libcholmod.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libsuitesparseconfig.so.7 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libpunc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libmc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libcgcode.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libccolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libstdc++.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libmpi.so.40 (they use none of the library's symbols) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package libapbs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libfetk-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: package apbs-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'apbs' in '../apbs_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'apbs-data' in '../apbs-data_3.4.1-5.1_all.deb'. dpkg-deb: building package 'libfetk1.9t64' in '../libfetk1.9t64_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libfetk1.9t64-dbgsym' in '../libfetk1.9t64-dbgsym_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libapbs3t64' in '../libapbs3t64_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'apbs-doc' in '../apbs-doc_3.4.1-5.1_all.deb'. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'python3-apbslib-dbgsym' in '../python3-apbslib-dbgsym_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libfetk-dev' in '../libfetk-dev_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libapbs3t64-dbgsym' in '../libapbs3t64-dbgsym_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'apbs-dbgsym' in '../apbs-dbgsym_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-5.1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../apbs_3.4.1-5.1_arm64.buildinfo dpkg-genchanges --build=binary -O../apbs_3.4.1-5.1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2021122 and its subdirectories I: Current time: Thu Jun 19 15:53:37 -12 2025 I: pbuilder-time-stamp: 1750391617 Fri May 17 21:30:42 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri May 17 21:30:42 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri May 17 21:40:34 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri May 17 21:40:35 UTC 2024 I: apbs_3.4.1-5.1_arm64.changes: Format: 1.8 Date: Wed, 28 Feb 2024 01:04:53 +0000 Source: apbs Binary: apbs apbs-data apbs-dbgsym apbs-doc libapbs-dev libapbs3t64 libapbs3t64-dbgsym libfetk-dev libfetk1.9t64 libfetk1.9t64-dbgsym python3-apbslib python3-apbslib-dbgsym Architecture: all arm64 Version: 3.4.1-5.1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Steve Langasek Description: apbs - Adaptive Poisson Boltzmann Solver apbs-data - data files for APBS (Adaptive Poisson Boltzmann Solver) apbs-doc - Adaptive Poisson Boltzmann Solver libapbs-dev - Adaptive Poisson Boltzmann Solver libapbs3t64 - Adaptive Poisson Boltzmann Solver libfetk-dev - FETK libraries for APBS (development headers) libfetk1.9t64 - FETK libraries for APBS (shared libraries) python3-apbslib - Adaptive Poisson Boltzmann Solver Closes: 1061891 Changes: apbs (3.4.1-5.1) unstable; urgency=medium . * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. Closes: #1061891 Checksums-Sha1: 9111a462133ec2bd5f2c0ef5dd69feb35889bfc6 1480936 apbs-data_3.4.1-5.1_all.deb 80d683659f973b3c72e24b9bf9aacbd7d5f5f010 111380 apbs-dbgsym_3.4.1-5.1_arm64.deb f1e4ccdbb7de2dd9d768e65d3e14b6a8cdd2ea21 5851636 apbs-doc_3.4.1-5.1_all.deb 36b3e6d7572faf944c7fb634a307a2c538b7e95e 14093 apbs_3.4.1-5.1_arm64.buildinfo fb63337414fe2b566d4a8fa3a1d19a2fcb43cf94 76212 apbs_3.4.1-5.1_arm64.deb d41ac4818a7151ebf4c2de41c4450cd00fe9c301 103032 libapbs-dev_3.4.1-5.1_arm64.deb 1b1334b29d575293f9a7b8025fb49cecbf311850 590536 libapbs3t64-dbgsym_3.4.1-5.1_arm64.deb e6dece0db2b530c952d3cdb27979eb961dfc42ef 234480 libapbs3t64_3.4.1-5.1_arm64.deb 788d7e701a49979b4a742e264c7c0971cf642f00 148636 libfetk-dev_3.4.1-5.1_arm64.deb 006e4ed751a08e496e0f001d67f647c8df7ef750 1608964 libfetk1.9t64-dbgsym_3.4.1-5.1_arm64.deb 878f3a8ef6f2831bb48d338f254dd4fa1688c702 499900 libfetk1.9t64_3.4.1-5.1_arm64.deb 5ce241e72118276558ed57e612a57ad6ec7402a7 3255736 python3-apbslib-dbgsym_3.4.1-5.1_arm64.deb ea82ad8695629628b2864f29dd7e1700b864810f 205832 python3-apbslib_3.4.1-5.1_arm64.deb Checksums-Sha256: c95e4d3a8ecf802d5bc9d86adbab720193cd2b6d35e496859a584f077079abea 1480936 apbs-data_3.4.1-5.1_all.deb f6f95dca6d45f6b7c155b0a158d5b38cdf88f34698bf1d5304e6bc6e5acdfb2c 111380 apbs-dbgsym_3.4.1-5.1_arm64.deb e61617f6651a484d38196ff85a1c9804348c65fb39c5ee7155faecdc3189cf4c 5851636 apbs-doc_3.4.1-5.1_all.deb d7e2da9c531853b67e1e3aefe545517eb56160c9279d782e724804ddcbe5f353 14093 apbs_3.4.1-5.1_arm64.buildinfo 7dffbdddcccaa8a36c1c2b31ec7774f8cc003df2b0229203ebfd962b4cd3bcb3 76212 apbs_3.4.1-5.1_arm64.deb 586bfe92d56bf49d7e5671023e52cfac6c3cf5b87698bbda2ff3b4e08a4f696f 103032 libapbs-dev_3.4.1-5.1_arm64.deb 88f88dbf1babb5e3336a390efe70355f93235dee6334cf823990249d79b81858 590536 libapbs3t64-dbgsym_3.4.1-5.1_arm64.deb 8ec2ede681f7a4776038a602cd64b32755b41cb30e97a533d72d97f9a25d21bb 234480 libapbs3t64_3.4.1-5.1_arm64.deb 97c903181975ba1d78f3d79436e908596d277b1dc8a82e0a942aedb2392949ce 148636 libfetk-dev_3.4.1-5.1_arm64.deb 57ebd0a0da450e8ef9bac4ce5266b91ae4ea193c95bae5eaf7ec591777dbd7d0 1608964 libfetk1.9t64-dbgsym_3.4.1-5.1_arm64.deb c78d639b72b1cae4db23e3d28475bb97302914b20b768b0eae738e2fce553fd3 499900 libfetk1.9t64_3.4.1-5.1_arm64.deb 18c45d8a9ec94a68c1f44523e967b6752529ba73256bf5a42eecfe26112e521b 3255736 python3-apbslib-dbgsym_3.4.1-5.1_arm64.deb 6465c86d37abb5b2e876b60914dbcae6ec6afe8a252a9a5c6a0e874323c252ea 205832 python3-apbslib_3.4.1-5.1_arm64.deb Files: aee66690eeb8d82ffdd4ce0725b6a8ff 1480936 science optional apbs-data_3.4.1-5.1_all.deb 75e8c131ec6644d229707b4ce7b2e6d8 111380 debug optional apbs-dbgsym_3.4.1-5.1_arm64.deb 9899c571f0bdb920a412b12648afd3ab 5851636 science optional apbs-doc_3.4.1-5.1_all.deb 14b024d1eb593bcb111cad301263ea49 14093 science optional apbs_3.4.1-5.1_arm64.buildinfo 184948546eaf3ba2867c3541714559be 76212 science optional apbs_3.4.1-5.1_arm64.deb 6ec2a68b8e33b09bdd51b3a86292ae8a 103032 libdevel optional libapbs-dev_3.4.1-5.1_arm64.deb a3a678fc5502ceea9896854fbf0c4bdc 590536 debug optional libapbs3t64-dbgsym_3.4.1-5.1_arm64.deb 14f44cd099c61608c46a1fbd3f89b655 234480 libs optional libapbs3t64_3.4.1-5.1_arm64.deb 4e0fbb10094774a56f845b58900f8467 148636 libdevel optional libfetk-dev_3.4.1-5.1_arm64.deb 0f7345aa7a28814280a9124bee42da4a 1608964 debug optional libfetk1.9t64-dbgsym_3.4.1-5.1_arm64.deb c4e25ff8c80a385aab6775d70088e446 499900 libs optional libfetk1.9t64_3.4.1-5.1_arm64.deb 5aab760dca9f16287443494af5b876c9 3255736 debug optional python3-apbslib-dbgsym_3.4.1-5.1_arm64.deb 6d465c7c8f7a1faba4bc248dd251add6 205832 python optional python3-apbslib_3.4.1-5.1_arm64.deb Fri May 17 21:40:35 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Fri May 17 22:02:06 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 19 16:03:38 -12 2025 I: pbuilder-time-stamp: 1750392218 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [apbs_3.4.1-5.1.dsc] I: copying [./apbs_3.4.1.orig.tar.gz] I: copying [./apbs_3.4.1-5.1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Feb 28 01:10:02 2024 gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "vorlon@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-5.1.dsc: no acceptable signature found dpkg-source: info: extracting apbs in apbs-3.4.1 dpkg-source: info: unpacking apbs_3.4.1.orig.tar.gz dpkg-source: info: unpacking apbs_3.4.1-5.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying wrong-path-for-interpreter.patch dpkg-source: info: applying debian_testfiles.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying shared_library_soname.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying cmake.patch dpkg-source: info: applying docs.patch dpkg-source: info: applying open-U-obsolete.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2355443/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='02c1595e050c4854bcf601dc304385b7' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2355443' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/pbuilderrc_jB2P --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/b1 --logfile b1/build.log apbs_3.4.1-5.1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 19 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2355443/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19764 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libmaloc-dev; however: Package libmaloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libsuitesparse-dev; however: Package libsuitesparse-dev is not installed. pbuilder-satisfydepends-dummy depends on libsuperlu-dev; however: Package libsuperlu-dev is not installed. pbuilder-satisfydepends-dummy depends on libtirpc-dev; however: Package libtirpc-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx | sphinx; however: Package python3-sphinx is not installed. Package sphinx is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-aarch64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamd3{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbsd0{a} libbtf2{a} libcamd3{a} libcbor0.10{a} libccolamd3{a} libcholmod5{a} libcolamd3{a} libcom-err2{a} libcurl4t64{a} libcxsparse4{a} libdata-optlist-perl{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libklu2{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldl3{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmaloc-dev{a} libmaloc1{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libparams-util-perl{a} libparu0{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} librbio4{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libspex3{a} libspqr4{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libsuitesparse-dev{a} libsuitesparse-mongoose3{a} libsuitesparseconfig7{a} libsuperlu-dev{a} libsuperlu6{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libumfpack6{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libyaml-0-2{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} pybind11-dev{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-installer{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pybind11{a} python3-pygments{a} python3-pyproject-hooks{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-toml{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} swig{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libgraphblas-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libsasl2-modules lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 223 newly installed, 0 to remove and 0 not upgraded. Need to get 157 MB of archives. After unpacking 708 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.1-1 [93.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-1.2 [27.2 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.14.0-1+b2 [73.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 38 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:9.7p1-5 [902 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.2-2 [321 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.7.1-5 [412 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-4 [142 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.29.3-1 [2167 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.29.3-1+b2 [9058 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-3 [23.4 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libsub-prototype-perl arm64 0.03-2+b2 [9776 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.11-1 [10.4 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 75 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240422 [107 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.1.0-1 [361 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libgfortran-13-dev arm64 13.2.0-25 [401 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-25 [8827 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 gfortran-13 arm64 13.2.0-25 [12.8 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.7.0-0.3 [56.5 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [165 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 50.0-2+b1 [58.2 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 50.0-2+b1 [315 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-12 [21.3 MB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b1 [12.1 MB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libsuitesparseconfig7 arm64 1:7.7.0+dfsg-2 [22.3 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libamd3 arm64 1:7.7.0+dfsg-2 [36.5 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 104 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1 [21.4 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libhsakmt1 arm64 5.7.0-1 [57.6 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 5.7.1-2 [276 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libamdhip64-5 arm64 5.7.1-3 [8698 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libarpack2t64 arm64 3.9.1-1.1+b1 [81.4 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.0-3 [98.2 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.0-3 [3584 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libarpack2-dev arm64 3.9.1-1.1+b1 [98.2 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libbtf2 arm64 1:7.7.0+dfsg-2 [23.0 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libcamd3 arm64 1:7.7.0+dfsg-2 [33.3 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libccolamd3 arm64 1:7.7.0+dfsg-2 [36.1 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libcolamd3 arm64 1:7.7.0+dfsg-2 [29.9 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libcholmod5 arm64 1:7.7.0+dfsg-2 [507 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libcxsparse4 arm64 1:7.7.0+dfsg-2 [73.7 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [169 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [125 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [102 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [54.3 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [60.3 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-8.1+b3 [303 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 50.0-2+b1 [66.6 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 1.17.0-3+b1 [479 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.10.0-1+b1 [140 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.18-1 [37.4 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.4.7-7+b1 [165 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.10.0-1+b1 [234 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b1 [51.1 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-1 [143 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1 [13.8 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b1 [39.3 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.10.0-1+b1 [18.0 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.7.0-0.3 [101 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.7.0-0.3 [197 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 50.0-2+b1 [626 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libklu2 arm64 1:7.7.0+dfsg-2 [76.3 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libldl3 arm64 1:7.7.0+dfsg-2 [22.7 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libmaloc1 arm64 1.5-1+b1 [76.9 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libmaloc-dev arm64 1.5-1+b1 [122 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.15-4 [19.2 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 5.0.2-3 [580 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.16.0+ds-5 [938 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libopenmpi3t64 arm64 4.1.6-13.3 [2170 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libpmix-dev arm64 5.0.2-3 [3921 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 4.1.6-13.3 [225 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 4.1.6-13.3 [972 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libumfpack6 arm64 1:7.7.0+dfsg-2 [214 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libparu0 arm64 1:7.7.0+dfsg-2 [56.5 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libpython3.11t64 arm64 3.11.9-1 [1814 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libpython3.11-dev arm64 3.11.9-1 [4358 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.11.8-1 [9564 B] Get: 174 http://deb.debian.org/debian unstable/main arm64 librbio4 arm64 1:7.7.0+dfsg-2 [36.5 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libspex3 arm64 1:7.7.0+dfsg-2 [51.7 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libspqr4 arm64 1:7.7.0+dfsg-2 [122 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libsuitesparse-mongoose3 arm64 1:7.7.0+dfsg-2 [42.1 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libsuitesparse-dev arm64 1:7.7.0+dfsg-2 [1253 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libsuperlu6 arm64 6.0.1+dfsg1-1+b1 [141 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libsuperlu-dev arm64 6.0.1+dfsg1-1+b1 [21.8 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [192 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 mpi-default-dev arm64 1.15 [3152 B] Get: 186 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 pybind11-dev all 2.11.1-2 [191 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.0.0-2 [10.6 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.1-1 [34.1 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 pybuild-plugin-pyproject all 6.20240422 [11.1 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.14.0-1 [111 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2023.11.17-1 [155 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3.11-dev arm64 3.11.9-1 [501 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.11.8-1 [26.1 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-roman all 3.3-3 [9880 B] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.6-2 [37.0 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 209 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1 [14.6 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.11.1-2 [201 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.16.0-6 [16.3 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.31.0+dfsg-2 [68.7 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.2.6-7 [702 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.2.6-7 [552 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 221 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.1-2 [153 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 swig arm64 4.2.1-1 [1350 kB] Fetched 157 MB in 1s (136 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21098 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... 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Setting up libldl3:arm64 (1:7.7.0+dfsg-2) ... Setting up file (1:5.45-3) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jun 20 04:04:41 UTC 2025. Universal Time is now: Fri Jun 20 04:04:41 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libbtf2:arm64 (1:7.7.0+dfsg-2) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1+b2) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up libmunge2:arm64 (0.5.15-4) ... Setting up libexpat1-dev:arm64 (2.6.2-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libproc2-0:arm64 (2:4.0.4-4) ... Setting up libhwloc15:arm64 (2.10.0-1+b1) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:arm64 (1.9.5-6+b2) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libltdl7:arm64 (2.4.7-7+b1) ... Setting up libparams-util-perl (1.102-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:arm64 (14.1.0-1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libnuma1:arm64 (2.0.18-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:arm64 (2.3.2-1+b1) ... Setting up librhash0:arm64 (1.4.3-3+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:arm64 (3.7.0-0.3) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up libsuitesparseconfig7:arm64 (1:7.7.0+dfsg-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.29.3-1) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:arm64 (1.14.0-1+b2) ... Setting up libgfortran-13-dev:arm64 (13.2.0-25) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up libblas-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libarpack2t64:arm64 (3.9.1-1.1+b1) ... Setting up libamd3:arm64 (1:7.7.0+dfsg-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:arm64 (1:7.7.0+dfsg-2) ... Setting up libspex3:arm64 (1:7.7.0+dfsg-2) ... 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Setting up gfortran-13 (13.2.0-25) ... Setting up librbio4:arm64 (1:7.7.0+dfsg-2) ... Setting up liblapack-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up pkg-config:arm64 (1.8.1-1+b2) ... Setting up libjs-sphinxdoc (7.2.6-7) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libccolamd3:arm64 (1:7.7.0+dfsg-2) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up libdrm2:arm64 (2.4.120-2) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libhwloc-dev:arm64 (2.10.0-1+b1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libsuperlu-dev:arm64 (6.0.1+dfsg1-1+b1) ... Setting up libarchive13t64:arm64 (3.7.2-2) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... Setting up libmaloc1 (1.5-1+b1) ... Setting up libibverbs1:arm64 (50.0-2+b1) ... Setting up libcholmod5:arm64 (1:7.7.0+dfsg-2) ... Setting up libarpack2-dev:arm64 (3.9.1-1.1+b1) ... Setting up libcurl4t64:arm64 (8.7.1-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up ibverbs-providers:arm64 (50.0-2+b1) ... Setting up libspqr4:arm64 (1:7.7.0+dfsg-2) ... Setting up openssh-client (1:9.7p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libpython3.11t64:arm64 (3.11.9-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libsub-prototype-perl (0.03-2+b2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:arm64 (535.171.04-1) ... 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Setting up libhwloc-plugins:arm64 (2.10.0-1+b1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-wheel (0.43.0-1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.6-2) ... Setting up libpmix2t64:arm64 (5.0.2-3) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up python3-build (1.2.1-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up libpmix-dev:arm64 (5.0.2-3) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up libsuitesparse-dev:arm64 (1:7.7.0+dfsg-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up debhelper (13.15.3) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-requests (2.31.0+dfsg-2) ... Setting up dh-python (6.20240422) ... Setting up libucx0:arm64 (1.16.0+ds-5) ... Setting up pybuild-plugin-pyproject (6.20240422) ... Setting up libopenmpi3t64:arm64 (4.1.6-13.3) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:arm64 (4.1.6-13.3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up mpi-default-dev (1.15) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-7) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.34-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/apbs-3.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../apbs_3.4.1-5.1_source.changes dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 3.4.1-5.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steve Langasek dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules build dh build --with python3,sphinxdoc --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=None \ -DAPBS_STATIC_BUILD=Off \ -DBUILD_DOC=Off -DBUILD_TOOLS=On \ -DENABLE_OPENMP=On -DENABLE_MPI=On \ -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On \ -DENABLE_READLINE=Off -DENABLE_ZLIB=On \ -DFETCHCONTENT_SOURCE_DIR_FETK=/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk \ -DRPC_CFLAGS=-I/usr/include/tirpc \ -DBUILD_MALOC=Off cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_BUILD_TYPE=None -DAPBS_STATIC_BUILD=Off -DBUILD_DOC=Off -DBUILD_TOOLS=On -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On -DENABLE_READLINE=Off -DENABLE_ZLIB=On -DFETCHCONTENT_SOURCE_DIR_FETK=/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk -DRPC_CFLAGS=-I/usr/include/tirpc -DBUILD_MALOC=Off .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Install prefix: /usr -- -- APBS Static build: Off -- Building shared libs: ON -- Find-library suffixes: .so;.so;.a -- -- Building FETK from commit 57195e55351e04ce6ee0ef56a143c996a9aee7e2 -- FETK set_basic_vars_and_paths: FALSE, FETK -- Setting project paths -- Install prefix: /usr -- FETK static build: OFF -- Building shared libs: ON -- Find-library suffixes: .so;.so;.so;.a Configuring build for PUNC -- FETK set_basic_vars_and_paths: FALSE, punc -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of mode_t -- Check size of mode_t - done -- Check size of pid_t -- Check size of pid_t - done -- Check size of size_t -- Check size of size_t - done -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file sys/socket.h -- Looking for include file sys/socket.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file sys/un.h -- Looking for include file sys/un.h - found -- Looking for include file sys/wait.h -- Looking for include file sys/wait.h - found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Looking for include file arpa/inet.h -- Looking for include file arpa/inet.h - found -- Looking for include file netdb.h -- Looking for include file netdb.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file fcntl.h -- Looking for include file fcntl.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for O_NONBLOCK -- Looking for O_NONBLOCK - found -- Will build vf2c -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T - Success -- Performing Test SUPERLU_HAS_CLEAN_ENUMS -- Performing Test SUPERLU_HAS_CLEAN_ENUMS - Success -- Performing Test SUPERLU_HAS_GLOBALLU_T -- Performing Test SUPERLU_HAS_GLOBALLU_T - Success -- Found SuperLU: /usr/include/superlu (found version "5.0") -- Found ARPACK: libraries at /usr/lib/aarch64-linux-gnu/libarpack.so -- Will build CGCODE -- Building vf2c -- Type: EXTERNAL_HEADERS -- Items: punc/varpack.h;punc/vblas.h;punc/vcgcode.h;punc/vlapack.h;punc/vpmg.h;punc/vf2c.h -- Type: INTERNAL_HEADERS -- Items: f2c.h;fio.h;fmt.h;fp.h;lio.h;rawio.h;signal1.h;sysdep1.h -- Type: SOURCES -- Items: f77vers.c;i77vers.c;s_rnge.c;abort_.c;exit_.c;getarg_.c;iargc_.c;getenv_.c;signal_.c;s_stop.c;s_paus.c;system_.c;cabs.c;derf_.c;derfc_.c;erf_.c;erfc_.c;sig_die.c;uninit.c;pow_ci.c;pow_dd.c;pow_di.c;pow_hh.c;pow_ii.c;pow_ri.c;pow_zi.c;pow_zz.c;c_abs.c;c_cos.c;c_div.c;c_exp.c;c_log.c;c_sin.c;c_sqrt.c;z_abs.c;z_cos.c;z_div.c;z_exp.c;z_log.c;z_sin.c;z_sqrt.c;r_abs.c;r_acos.c;r_asin.c;r_atan.c;r_atn2.c;r_cnjg.c;r_cos.c;r_cosh.c;r_dim.c;r_exp.c;r_imag.c;r_int.c;r_lg10.c;r_log.c;r_mod.c;r_nint.c;r_sign.c;r_sin.c;r_sinh.c;r_sqrt.c;r_tan.c;r_tanh.c;d_abs.c;d_acos.c;d_asin.c;d_atan.c;d_atn2.c;d_cnjg.c;d_cos.c;d_cosh.c;d_dim.c;d_exp.c;d_imag.c;d_int.c;d_lg10.c;d_log.c;d_mod.c;d_nint.c;d_prod.c;d_sign.c;d_sin.c;d_sinh.c;d_sqrt.c;d_tan.c;d_tanh.c;i_abs.c;i_dim.c;i_dnnt.c;i_indx.c;i_len.c;i_mod.c;i_nint.c;i_sign.c;lbitbits.c;lbitshft.c;h_abs.c;h_dim.c;h_dnnt.c;h_indx.c;h_len.c;h_mod.c;h_nint.c;h_sign.c;l_ge.c;l_gt.c;l_le.c;l_lt.c;hl_ge.c;hl_gt.c;hl_le.c;hl_lt.c;ef1asc_.c;ef1cmc_.c;f77_aloc.c;s_cat.c;s_cmp.c;s_copy.c;dtime_.c;etime_.c;backspac.c;close.c;dfe.c;dolio.c;due.c;endfile.c;err.c;fmt.c;fmtlib.c;ftell_.c;iio.c;ilnw.c;inquire.c;lread.c;lwrite.c;open.c;rdfmt.c;rewind.c;rsfe.c;rsli.c;rsne.c;sfe.c;sue.c;typesize.c;uio.c;util.c;wref.c;wrtfmt.c;wsfe.c;wsle.c;wsne.c;xwsne.c;main.c -- Building cgcode -- Type: INTERNAL_HEADERS -- Items: vcgcode.h -- Type: SOURCES -- Items: scgdrv.c;scg.c;scr.c;scrind.c;spcg.c;scgnr.c;scgne.c;spcgnr.c;spcgne.c;sppcg.c;spcgca.c;sdpchb.c;scbfix.c;sckchb.c;scgchk.c;sonest.c;msstop.c;r1mach.c;sratqr.c;dcgdrv.c;dcg.c;dcr.c;dcrind.c;dpcg.c;dcgnr.c;dcgne.c;dpcgnr.c;dpcgne.c;dppcg.c;dpcgca.c;ddpchb.c;dcbfix.c;dckchb.c;dcgchk.c;donest.c;mdstop.c;d1mach.c;dratqr.c;depsln.c -- Type: INTERNAL_HEADERS -- Items: /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/punccf.h -- Type: SOURCES -- Items: punc_base.c -- Type: EXTERNAL_HEADERS -- Items: punc/punc.h;punc/punc_base.h -- Type: INTERNAL_HEADERS -- Items: punc_base_p.h Configuring build for GAMER -- FETK set_basic_vars_and_paths: FALSE, gamer -- Type: INTERNAL_HEADERS -- Items: /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src/gamercf.h -- Type: SOURCES -- Items: gamer_base.c -- Type: EXTERNAL_HEADERS -- Items: gamer/gamer.h;gamer/gamer_base.h -- Type: INTERNAL_HEADERS -- Items: gamer_base_p.h -- Type: SOURCES -- Items: triangle.c -- Type: EXTERNAL_HEADERS -- Items: gamer/triangle.h -- Type: INTERNAL_HEADERS -- Items: triangle_p.h -- Type: SOURCES -- Items: predicates.cpp;tetgen.cpp -- Type: EXTERNAL_HEADERS -- Items: gamer/tetgen.h -- Type: INTERNAL_HEADERS -- Items: tetgen_p.h -- Type: SOURCES -- Items: CorrectNormals.C;GenerateSphereMesh.C;MarchingCube.C;PDB2Mesh.C;PDB2Volume.C;ReadLattice.C;ReadPDB.C;ReadWriteMesh.C;RegionGrowing.C;SurfaceMesh.C;SurfExtract.C;SurfRefine.C;SurfSmooth.C -- Type: EXTERNAL_HEADERS -- Items: gamer/biom.h -- Type: INTERNAL_HEADERS -- Items: MarchingCube.h;PDB2Volume.h Configuring build for MC -- FETK set_basic_vars_and_paths: FALSE, mc -- Found UMFPACK: /usr/include/suitesparse -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/aarch64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/aarch64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/aarch64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/aarch64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/aarch64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/aarch64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/aarch64-linux-gnu/librt.a -- Adding librt: /usr/lib/aarch64-linux-gnu/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- Found SuiteSparse: TRUE (found version "..") -- Type: INTERNAL_HEADERS -- Items: /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src/mccf.h -- Type: SOURCES -- Items: mc_base.c -- Type: EXTERNAL_HEADERS -- Items: mc/mc_base.h;mc/mc.h -- Type: INTERNAL_HEADERS -- Items: mc_base_p.h -- Type: SOURCES -- Items: bmat.c;bsolv.c;bvec.c;mat.c;matcopy.c;matln.c;mtool.c;slu.c;vec.c;vec3.c;zslu.c -- Type: EXTERNAL_HEADERS -- Items: mc/bam.h;mc/bmat.h;mc/bvec.h;mc/mat.h;mc/mtool.h;mc/slu.h;mc/vec.h;mc/vec3.h;mc/zslu.h -- Type: INTERNAL_HEADERS -- Items: bam_p.h;bmat_p.h;bvec_p.h;mat_p.h;mtool_p.h;slu_p.h;vec_p.h;vec3_p.h;zslu_p.h -- Type: SOURCES -- Items: whb.c;bvechb.c;hbtools.c;rcmat.c;brcmat.c;subopt.c -- Type: EXTERNAL_HEADERS -- Items: mc/whb.h -- Type: INTERNAL_HEADERS -- Items: brcmat_p.h;bvechb_p.h;cholesky_p.h;hbtools_p.h;rcmat_p.h;subopt_p.h;whb_p.h -- Type: SOURCES -- Items: aprx.c;assem.c;bnode.c;estim.c;eval.c;io.c;node.c;parti.c;re.c -- Type: EXTERNAL_HEADERS -- Items: mc/aprx.h;mc/bnode.h;mc/node.h;mc/re.h -- Type: INTERNAL_HEADERS -- Items: aprx_p.h;bnode_p.h;node_p.h;re_p.h -- Type: SOURCES -- Items: vel.c;ves.c;gem.c;gemchk.c;gemdisp.c;gemg.c;gemgen.c;gemio.c;gemref.c;gemunref.c;gemcube.c -- Type: EXTERNAL_HEADERS -- Items: mc/gem.h;mc/vel.h;mc/ves.h -- Type: INTERNAL_HEADERS -- Items: gem_p.h;vel_p.h;ves_p.h -- Type: SOURCES -- Items: pde.c -- Type: EXTERNAL_HEADERS -- Items: mc/pde.h -- Type: INTERNAL_HEADERS -- Items: pde_p.h -- Type: SOURCES -- Items: am.c;lsolv.c;nsolv.c -- Type: EXTERNAL_HEADERS -- Items: mc/am.h;mc/nam.h -- Type: INTERNAL_HEADERS -- Items: am_p.h;nam_p.h -- Type: SOURCES -- Items: dyn.c;svio.c -- Type: EXTERNAL_HEADERS -- Items: mc/dyn.h -- Type: INTERNAL_HEADERS -- Items: dyn_p.h;svio_p.h -- Type: SOURCES -- Items: mcsh.c -- Type: EXTERNAL_HEADERS -- Items: mc/mcsh.h -- Type: INTERNAL_HEADERS -- Items: mcsh_p.h -- ############################################################# -- ** PROJECT NAME: APBS -- ** PROJECT DESC: Adaptive Poisson-Boltzmann Solver -- ** PROJECT URL: http://www.poissonboltzmann.org/ -- ** VERSION_DATA: 3.4.1 -- ** CURRENT_TIME: 2024-02-27T13:04:53 -- ** CURRENT_YEAR: 2024 -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Found Intl: built in to C library -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/aarch64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/aarch64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/aarch64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/aarch64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/aarch64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/aarch64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/aarch64-linux-gnu/librt.a -- Adding librt: /usr/lib/aarch64-linux-gnu/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- UMFPack libraries: /usr/lib/aarch64-linux-gnu/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a -- Checking for MPI -- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI support enabled -- Inline functions enabled -- Verbose debugging mode enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled -- Building of iAPBS interface disabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_fem -- With source files vcsm.c;vfetk.c;vpee.c -- With external header files vcsm.h;vfetk.h;vpee.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic -- Added apbs_fem -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem -- Added apbs_routines -- External Headers: -- -- APBS Libraries: mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- -- -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines CMake Deprecation Warning at tools/python/CMakeLists.txt:2 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig (found version "4.2.1") -- Found Python3: /usr/bin/python3 (found suitable version "3.11.9", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- ***** Python3 include path is: /usr/include/python3.11 -- ***** Python3 library path is: /usr/lib/aarch64-linux-gnu/libpython3.11.so -- ***** Python3 library dir is: /usr/lib/aarch64-linux-gnu CMake Warning at /usr/lib/cmake/pybind11/pybind11Tools.cmake:24 (message): Set PYBIND11_PYTHON_VERSION to search for a specific version, not PYTHON_VERSION (which is an output). Assuming that is what you meant to do and continuing anyway. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) CMake Warning (dev) at /usr/lib/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.11.9", minimum required is "3.6") -- Found PythonLibs: /usr/lib/aarch64-linux-gnu/libpython3.11.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.11.1") -- LIBS mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- INTERNAL_LIBS apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- ******* TESTING ADDED ***************** -- Found Python3: /usr/bin/python3 (found suitable exact version "3.11.9") found components: Interpreter -- ******* FOUND TEST CASE born, born -- TEST born_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t born -- ******* FOUND TEST CASE actin, actin-dimer-auto -- TEST actin-dimer-auto_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t actin-dimer-auto -- ******* FOUND TEST CASE alkanes, alkanes -- TEST alkanes_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t alkanes -- ******* FOUND TEST CASE FKBP, FKBP -- TEST FKBP_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t FKBP -- ******* FOUND TEST CASE hca, hca-bind -- TEST hca-bind_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t hca-bind -- ******* FOUND TEST CASE ionize, ionize -- TEST ionize_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t ionize -- ******* FOUND TEST CASE ion, ion-pmf -- TEST ion-pmf_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t ion-pmf -- ******* FOUND TEST CASE pka, pka-lig -- TEST pka-lig_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t pka-lig -- ******* FOUND TEST CASE point, point-pmf -- TEST point-pmf_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t point-pmf -- ******* FOUND TEST CASE solv, solv -- TEST solv_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t solv -- Configuring done (28.8s) -- Generating done (0.4s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY ENABLE_READLINE ENABLE_ZLIB -- Build files have been written to: /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' dh_auto_build -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/apbs-3.4.1 -B/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depend make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build Dependee "/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". Dependee "/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' Scanning dependencies of target apbslib_swig_compilation make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build [ 0%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o -MF CMakeFiles/cgcode.dir/scgdrv.c.o.d -o CMakeFiles/cgcode.dir/scgdrv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgdrv.c [ 0%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o [ 2%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC 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_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o -MF CMakeFiles/cgcode.dir/scr.c.o.d -o CMakeFiles/cgcode.dir/scr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scr.c [ 2%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o [ 2%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o -MF CMakeFiles/cgcode.dir/scrind.c.o.d -o CMakeFiles/cgcode.dir/scrind.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scrind.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o -MF CMakeFiles/vf2c.dir/f77vers.c.o.d -o CMakeFiles/vf2c.dir/f77vers.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77vers.c [ 3%] Swig compile apbslib.i for python cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o -MF CMakeFiles/cgcode.dir/scg.c.o.d -o CMakeFiles/cgcode.dir/scg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scg.c [ 3%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -MF CMakeFiles/gamer.dir/tetgen/predicates.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp [ 3%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o [ 3%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g 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CMakeFiles/vf2c.dir/s_rnge.c.o.d -o CMakeFiles/vf2c.dir/s_rnge.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_rnge.c [ 4%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o -MF CMakeFiles/cgcode.dir/spcg.c.o.d -o CMakeFiles/cgcode.dir/spcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcg.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o -MF CMakeFiles/gamer.dir/triangle/triangle.c.o.d -o CMakeFiles/gamer.dir/triangle/triangle.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle/triangle.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E touch /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o -MF CMakeFiles/vf2c.dir/abort_.c.o.d -o CMakeFiles/vf2c.dir/abort_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/abort_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -python -outdir /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python -interface _apbslib -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/python3.11 -I/build/reproducible-path/apbs-3.4.1/tools/python -o /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /build/reproducible-path/apbs-3.4.1/tools/python/apbslib.i [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC 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-Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o -MF CMakeFiles/cgcode.dir/scgnr.c.o.d -o CMakeFiles/cgcode.dir/scgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgnr.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -MF CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp [ 5%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -MF CMakeFiles/gamer.dir/biom/CorrectNormals.C.o.d -o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o -MF CMakeFiles/vf2c.dir/getarg_.c.o.d -o CMakeFiles/vf2c.dir/getarg_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getarg_.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o -MF CMakeFiles/cgcode.dir/spcgnr.c.o.d -o CMakeFiles/cgcode.dir/spcgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgnr.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o -MF CMakeFiles/vf2c.dir/signal_.c.o.d -o CMakeFiles/vf2c.dir/signal_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/signal_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o -MF CMakeFiles/vf2c.dir/s_stop.c.o.d -o CMakeFiles/vf2c.dir/s_stop.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_stop.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o -MF CMakeFiles/cgcode.dir/sppcg.c.o.d -o CMakeFiles/cgcode.dir/sppcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sppcg.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o -MF CMakeFiles/vf2c.dir/s_paus.c.o.d -o CMakeFiles/vf2c.dir/s_paus.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_paus.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o -MF CMakeFiles/vf2c.dir/system_.c.o.d -o CMakeFiles/vf2c.dir/system_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/system_.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o -MF CMakeFiles/vf2c.dir/cabs.c.o.d -o CMakeFiles/vf2c.dir/cabs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/cabs.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o -MF CMakeFiles/cgcode.dir/spcgca.c.o.d -o CMakeFiles/cgcode.dir/spcgca.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgca.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && 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/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o -MF CMakeFiles/cgcode.dir/sdpchb.c.o.d -o CMakeFiles/cgcode.dir/sdpchb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o -MF CMakeFiles/cgcode.dir/scbfix.c.o.d -o CMakeFiles/cgcode.dir/scbfix.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scbfix.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o [ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o -MF CMakeFiles/cgcode.dir/sckchb.c.o.d -o CMakeFiles/cgcode.dir/sckchb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sckchb.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o -MF CMakeFiles/vf2c.dir/derfc_.c.o.d -o CMakeFiles/vf2c.dir/derfc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derfc_.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o -MF CMakeFiles/vf2c.dir/erf_.c.o.d -o CMakeFiles/vf2c.dir/erf_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erf_.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o -MF CMakeFiles/vf2c.dir/erfc_.c.o.d -o CMakeFiles/vf2c.dir/erfc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erfc_.c [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o -MF CMakeFiles/cgcode.dir/scgchk.c.o.d -o CMakeFiles/cgcode.dir/scgchk.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgchk.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o -MF CMakeFiles/cgcode.dir/sonest.c.o.d -o CMakeFiles/cgcode.dir/sonest.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sonest.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function 'void tetgenmesh::constrainedfacets()': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20804:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 20804 | equatptlist = new list("point *"); | ^~~~~~~~~ cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o -MF CMakeFiles/cgcode.dir/msstop.c.o.d -o CMakeFiles/cgcode.dir/msstop.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/msstop.c [ 12%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20809:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 20809 | horizptlist = new list("point *"); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20810:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 20810 | belowptlist = new list("point *"); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20811:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 20811 | aboveptlist = new list("point *"); | ^~~~~~~~~ [ 12%] Built target apbslib_swig_compilation cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -MF CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o.d -o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o -MF CMakeFiles/vf2c.dir/sig_die.c.o.d -o CMakeFiles/vf2c.dir/sig_die.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sig_die.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o -MF CMakeFiles/vf2c.dir/uninit.c.o.d -o CMakeFiles/vf2c.dir/uninit.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uninit.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o -MF CMakeFiles/vf2c.dir/pow_ci.c.o.d -o CMakeFiles/vf2c.dir/pow_ci.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ci.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function 'long int tetgenmesh::reconstructmesh()': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:24383:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 24383 | markerlist = new list("int"); | ^~~~~ cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o -MF CMakeFiles/vf2c.dir/pow_dd.c.o.d -o CMakeFiles/vf2c.dir/pow_dd.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_dd.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o -MF CMakeFiles/cgcode.dir/r1mach.c.o.d -o CMakeFiles/cgcode.dir/r1mach.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/r1mach.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o -MF CMakeFiles/cgcode.dir/sratqr.c.o.d -o CMakeFiles/cgcode.dir/sratqr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sratqr.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o -MF CMakeFiles/cgcode.dir/dcgdrv.c.o.d -o CMakeFiles/cgcode.dir/dcgdrv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o -MF CMakeFiles/vf2c.dir/pow_di.c.o.d -o CMakeFiles/vf2c.dir/pow_di.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_di.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o -MF CMakeFiles/vf2c.dir/pow_hh.c.o.d -o CMakeFiles/vf2c.dir/pow_hh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c [ 14%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o -MF CMakeFiles/gamer.dir/biom/MarchingCube.C.o.d -o CMakeFiles/gamer.dir/biom/MarchingCube.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o -MF CMakeFiles/vf2c.dir/pow_ii.c.o.d -o CMakeFiles/vf2c.dir/pow_ii.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o -MF CMakeFiles/vf2c.dir/pow_ri.c.o.d -o CMakeFiles/vf2c.dir/pow_ri.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o -MF CMakeFiles/cgcode.dir/dcg.c.o.d -o CMakeFiles/cgcode.dir/dcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcg.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG 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_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o -MF CMakeFiles/vf2c.dir/c_abs.c.o.d -o CMakeFiles/vf2c.dir/c_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_abs.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o -MF CMakeFiles/vf2c.dir/pow_zz.c.o.d -o CMakeFiles/vf2c.dir/pow_zz.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zz.c [ 17%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Mesh.C [ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o -MF CMakeFiles/cgcode.dir/dcr.c.o.d -o CMakeFiles/cgcode.dir/dcr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcr.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time 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CMakeFiles/vf2c.dir/c_cos.c.o.d -o CMakeFiles/vf2c.dir/c_cos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_cos.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o -MF CMakeFiles/cgcode.dir/dcrind.c.o.d -o CMakeFiles/cgcode.dir/dcrind.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcrind.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o -MF CMakeFiles/vf2c.dir/c_exp.c.o.d -o CMakeFiles/vf2c.dir/c_exp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_exp.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o -MF CMakeFiles/cgcode.dir/dpcg.c.o.d -o CMakeFiles/cgcode.dir/dpcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcg.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o -MF CMakeFiles/vf2c.dir/c_log.c.o.d -o CMakeFiles/vf2c.dir/c_log.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_log.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o -MF CMakeFiles/vf2c.dir/c_sin.c.o.d -o CMakeFiles/vf2c.dir/c_sin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sin.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT 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/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c [ 20%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o -MF CMakeFiles/vf2c.dir/z_abs.c.o.d -o CMakeFiles/vf2c.dir/z_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_abs.c [ 20%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o -MF CMakeFiles/gamer.dir/biom/ReadLattice.C.o.d -o CMakeFiles/gamer.dir/biom/ReadLattice.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C [ 20%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o -MF CMakeFiles/gamer.dir/biom/ReadPDB.C.o.d -o CMakeFiles/gamer.dir/biom/ReadPDB.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o -MF CMakeFiles/vf2c.dir/z_cos.c.o.d -o CMakeFiles/vf2c.dir/z_cos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_cos.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o -MF CMakeFiles/cgcode.dir/dcgne.c.o.d -o CMakeFiles/cgcode.dir/dcgne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgne.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o -MF CMakeFiles/vf2c.dir/z_div.c.o.d -o CMakeFiles/vf2c.dir/z_div.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_div.c [ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o -MF CMakeFiles/cgcode.dir/dpcgnr.c.o.d -o CMakeFiles/cgcode.dir/dpcgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgnr.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o -MF CMakeFiles/vf2c.dir/z_exp.c.o.d -o CMakeFiles/vf2c.dir/z_exp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_exp.c [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o -MF CMakeFiles/cgcode.dir/dpcgne.c.o.d -o CMakeFiles/cgcode.dir/dpcgne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o -MF CMakeFiles/vf2c.dir/z_log.c.o.d -o CMakeFiles/vf2c.dir/z_log.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_log.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o -MF CMakeFiles/vf2c.dir/z_sin.c.o.d -o CMakeFiles/vf2c.dir/z_sin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sin.c [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o -MF CMakeFiles/cgcode.dir/dppcg.c.o.d -o CMakeFiles/cgcode.dir/dppcg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dppcg.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C: In function 'float PDB2Volume(char*, float**, int*, int*, int*, float*, float*, ATOM**, int*, char)': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:85:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 85 | fscanf(fp,"%d\n",&m); | ~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:88:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fscanf(fp,"%f %f %f %f\n",&x,&y,&z,&radius); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o -MF CMakeFiles/vf2c.dir/z_sqrt.c.o.d -o CMakeFiles/vf2c.dir/z_sqrt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o -MF CMakeFiles/vf2c.dir/r_abs.c.o.d -o CMakeFiles/vf2c.dir/r_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_abs.c [ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o -MF CMakeFiles/cgcode.dir/dpcgca.c.o.d -o CMakeFiles/cgcode.dir/dpcgca.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgca.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o -MF CMakeFiles/vf2c.dir/r_acos.c.o.d -o CMakeFiles/vf2c.dir/r_acos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_acos.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o -MF CMakeFiles/vf2c.dir/r_asin.c.o.d -o CMakeFiles/vf2c.dir/r_asin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_asin.c [ 25%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o [ 25%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -MF CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o.d -o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -MF CMakeFiles/gamer.dir/biom/RegionGrowing.C.o.d -o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C [ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o [ 25%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o -MF CMakeFiles/cgcode.dir/ddpchb.c.o.d -o CMakeFiles/cgcode.dir/ddpchb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -MF CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o.d -o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o -MF CMakeFiles/vf2c.dir/r_atan.c.o.d -o CMakeFiles/vf2c.dir/r_atan.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atan.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o -MF CMakeFiles/vf2c.dir/r_atn2.c.o.d -o CMakeFiles/vf2c.dir/r_atn2.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atn2.c [ 26%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o -MF CMakeFiles/cgcode.dir/dcbfix.c.o.d -o CMakeFiles/cgcode.dir/dcbfix.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c [ 27%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o -MF CMakeFiles/gamer.dir/biom/SurfExtract.C.o.d -o CMakeFiles/gamer.dir/biom/SurfExtract.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o -MF CMakeFiles/vf2c.dir/r_cnjg.c.o.d -o CMakeFiles/vf2c.dir/r_cnjg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o [ 28%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o -MF CMakeFiles/vf2c.dir/r_cos.c.o.d -o CMakeFiles/vf2c.dir/r_cos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cos.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o -MF CMakeFiles/cgcode.dir/dckchb.c.o.d -o CMakeFiles/cgcode.dir/dckchb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dckchb.c [ 29%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o -MF CMakeFiles/cgcode.dir/dcgchk.c.o.d -o CMakeFiles/cgcode.dir/dcgchk.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgchk.c [ 29%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o -MF CMakeFiles/gamer.dir/biom/SurfRefine.C.o.d -o CMakeFiles/gamer.dir/biom/SurfRefine.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o -MF CMakeFiles/vf2c.dir/r_cosh.c.o.d -o CMakeFiles/vf2c.dir/r_cosh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cosh.c [ 29%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o -MF CMakeFiles/cgcode.dir/donest.c.o.d -o CMakeFiles/cgcode.dir/donest.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/donest.c [ 29%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o [ 29%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o -MF CMakeFiles/cgcode.dir/mdstop.c.o.d -o CMakeFiles/cgcode.dir/mdstop.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/mdstop.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -MF CMakeFiles/gamer.dir/biom/SurfSmooth.C.o.d -o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfSmooth.C [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function 'SurfaceMesh* SurfaceMesh_readOFF(char*)': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:401:14: warning: too many arguments for format [-Wformat-extra-args] 401 | printf("Read error. Expected 3 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o -MF CMakeFiles/vf2c.dir/r_dim.c.o.d -o CMakeFiles/vf2c.dir/r_dim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_dim.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:494:14: warning: too many arguments for format [-Wformat-extra-args] 494 | printf("Read error. Expected 4 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function 'GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:754:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 754 | in.save_nodes("plc"); | ^~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:755:16: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 755 | in.save_poly("plc"); | ^~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:761:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 761 | out.save_nodes("result"); | ^~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:762:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 762 | out.save_elements("result"); | ^~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:763:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 763 | out.save_faces("result"); | ^~~~~~~~ [ 30%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o -MF CMakeFiles/cgcode.dir/d1mach.c.o.d -o CMakeFiles/cgcode.dir/d1mach.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/d1mach.c [ 30%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o -MF CMakeFiles/cgcode.dir/dratqr.c.o.d -o CMakeFiles/cgcode.dir/dratqr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dratqr.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o [ 30%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o -MF CMakeFiles/vf2c.dir/r_exp.c.o.d -o CMakeFiles/vf2c.dir/r_exp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_exp.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o -MF CMakeFiles/cgcode.dir/depsln.c.o.d -o CMakeFiles/cgcode.dir/depsln.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/depsln.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o -MF CMakeFiles/vf2c.dir/r_imag.c.o.d -o CMakeFiles/vf2c.dir/r_imag.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_imag.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o -MF CMakeFiles/vf2c.dir/r_int.c.o.d -o CMakeFiles/vf2c.dir/r_int.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_int.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o -MF CMakeFiles/vf2c.dir/r_lg10.c.o.d -o CMakeFiles/vf2c.dir/r_lg10.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_lg10.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o -MF CMakeFiles/vf2c.dir/r_log.c.o.d -o CMakeFiles/vf2c.dir/r_log.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_log.c [ 32%] Linking C shared library libcgcode.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1 [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o -MF CMakeFiles/vf2c.dir/r_mod.c.o.d -o CMakeFiles/vf2c.dir/r_mod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_mod.c /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libcgcode.so.1.9 -o libcgcode.so.1.9.3 CMakeFiles/cgcode.dir/scgdrv.c.o CMakeFiles/cgcode.dir/scg.c.o CMakeFiles/cgcode.dir/scr.c.o CMakeFiles/cgcode.dir/scrind.c.o CMakeFiles/cgcode.dir/spcg.c.o CMakeFiles/cgcode.dir/scgnr.c.o CMakeFiles/cgcode.dir/scgne.c.o CMakeFiles/cgcode.dir/spcgnr.c.o CMakeFiles/cgcode.dir/spcgne.c.o CMakeFiles/cgcode.dir/sppcg.c.o CMakeFiles/cgcode.dir/spcgca.c.o CMakeFiles/cgcode.dir/sdpchb.c.o CMakeFiles/cgcode.dir/scbfix.c.o CMakeFiles/cgcode.dir/sckchb.c.o CMakeFiles/cgcode.dir/scgchk.c.o CMakeFiles/cgcode.dir/sonest.c.o CMakeFiles/cgcode.dir/msstop.c.o CMakeFiles/cgcode.dir/r1mach.c.o CMakeFiles/cgcode.dir/sratqr.c.o CMakeFiles/cgcode.dir/dcgdrv.c.o CMakeFiles/cgcode.dir/dcg.c.o CMakeFiles/cgcode.dir/dcr.c.o CMakeFiles/cgcode.dir/dcrind.c.o CMakeFiles/cgcode.dir/dpcg.c.o CMakeFiles/cgcode.dir/dcgnr.c.o CMakeFiles/cgcode.dir/dcgne.c.o CMakeFiles/cgcode.dir/dpcgnr.c.o CMakeFiles/cgcode.dir/dpcgne.c.o CMakeFiles/cgcode.dir/dppcg.c.o CMakeFiles/cgcode.dir/dpcgca.c.o CMakeFiles/cgcode.dir/ddpchb.c.o CMakeFiles/cgcode.dir/dcbfix.c.o CMakeFiles/cgcode.dir/dckchb.c.o CMakeFiles/cgcode.dir/dcgchk.c.o CMakeFiles/cgcode.dir/donest.c.o CMakeFiles/cgcode.dir/mdstop.c.o CMakeFiles/cgcode.dir/d1mach.c.o CMakeFiles/cgcode.dir/dratqr.c.o CMakeFiles/cgcode.dir/depsln.c.o [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o -MF CMakeFiles/vf2c.dir/r_nint.c.o.d -o CMakeFiles/vf2c.dir/r_nint.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_nint.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o -MF CMakeFiles/vf2c.dir/r_sign.c.o.d -o CMakeFiles/vf2c.dir/r_sign.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sign.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o -MF CMakeFiles/vf2c.dir/r_sin.c.o.d -o CMakeFiles/vf2c.dir/r_sin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sin.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_symlink_library libcgcode.so.1.9.3 libcgcode.so.1.9 libcgcode.so [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o -MF CMakeFiles/vf2c.dir/r_sinh.c.o.d -o CMakeFiles/vf2c.dir/r_sinh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sinh.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o -MF CMakeFiles/vf2c.dir/r_sqrt.c.o.d -o CMakeFiles/vf2c.dir/r_sqrt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sqrt.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o -MF CMakeFiles/vf2c.dir/r_tan.c.o.d -o CMakeFiles/vf2c.dir/r_tan.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tan.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o -MF CMakeFiles/vf2c.dir/r_tanh.c.o.d -o CMakeFiles/vf2c.dir/r_tanh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c [ 34%] Built target cgcode [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o -MF CMakeFiles/vf2c.dir/d_abs.c.o.d -o CMakeFiles/vf2c.dir/d_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_abs.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o -MF CMakeFiles/vf2c.dir/d_acos.c.o.d -o CMakeFiles/vf2c.dir/d_acos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_acos.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o -MF CMakeFiles/vf2c.dir/d_asin.c.o.d -o CMakeFiles/vf2c.dir/d_asin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_asin.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o -MF CMakeFiles/vf2c.dir/d_atan.c.o.d -o CMakeFiles/vf2c.dir/d_atan.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atan.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o -MF CMakeFiles/vf2c.dir/d_atn2.c.o.d -o CMakeFiles/vf2c.dir/d_atn2.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o -MF CMakeFiles/vf2c.dir/d_cnjg.c.o.d -o CMakeFiles/vf2c.dir/d_cnjg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o -MF CMakeFiles/vf2c.dir/d_cos.c.o.d -o CMakeFiles/vf2c.dir/d_cos.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cos.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o -MF CMakeFiles/vf2c.dir/d_cosh.c.o.d -o CMakeFiles/vf2c.dir/d_cosh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o -MF CMakeFiles/vf2c.dir/d_dim.c.o.d -o CMakeFiles/vf2c.dir/d_dim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_dim.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o -MF CMakeFiles/vf2c.dir/d_exp.c.o.d -o CMakeFiles/vf2c.dir/d_exp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_exp.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o -MF CMakeFiles/vf2c.dir/d_imag.c.o.d -o CMakeFiles/vf2c.dir/d_imag.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_imag.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o -MF CMakeFiles/vf2c.dir/d_int.c.o.d -o CMakeFiles/vf2c.dir/d_int.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_int.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o -MF CMakeFiles/vf2c.dir/d_lg10.c.o.d -o CMakeFiles/vf2c.dir/d_lg10.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o -MF CMakeFiles/vf2c.dir/d_log.c.o.d -o CMakeFiles/vf2c.dir/d_log.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_log.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o cd 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o -MF CMakeFiles/vf2c.dir/d_nint.c.o.d -o CMakeFiles/vf2c.dir/d_nint.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_nint.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o -MF CMakeFiles/vf2c.dir/d_prod.c.o.d -o CMakeFiles/vf2c.dir/d_prod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_prod.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o -MF CMakeFiles/vf2c.dir/d_sign.c.o.d -o CMakeFiles/vf2c.dir/d_sign.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sign.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o -MF CMakeFiles/vf2c.dir/d_sin.c.o.d -o CMakeFiles/vf2c.dir/d_sin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sin.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o -MF CMakeFiles/vf2c.dir/d_sinh.c.o.d -o CMakeFiles/vf2c.dir/d_sinh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o -MF CMakeFiles/vf2c.dir/d_tan.c.o.d -o CMakeFiles/vf2c.dir/d_tan.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tan.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o -MF CMakeFiles/vf2c.dir/d_sqrt.c.o.d -o CMakeFiles/vf2c.dir/d_sqrt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o -MF CMakeFiles/vf2c.dir/d_tanh.c.o.d -o CMakeFiles/vf2c.dir/d_tanh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o -MF CMakeFiles/vf2c.dir/i_abs.c.o.d -o CMakeFiles/vf2c.dir/i_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_abs.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o -MF CMakeFiles/vf2c.dir/i_dim.c.o.d -o CMakeFiles/vf2c.dir/i_dim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dim.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o -MF CMakeFiles/vf2c.dir/i_dnnt.c.o.d -o CMakeFiles/vf2c.dir/i_dnnt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o -MF CMakeFiles/vf2c.dir/i_indx.c.o.d -o CMakeFiles/vf2c.dir/i_indx.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_indx.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o -MF CMakeFiles/vf2c.dir/i_len.c.o.d -o CMakeFiles/vf2c.dir/i_len.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_len.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o -MF CMakeFiles/vf2c.dir/i_mod.c.o.d -o CMakeFiles/vf2c.dir/i_mod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_mod.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o -MF CMakeFiles/vf2c.dir/i_nint.c.o.d -o CMakeFiles/vf2c.dir/i_nint.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_nint.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o -MF CMakeFiles/vf2c.dir/i_sign.c.o.d -o CMakeFiles/vf2c.dir/i_sign.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_sign.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o -MF CMakeFiles/vf2c.dir/lbitbits.c.o.d -o CMakeFiles/vf2c.dir/lbitbits.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitbits.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o -MF CMakeFiles/vf2c.dir/lbitshft.c.o.d -o CMakeFiles/vf2c.dir/lbitshft.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitshft.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o -MF CMakeFiles/vf2c.dir/h_abs.c.o.d -o CMakeFiles/vf2c.dir/h_abs.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_abs.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o -MF CMakeFiles/vf2c.dir/h_dim.c.o.d -o CMakeFiles/vf2c.dir/h_dim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dim.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o -MF CMakeFiles/vf2c.dir/h_dnnt.c.o.d -o CMakeFiles/vf2c.dir/h_dnnt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o -MF CMakeFiles/vf2c.dir/h_indx.c.o.d -o CMakeFiles/vf2c.dir/h_indx.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_indx.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o -MF CMakeFiles/vf2c.dir/h_len.c.o.d -o CMakeFiles/vf2c.dir/h_len.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_len.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o -MF CMakeFiles/vf2c.dir/h_mod.c.o.d -o CMakeFiles/vf2c.dir/h_mod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_mod.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o -MF CMakeFiles/vf2c.dir/h_nint.c.o.d -o CMakeFiles/vf2c.dir/h_nint.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_nint.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o -MF CMakeFiles/vf2c.dir/h_sign.c.o.d -o CMakeFiles/vf2c.dir/h_sign.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_sign.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o -MF CMakeFiles/vf2c.dir/l_gt.c.o.d -o CMakeFiles/vf2c.dir/l_gt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_gt.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o -MF CMakeFiles/vf2c.dir/l_ge.c.o.d -o CMakeFiles/vf2c.dir/l_ge.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_ge.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o -MF CMakeFiles/vf2c.dir/l_le.c.o.d -o CMakeFiles/vf2c.dir/l_le.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_le.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o -MF CMakeFiles/vf2c.dir/l_lt.c.o.d -o CMakeFiles/vf2c.dir/l_lt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_lt.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o -MF CMakeFiles/vf2c.dir/hl_ge.c.o.d -o CMakeFiles/vf2c.dir/hl_ge.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_ge.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o -MF CMakeFiles/vf2c.dir/hl_le.c.o.d -o CMakeFiles/vf2c.dir/hl_le.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_le.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o -MF CMakeFiles/vf2c.dir/hl_gt.c.o.d -o CMakeFiles/vf2c.dir/hl_gt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_gt.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o -MF CMakeFiles/vf2c.dir/hl_lt.c.o.d -o CMakeFiles/vf2c.dir/hl_lt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_lt.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG 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-I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o -MF CMakeFiles/vf2c.dir/ef1cmc_.c.o.d -o CMakeFiles/vf2c.dir/ef1cmc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1cmc_.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o -MF CMakeFiles/vf2c.dir/f77_aloc.c.o.d -o CMakeFiles/vf2c.dir/f77_aloc.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77_aloc.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o -MF CMakeFiles/vf2c.dir/s_cat.c.o.d -o CMakeFiles/vf2c.dir/s_cat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_cat.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o -MF CMakeFiles/vf2c.dir/s_cmp.c.o.d -o CMakeFiles/vf2c.dir/s_cmp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_cmp.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o -MF CMakeFiles/vf2c.dir/s_copy.c.o.d -o CMakeFiles/vf2c.dir/s_copy.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_copy.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o -MF CMakeFiles/vf2c.dir/dtime_.c.o.d -o CMakeFiles/vf2c.dir/dtime_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dtime_.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o -MF CMakeFiles/vf2c.dir/etime_.c.o.d -o CMakeFiles/vf2c.dir/etime_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/etime_.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o -MF CMakeFiles/vf2c.dir/backspac.c.o.d -o CMakeFiles/vf2c.dir/backspac.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o -MF CMakeFiles/vf2c.dir/close.c.o.d -o CMakeFiles/vf2c.dir/close.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/close.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function 'f_back': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c:47:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 47 | fread((char *)&n,sizeof(uiolen),1,f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC 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CMakeFiles/vf2c.dir/dolio.c.o.d -o CMakeFiles/vf2c.dir/dolio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dolio.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o -MF CMakeFiles/vf2c.dir/due.c.o.d -o CMakeFiles/vf2c.dir/due.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/due.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o -MF CMakeFiles/vf2c.dir/fmt.c.o.d -o CMakeFiles/vf2c.dir/fmt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmt.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o -MF CMakeFiles/vf2c.dir/endfile.c.o.d -o CMakeFiles/vf2c.dir/endfile.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/endfile.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o -MF CMakeFiles/vf2c.dir/err.c.o.d -o CMakeFiles/vf2c.dir/err.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/err.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o -MF CMakeFiles/vf2c.dir/fmtlib.c.o.d -o CMakeFiles/vf2c.dir/fmtlib.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmtlib.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o cd 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_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o -MF CMakeFiles/vf2c.dir/lread.c.o.d -o CMakeFiles/vf2c.dir/lread.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lread.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o -MF CMakeFiles/vf2c.dir/lwrite.c.o.d -o CMakeFiles/vf2c.dir/lwrite.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lwrite.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o -MF CMakeFiles/vf2c.dir/open.c.o.d -o CMakeFiles/vf2c.dir/open.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/open.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o -MF CMakeFiles/vf2c.dir/rdfmt.c.o.d -o CMakeFiles/vf2c.dir/rdfmt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o -MF CMakeFiles/vf2c.dir/rewind.c.o.d -o CMakeFiles/vf2c.dir/rewind.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rewind.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o -MF CMakeFiles/vf2c.dir/rsfe.c.o.d -o CMakeFiles/vf2c.dir/rsfe.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o -MF CMakeFiles/vf2c.dir/rsli.c.o.d -o CMakeFiles/vf2c.dir/rsli.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsli.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o -MF CMakeFiles/vf2c.dir/rsne.c.o.d -o CMakeFiles/vf2c.dir/rsne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsne.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o -MF CMakeFiles/vf2c.dir/sfe.c.o.d -o CMakeFiles/vf2c.dir/sfe.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o -MF CMakeFiles/vf2c.dir/sue.c.o.d -o CMakeFiles/vf2c.dir/sue.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sue.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o -MF CMakeFiles/vf2c.dir/typesize.c.o.d -o CMakeFiles/vf2c.dir/typesize.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/typesize.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o -MF CMakeFiles/vf2c.dir/uio.c.o.d -o CMakeFiles/vf2c.dir/uio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uio.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o -MF CMakeFiles/vf2c.dir/util.c.o.d -o CMakeFiles/vf2c.dir/util.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/util.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o -MF CMakeFiles/vf2c.dir/wref.c.o.d -o CMakeFiles/vf2c.dir/wref.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wref.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o -MF CMakeFiles/vf2c.dir/wrtfmt.c.o.d -o CMakeFiles/vf2c.dir/wrtfmt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wrtfmt.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o -MF CMakeFiles/vf2c.dir/wsfe.c.o.d -o CMakeFiles/vf2c.dir/wsfe.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsfe.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o -MF CMakeFiles/vf2c.dir/wsle.c.o.d -o CMakeFiles/vf2c.dir/wsle.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsle.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o -MF CMakeFiles/vf2c.dir/wsne.c.o.d -o CMakeFiles/vf2c.dir/wsne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsne.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o -MF CMakeFiles/vf2c.dir/xwsne.c.o.d -o CMakeFiles/vf2c.dir/xwsne.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/xwsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o -MF CMakeFiles/vf2c.dir/main.c.o.d -o CMakeFiles/vf2c.dir/main.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c:115:1: warning: return type defaults to 'int' [-Wimplicit-int] 115 | main(int argc, char **argv) | ^~~~ [ 60%] Linking C shared library libvf2c.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_link_script CMakeFiles/vf2c.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libvf2c.so.1.9 -o libvf2c.so.1.9.3 CMakeFiles/vf2c.dir/f77vers.c.o CMakeFiles/vf2c.dir/i77vers.c.o CMakeFiles/vf2c.dir/s_rnge.c.o CMakeFiles/vf2c.dir/abort_.c.o CMakeFiles/vf2c.dir/exit_.c.o CMakeFiles/vf2c.dir/getarg_.c.o CMakeFiles/vf2c.dir/iargc_.c.o CMakeFiles/vf2c.dir/getenv_.c.o CMakeFiles/vf2c.dir/signal_.c.o CMakeFiles/vf2c.dir/s_stop.c.o CMakeFiles/vf2c.dir/s_paus.c.o CMakeFiles/vf2c.dir/system_.c.o CMakeFiles/vf2c.dir/cabs.c.o CMakeFiles/vf2c.dir/derf_.c.o CMakeFiles/vf2c.dir/derfc_.c.o CMakeFiles/vf2c.dir/erf_.c.o CMakeFiles/vf2c.dir/erfc_.c.o CMakeFiles/vf2c.dir/sig_die.c.o CMakeFiles/vf2c.dir/uninit.c.o CMakeFiles/vf2c.dir/pow_ci.c.o CMakeFiles/vf2c.dir/pow_dd.c.o CMakeFiles/vf2c.dir/pow_di.c.o CMakeFiles/vf2c.dir/pow_hh.c.o CMakeFiles/vf2c.dir/pow_ii.c.o CMakeFiles/vf2c.dir/pow_ri.c.o CMakeFiles/vf2c.dir/pow_zi.c.o CMakeFiles/vf2c.dir/pow_zz.c.o CMakeFiles/vf2c.dir/c_abs.c.o CMakeFiles/vf2c.dir/c_cos.c.o CMakeFiles/vf2c.dir/c_div.c.o CMakeFiles/vf2c.dir/c_exp.c.o CMakeFiles/vf2c.dir/c_log.c.o CMakeFiles/vf2c.dir/c_sin.c.o CMakeFiles/vf2c.dir/c_sqrt.c.o CMakeFiles/vf2c.dir/z_abs.c.o CMakeFiles/vf2c.dir/z_cos.c.o CMakeFiles/vf2c.dir/z_div.c.o CMakeFiles/vf2c.dir/z_exp.c.o CMakeFiles/vf2c.dir/z_log.c.o CMakeFiles/vf2c.dir/z_sin.c.o CMakeFiles/vf2c.dir/z_sqrt.c.o CMakeFiles/vf2c.dir/r_abs.c.o CMakeFiles/vf2c.dir/r_acos.c.o CMakeFiles/vf2c.dir/r_asin.c.o CMakeFiles/vf2c.dir/r_atan.c.o CMakeFiles/vf2c.dir/r_atn2.c.o CMakeFiles/vf2c.dir/r_cnjg.c.o CMakeFiles/vf2c.dir/r_cos.c.o CMakeFiles/vf2c.dir/r_cosh.c.o CMakeFiles/vf2c.dir/r_dim.c.o CMakeFiles/vf2c.dir/r_exp.c.o CMakeFiles/vf2c.dir/r_imag.c.o CMakeFiles/vf2c.dir/r_int.c.o CMakeFiles/vf2c.dir/r_lg10.c.o CMakeFiles/vf2c.dir/r_log.c.o CMakeFiles/vf2c.dir/r_mod.c.o CMakeFiles/vf2c.dir/r_nint.c.o CMakeFiles/vf2c.dir/r_sign.c.o CMakeFiles/vf2c.dir/r_sin.c.o CMakeFiles/vf2c.dir/r_sinh.c.o CMakeFiles/vf2c.dir/r_sqrt.c.o CMakeFiles/vf2c.dir/r_tan.c.o CMakeFiles/vf2c.dir/r_tanh.c.o CMakeFiles/vf2c.dir/d_abs.c.o CMakeFiles/vf2c.dir/d_acos.c.o CMakeFiles/vf2c.dir/d_asin.c.o CMakeFiles/vf2c.dir/d_atan.c.o CMakeFiles/vf2c.dir/d_atn2.c.o CMakeFiles/vf2c.dir/d_cnjg.c.o CMakeFiles/vf2c.dir/d_cos.c.o CMakeFiles/vf2c.dir/d_cosh.c.o CMakeFiles/vf2c.dir/d_dim.c.o CMakeFiles/vf2c.dir/d_exp.c.o CMakeFiles/vf2c.dir/d_imag.c.o CMakeFiles/vf2c.dir/d_int.c.o CMakeFiles/vf2c.dir/d_lg10.c.o CMakeFiles/vf2c.dir/d_log.c.o CMakeFiles/vf2c.dir/d_mod.c.o CMakeFiles/vf2c.dir/d_nint.c.o CMakeFiles/vf2c.dir/d_prod.c.o CMakeFiles/vf2c.dir/d_sign.c.o CMakeFiles/vf2c.dir/d_sin.c.o CMakeFiles/vf2c.dir/d_sinh.c.o CMakeFiles/vf2c.dir/d_sqrt.c.o CMakeFiles/vf2c.dir/d_tan.c.o CMakeFiles/vf2c.dir/d_tanh.c.o CMakeFiles/vf2c.dir/i_abs.c.o CMakeFiles/vf2c.dir/i_dim.c.o CMakeFiles/vf2c.dir/i_dnnt.c.o CMakeFiles/vf2c.dir/i_indx.c.o CMakeFiles/vf2c.dir/i_len.c.o CMakeFiles/vf2c.dir/i_mod.c.o CMakeFiles/vf2c.dir/i_nint.c.o CMakeFiles/vf2c.dir/i_sign.c.o CMakeFiles/vf2c.dir/lbitbits.c.o CMakeFiles/vf2c.dir/lbitshft.c.o CMakeFiles/vf2c.dir/h_abs.c.o CMakeFiles/vf2c.dir/h_dim.c.o CMakeFiles/vf2c.dir/h_dnnt.c.o CMakeFiles/vf2c.dir/h_indx.c.o CMakeFiles/vf2c.dir/h_len.c.o CMakeFiles/vf2c.dir/h_mod.c.o CMakeFiles/vf2c.dir/h_nint.c.o CMakeFiles/vf2c.dir/h_sign.c.o CMakeFiles/vf2c.dir/l_ge.c.o CMakeFiles/vf2c.dir/l_gt.c.o CMakeFiles/vf2c.dir/l_le.c.o CMakeFiles/vf2c.dir/l_lt.c.o CMakeFiles/vf2c.dir/hl_ge.c.o CMakeFiles/vf2c.dir/hl_gt.c.o CMakeFiles/vf2c.dir/hl_le.c.o CMakeFiles/vf2c.dir/hl_lt.c.o CMakeFiles/vf2c.dir/ef1asc_.c.o CMakeFiles/vf2c.dir/ef1cmc_.c.o CMakeFiles/vf2c.dir/f77_aloc.c.o CMakeFiles/vf2c.dir/s_cat.c.o CMakeFiles/vf2c.dir/s_cmp.c.o CMakeFiles/vf2c.dir/s_copy.c.o CMakeFiles/vf2c.dir/dtime_.c.o CMakeFiles/vf2c.dir/etime_.c.o CMakeFiles/vf2c.dir/backspac.c.o CMakeFiles/vf2c.dir/close.c.o CMakeFiles/vf2c.dir/dfe.c.o CMakeFiles/vf2c.dir/dolio.c.o CMakeFiles/vf2c.dir/due.c.o CMakeFiles/vf2c.dir/endfile.c.o CMakeFiles/vf2c.dir/err.c.o CMakeFiles/vf2c.dir/fmt.c.o CMakeFiles/vf2c.dir/fmtlib.c.o CMakeFiles/vf2c.dir/ftell_.c.o CMakeFiles/vf2c.dir/iio.c.o CMakeFiles/vf2c.dir/ilnw.c.o CMakeFiles/vf2c.dir/inquire.c.o CMakeFiles/vf2c.dir/lread.c.o CMakeFiles/vf2c.dir/lwrite.c.o CMakeFiles/vf2c.dir/open.c.o CMakeFiles/vf2c.dir/rdfmt.c.o CMakeFiles/vf2c.dir/rewind.c.o CMakeFiles/vf2c.dir/rsfe.c.o CMakeFiles/vf2c.dir/rsli.c.o CMakeFiles/vf2c.dir/rsne.c.o CMakeFiles/vf2c.dir/sfe.c.o CMakeFiles/vf2c.dir/sue.c.o CMakeFiles/vf2c.dir/typesize.c.o CMakeFiles/vf2c.dir/uio.c.o CMakeFiles/vf2c.dir/util.c.o CMakeFiles/vf2c.dir/wref.c.o CMakeFiles/vf2c.dir/wrtfmt.c.o CMakeFiles/vf2c.dir/wsfe.c.o CMakeFiles/vf2c.dir/wsle.c.o CMakeFiles/vf2c.dir/wsne.c.o CMakeFiles/vf2c.dir/xwsne.c.o CMakeFiles/vf2c.dir/main.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_symlink_library libvf2c.so.1.9.3 libvf2c.so.1.9 libvf2c.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 60%] Built target vf2c make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o -MF CMakeFiles/punc.dir/base/punc_base.c.o.d -o CMakeFiles/punc.dir/base/punc_base.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base/punc_base.c [ 60%] Linking C shared library libpunc.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/punc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libpunc.so.1.9 -o libpunc.so.1.9.3 CMakeFiles/punc.dir/base/punc_base.c.o -lmaloc /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_symlink_library libpunc.so.1.9.3 libpunc.so.1.9 libpunc.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 60%] Built target punc make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o -MF CMakeFiles/mc.dir/base/mc_base.c.o.d -o CMakeFiles/mc.dir/base/mc_base.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc_base.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o -MF CMakeFiles/mc.dir/bam/bmat.c.o.d -o CMakeFiles/mc.dir/bam/bmat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o -MF CMakeFiles/mc.dir/bam/bsolv.c.o.d -o CMakeFiles/mc.dir/bam/bsolv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o -MF CMakeFiles/mc.dir/bam/bvec.c.o.d -o CMakeFiles/mc.dir/bam/bvec.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o -MF CMakeFiles/mc.dir/bam/mat.c.o.d -o CMakeFiles/mc.dir/bam/mat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mat.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o -MF CMakeFiles/mc.dir/bam/matcopy.c.o.d -o CMakeFiles/mc.dir/bam/matcopy.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/matcopy.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o -MF CMakeFiles/mc.dir/bam/matln.c.o.d -o CMakeFiles/mc.dir/bam/matln.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/matln.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o -MF CMakeFiles/mc.dir/bam/mtool.c.o.d -o CMakeFiles/mc.dir/bam/mtool.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mtool.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o -MF CMakeFiles/mc.dir/bam/slu.c.o.d -o CMakeFiles/mc.dir/bam/slu.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/slu.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o -MF CMakeFiles/mc.dir/bam/vec.c.o.d -o CMakeFiles/mc.dir/bam/vec.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o -MF CMakeFiles/mc.dir/bam/vec3.c.o.d -o CMakeFiles/mc.dir/bam/vec3.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec3.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o -MF CMakeFiles/mc.dir/bam/zslu.c.o.d -o CMakeFiles/mc.dir/bam/zslu.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/zslu.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function 'Bmat_ctor': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:36: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 2147483646] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 3] In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:34: In function 'sprintf', inlined from 'Bmat_ctor' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 22 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_bcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:29: warning: '%s' directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 922 | sprintf(rn,"Bvec_bcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: In function 'sprintf', inlined from 'Bvec_bcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_bcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:33: warning: '%s' directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 919 | sprintf(rn,"--->Bvec_bcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_bcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o -MF CMakeFiles/mc.dir/whb/whb.c.o.d -o CMakeFiles/mc.dir/whb/whb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/whb.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:28: warning: '%s' directive writing up to 79 bytes into a region of size 73 [-Wformat-overflow=] 631 | sprintf(rn,"Bvec_cg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_cg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 87 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:32: warning: '%s' directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 628 | sprintf(rn,"--->Bvec_cg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_cg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function 'Bmat_galerkin': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:36: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] In function 'sprintf', inlined from 'Bmat_galerkin' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 31 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o -MF CMakeFiles/mc.dir/whb/bvechb.c.o.d -o CMakeFiles/mc.dir/whb/bvechb.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o -MF CMakeFiles/mc.dir/whb/hbtools.c.o.d -o CMakeFiles/mc.dir/whb/hbtools.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o -MF CMakeFiles/mc.dir/whb/rcmat.c.o.d -o CMakeFiles/mc.dir/whb/rcmat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/rcmat.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cgnr': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:30: warning: '%s' directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 1422 | sprintf(rn,"Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_cgnr' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cgnr': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:34: warning: '%s' directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 1419 | sprintf(rn,"--->Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_cgnr' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function 'Bvec_ctorPoint': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:28: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 2147483646] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:34: In function 'sprintf', inlined from 'Bvec_ctorPoint' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 21 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o -MF CMakeFiles/mc.dir/whb/brcmat.c.o.d -o CMakeFiles/mc.dir/whb/brcmat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/brcmat.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:29: warning: '%s' directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 267 | sprintf(rn,"Bvec_hcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: In function 'sprintf', inlined from 'Bvec_hcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:33: warning: '%s' directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 264 | sprintf(rn,"--->Bvec_hcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_hcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o -MF CMakeFiles/mc.dir/whb/subopt.c.o.d -o CMakeFiles/mc.dir/whb/subopt.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o -MF CMakeFiles/mc.dir/aprx/aprx.c.o.d -o CMakeFiles/mc.dir/aprx/aprx.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hbcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:30: warning: '%s' directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 474 | sprintf(rn,"Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_hbcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hbcg': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:34: warning: '%s' directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 471 | sprintf(rn,"--->Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_hbcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o -MF CMakeFiles/mc.dir/aprx/assem.c.o.d -o CMakeFiles/mc.dir/aprx/assem.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/assem.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o -MF CMakeFiles/mc.dir/aprx/bnode.c.o.d -o CMakeFiles/mc.dir/aprx/bnode.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/bnode.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o -MF CMakeFiles/mc.dir/aprx/eval.c.o.d -o CMakeFiles/mc.dir/aprx/eval.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam 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_deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o -MF CMakeFiles/mc.dir/aprx/estim.c.o.d -o CMakeFiles/mc.dir/aprx/estim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/estim.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o -MF CMakeFiles/mc.dir/aprx/node.c.o.d -o CMakeFiles/mc.dir/aprx/node.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/node.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o -MF CMakeFiles/mc.dir/aprx/parti.c.o.d -o CMakeFiles/mc.dir/aprx/parti.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/parti.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o -MF CMakeFiles/mc.dir/aprx/re.c.o.d -o CMakeFiles/mc.dir/aprx/re.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/re.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o -MF CMakeFiles/mc.dir/gem/vel.c.o.d -o CMakeFiles/mc.dir/gem/vel.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/vel.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src 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-I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o -MF CMakeFiles/mc.dir/gem/gem.c.o.d -o CMakeFiles/mc.dir/gem/gem.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o -MF CMakeFiles/mc.dir/gem/gemchk.c.o.d -o CMakeFiles/mc.dir/gem/gemchk.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemchk.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:40: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 368 | sprintf(filename, "f%dz.dat", block); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:34: In function 'sprintf', inlined from 'Aprx_fe2fd' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:40: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 366 | sprintf(filename, "f%dy.dat", block); | ^ In function 'sprintf', inlined from 'Aprx_fe2fd' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:40: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 364 | sprintf(filename, "f%dx.dat", block); | ^ In function 'sprintf', inlined from 'Aprx_fe2fd' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o -MF CMakeFiles/mc.dir/gem/gemdisp.c.o.d -o CMakeFiles/mc.dir/gem/gemdisp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:31: warning: '%s' directive writing up to 79 bytes into a region of size 70 [-Wformat-overflow=] 495 | sprintf(rn,"Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: In function 'sprintf', inlined from 'Bvec_sfpcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 11 and 90 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:35: warning: '%s' directive writing up to 79 bytes into a region of size 66 [-Wformat-overflow=] 492 | sprintf(rn,"--->Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_sfpcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 94 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:32: warning: '%s' directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 776 | sprintf(rn,"Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_sfpbcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:36: warning: '%s' directive writing up to 79 bytes into a region of size 65 [-Wformat-overflow=] 773 | sprintf(rn,"--->Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function 'sprintf', inlined from 'Bvec_sfpbcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 95 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o -MF CMakeFiles/mc.dir/gem/gemg.c.o.d -o CMakeFiles/mc.dir/gem/gemg.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemg.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o -MF CMakeFiles/mc.dir/gem/gemgen.c.o.d -o CMakeFiles/mc.dir/gem/gemgen.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o -MF CMakeFiles/mc.dir/gem/gemio.c.o.d -o CMakeFiles/mc.dir/gem/gemio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemio.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o -MF CMakeFiles/mc.dir/gem/gemref.c.o.d -o CMakeFiles/mc.dir/gem/gemref.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o -MF CMakeFiles/mc.dir/gem/gemunref.c.o.d -o CMakeFiles/mc.dir/gem/gemunref.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemunref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o -MF CMakeFiles/mc.dir/gem/gemcube.c.o.d -o CMakeFiles/mc.dir/gem/gemcube.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemcube.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o -MF CMakeFiles/mc.dir/pde/pde.c.o.d -o CMakeFiles/mc.dir/pde/pde.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde/pde.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function 'Gem_delaunay': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: warning: 'Gem_writeGV' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 522 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type 'double *[4]' In file included from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function 'Gem_writeGV' 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: warning: 'Gem_writeGV' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 659 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function 'Gem_writeGV' 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: warning: 'Gem_writeGV' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 743 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function 'Gem_writeGV' 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o -MF CMakeFiles/mc.dir/nam/am.c.o.d -o CMakeFiles/mc.dir/nam/am.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/am.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o -MF CMakeFiles/mc.dir/nam/lsolv.c.o.d -o CMakeFiles/mc.dir/nam/lsolv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/lsolv.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o -MF CMakeFiles/mc.dir/nam/nsolv.c.o.d -o CMakeFiles/mc.dir/nam/nsolv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/nsolv.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o -MF CMakeFiles/mc.dir/dyn/dyn.c.o.d -o CMakeFiles/mc.dir/dyn/dyn.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/dyn.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o -MF CMakeFiles/mc.dir/dyn/svio.c.o.d -o CMakeFiles/mc.dir/dyn/svio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/svio.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o -MF CMakeFiles/mc.dir/mcsh/mcsh.c.o.d -o CMakeFiles/mc.dir/mcsh/mcsh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function 'MCsh_builtIn': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: warning: 'Gem_writeGEOM' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 765 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 766 | sock, | ~~~~~ 767 | defKey, | ~~~~~~~ 768 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 769 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 770 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 771 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 | defX, | ~~~~~ 773 | "GV"); | ~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type 'double *[4]' In file included from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function 'Gem_writeGEOM' 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: warning: 'Gem_writeGEOM' accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 810 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 811 | sock, | ~~~~~ 812 | defKey, | ~~~~~~~ 813 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 814 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 815 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 816 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 817 | defX, | ~~~~~ 818 | "MATH"); | ~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function 'Gem_writeGEOM' 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function 'Gem_writeTEC': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:33: warning: '__builtin___sprintf_chk' writing a terminating nul past the end of the destination [-Wformat-overflow=] 1656 | sprintf(str1,"TETRAHEDRA"); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: In function 'sprintf', inlined from 'Gem_writeTEC' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function 'Gem_writeTEC': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:33: warning: 'TETRAHEDRON' directive writing 11 bytes into a region of size 10 [-Wformat-overflow=] 1657 | sprintf(str2,"TETRAHEDRON"); | ~~~~~~~~~~^ In function 'sprintf', inlined from 'Gem_writeTEC' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 73%] Linking C shared library libmc.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/mc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libmc.so.1.9 -o libmc.so.1.9.3 CMakeFiles/mc.dir/base/mc_base.c.o CMakeFiles/mc.dir/bam/bmat.c.o CMakeFiles/mc.dir/bam/bsolv.c.o CMakeFiles/mc.dir/bam/bvec.c.o CMakeFiles/mc.dir/bam/mat.c.o CMakeFiles/mc.dir/bam/matcopy.c.o CMakeFiles/mc.dir/bam/matln.c.o CMakeFiles/mc.dir/bam/mtool.c.o CMakeFiles/mc.dir/bam/slu.c.o CMakeFiles/mc.dir/bam/vec.c.o CMakeFiles/mc.dir/bam/vec3.c.o CMakeFiles/mc.dir/bam/zslu.c.o CMakeFiles/mc.dir/whb/whb.c.o CMakeFiles/mc.dir/whb/bvechb.c.o CMakeFiles/mc.dir/whb/hbtools.c.o CMakeFiles/mc.dir/whb/rcmat.c.o CMakeFiles/mc.dir/whb/brcmat.c.o CMakeFiles/mc.dir/whb/subopt.c.o CMakeFiles/mc.dir/aprx/aprx.c.o CMakeFiles/mc.dir/aprx/assem.c.o CMakeFiles/mc.dir/aprx/bnode.c.o CMakeFiles/mc.dir/aprx/estim.c.o CMakeFiles/mc.dir/aprx/eval.c.o CMakeFiles/mc.dir/aprx/io.c.o CMakeFiles/mc.dir/aprx/node.c.o CMakeFiles/mc.dir/aprx/parti.c.o CMakeFiles/mc.dir/aprx/re.c.o CMakeFiles/mc.dir/gem/vel.c.o CMakeFiles/mc.dir/gem/ves.c.o CMakeFiles/mc.dir/gem/gem.c.o CMakeFiles/mc.dir/gem/gemchk.c.o CMakeFiles/mc.dir/gem/gemdisp.c.o CMakeFiles/mc.dir/gem/gemg.c.o CMakeFiles/mc.dir/gem/gemgen.c.o CMakeFiles/mc.dir/gem/gemio.c.o CMakeFiles/mc.dir/gem/gemref.c.o CMakeFiles/mc.dir/gem/gemunref.c.o CMakeFiles/mc.dir/gem/gemcube.c.o CMakeFiles/mc.dir/pde/pde.c.o CMakeFiles/mc.dir/nam/am.c.o CMakeFiles/mc.dir/nam/lsolv.c.o CMakeFiles/mc.dir/nam/nsolv.c.o CMakeFiles/mc.dir/dyn/dyn.c.o CMakeFiles/mc.dir/dyn/svio.c.o CMakeFiles/mc.dir/mcsh/mcsh.c.o /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/aarch64-linux-gnu/libblas.so -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3 cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_symlink_library libmc.so.1.9.3 libmc.so.1.9 libmc.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 73%] Built target mc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/generic /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/pmgc /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o -MF CMakeFiles/apbs_generic.dir/nosh.c.o.d -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/nosh.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildAd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/buildAd.c [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o -MF CMakeFiles/apbs_generic.dir/mgparm.c.o.d -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/mgparm.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildBd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/buildBd.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildGd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/buildGd.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o -MF CMakeFiles/apbs_generic.dir/femparm.c.o.d -o CMakeFiles/apbs_generic.dir/femparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/femparm.c [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildPd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/buildPd.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbsamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/pbsamparm.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/pbamparm.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o -MF CMakeFiles/apbs_generic.dir/pbeparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/pbeparm.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o -MF CMakeFiles/apbs_generic.dir/bemparm.c.o.d -o CMakeFiles/apbs_generic.dir/bemparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/bemparm.c [ 78%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o -MF CMakeFiles/apbs_generic.dir/geoflowparm.c.o.d -o CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/geoflowparm.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o -MF CMakeFiles/apbs_pmgc.dir/cgd.c.o.d -o CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/cgd.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o -MF CMakeFiles/apbs_generic.dir/apolparm.c.o.d -o CMakeFiles/apbs_generic.dir/apolparm.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/apolparm.c [ 78%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o -MF CMakeFiles/apbs_pmgc.dir/gsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/gsd.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o -MF CMakeFiles/apbs_generic.dir/vacc.c.o.d -o CMakeFiles/apbs_generic.dir/vacc.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vacc.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/valist.c.o -MF CMakeFiles/apbs_generic.dir/valist.c.o.d -o CMakeFiles/apbs_generic.dir/valist.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/valist.c [ 78%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o -MF CMakeFiles/apbs_pmgc.dir/matvecd.c.o.d -o CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/matvecd.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o -MF CMakeFiles/apbs_generic.dir/vatom.c.o.d -o CMakeFiles/apbs_generic.dir/vatom.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vatom.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o -MF CMakeFiles/apbs_generic.dir/vpbe.c.o.d -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vpbe.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o -MF CMakeFiles/apbs_generic.dir/vcap.c.o.d -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vcap.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o -MF CMakeFiles/apbs_generic.dir/vclist.c.o.d -o CMakeFiles/apbs_generic.dir/vclist.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vclist.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o -MF CMakeFiles/apbs_generic.dir/vstring.c.o.d -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vstring.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o -MF CMakeFiles/apbs_generic.dir/vparam.c.o.d -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vparam.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o -MF CMakeFiles/apbs_generic.dir/vgreen.c.o.d -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vgreen.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgcsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mgcsd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mgdrvd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgsubd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mgsubd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mikpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mikpckd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mlinpckd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o -MF CMakeFiles/apbs_pmgc.dir/mypdec.c.o.d -o CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mypdec.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o -MF CMakeFiles/apbs_pmgc.dir/newtond.c.o.d -o CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/newtond.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/newdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/newdrvd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o -MF CMakeFiles/apbs_pmgc.dir/powerd.c.o.d -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/powerd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o -MF CMakeFiles/apbs_pmgc.dir/smoothd.c.o.d -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/smoothd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgfasd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /build/reproducible-path/apbs-3.4.1/src/pmgc/mgfasd.c [ 84%] Linking C shared library libapbs_generic.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.3 -o libapbs_generic.so.3 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/aarch64-linux-gnu/libblas.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_symlink_library libapbs_generic.so.3 libapbs_generic.so.3 libapbs_generic.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 84%] Built target apbs_generic make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/fem /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 84%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o -MF CMakeFiles/apbs_fem.dir/vcsm.c.o.d -o CMakeFiles/apbs_fem.dir/vcsm.c.o -c /build/reproducible-path/apbs-3.4.1/src/fem/vcsm.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o -MF CMakeFiles/apbs_fem.dir/vfetk.c.o.d -o CMakeFiles/apbs_fem.dir/vfetk.c.o -c /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o -MF CMakeFiles/apbs_fem.dir/vpee.c.o.d -o CMakeFiles/apbs_fem.dir/vpee.c.o -c /build/reproducible-path/apbs-3.4.1/src/fem/vpee.c /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Vfetk_PDE_ctor2': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1211:24: warning: assignment to 'void (*)(struct sPDE *, int, int, double *, double *, double (*)[3])' from incompatible pointer type 'void (*)(PDE *, int, int, double *, double *)' {aka 'void (*)(struct sPDE *, int, int, double *, double *)'} [-Wincompatible-pointer-types] 1211 | thee->u_T = Vfetk_PDE_u_T; | ^ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1073:28: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 1073 | sprintf(ptrfmt,"(%dI%d)",nptrline,numZdigits+1); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.h:67, from /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:57: In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1073:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1074:26: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1074:23: note: directive argument in the range [-2147483646, 2147483647] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~~~~~~ In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1074:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1075:28: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 1075 | sprintf(indfmt,"(%dI%d)",nindline,nrowdigits+1); | ^ In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1075:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1076:26: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~ /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1076:23: note: directive argument in the range [-2147483646, 2147483647] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~~~~~~ In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1076:5: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 85%] Linking C shared library libapbs_fem.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_fem.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_fem.so.3 -o libapbs_fem.so.3 CMakeFiles/apbs_fem.dir/vcsm.c.o CMakeFiles/apbs_fem.dir/vfetk.c.o CMakeFiles/apbs_fem.dir/vpee.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_symlink_library libapbs_fem.so.3 libapbs_fem.so.3 libapbs_fem.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 85%] Built target apbs_fem [ 86%] Linking C shared library libapbs_pmgc.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.3 -o libapbs_pmgc.so.3 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/aarch64-linux-gnu/libblas.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_symlink_library libapbs_pmgc.so.3 libapbs_pmgc.so.3 libapbs_pmgc.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 86%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/mg /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -MF CMakeFiles/apbs_mg.dir/vgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o -MF CMakeFiles/apbs_mg.dir/vmgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vmgrid.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o -MF CMakeFiles/apbs_mg.dir/vopot.c.o.d -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vopot.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o -MF CMakeFiles/apbs_mg.dir/vpmg.c.o.d -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vpmg.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -MF CMakeFiles/apbs_mg.dir/vpmgp.c.o.d -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /build/reproducible-path/apbs-3.4.1/src/mg/vpmgp.c /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c: In function 'Vgrid_readDXBIN': /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c:853:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c:831:7: warning: argument 1 null where non-null expected [-Wnonnull] 831 | fclose(fd); | ^~~~~~~~~~ In file included from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.h:67, from /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c:57: /usr/include/stdio.h:183:12: note: in a call to function 'fclose' declared 'nonnull' 183 | extern int fclose (FILE *__stream) __nonnull ((1)); | ^~~~~~ [ 87%] Linking C shared library libapbs_mg.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.3 -o libapbs_mg.so.3 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../pmgc/libapbs_pmgc.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_symlink_library libapbs_mg.so.3 libapbs_mg.so.3 libapbs_mg.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 87%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/CMakeFiles/apbs_routines.dir/routines.c.o -MF CMakeFiles/apbs_routines.dir/routines.c.o.d -o CMakeFiles/apbs_routines.dir/routines.c.o -c /build/reproducible-path/apbs-3.4.1/src/routines.c /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'initAPOL': /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5046 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 2 of type 'char[1024]' /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 3 of type 'char[1024]' In file included from /build/reproducible-path/apbs-3.4.1/src/generic/apolparm.h:73, from /build/reproducible-path/apbs-3.4.1/src/generic/nosh.h:73, from /build/reproducible-path/apbs-3.4.1/src/apbs.h:70, from /build/reproducible-path/apbs-3.4.1/src/routines.h:64, from /build/reproducible-path/apbs-3.4.1/src/routines.c:54: /build/reproducible-path/apbs-3.4.1/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5048 | atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 2 of type 'char[1024]' /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 3 of type 'char[1024]' /build/reproducible-path/apbs-3.4.1/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writematMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2020:30: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2020 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/reproducible-path/apbs-3.4.1/src/apbs.h:67: In function 'sprintf', inlined from 'writematMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2020:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2937:34: warning: '%s' directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2937 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2937:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2963:34: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2963 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2963:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2919:34: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2919 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2919:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2954:34: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2954 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2954:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2944:34: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2944 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2944:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2930:34: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2930 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2930:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/apbs-3.4.1/src/routines.c:2909:34: warning: '%s' directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2909 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function 'sprintf', inlined from 'writedataMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2909:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 87%] Linking CXX shared library libgamer.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgamer.so.1.9 -o libgamer.so.1.9.3 CMakeFiles/gamer.dir/base/gamer_base.c.o CMakeFiles/gamer.dir/triangle/triangle.c.o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o CMakeFiles/gamer.dir/biom/MarchingCube.C.o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o CMakeFiles/gamer.dir/biom/ReadLattice.C.o CMakeFiles/gamer.dir/biom/ReadPDB.C.o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o CMakeFiles/gamer.dir/biom/SurfExtract.C.o CMakeFiles/gamer.dir/biom/SurfRefine.C.o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -lmaloc cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_symlink_library libgamer.so.1.9.3 libgamer.so.1.9 libgamer.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 87%] Built target gamer /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/apbs-3.4.1/src/routines.c:4893:34: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4893 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataFE' at /build/reproducible-path/apbs-3.4.1/src/routines.c:4893:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/apbs-3.4.1/src/routines.c:4887:34: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4887 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataFE' at /build/reproducible-path/apbs-3.4.1/src/routines.c:4887:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/apbs-3.4.1/src/routines.c:4880:34: warning: '%s' directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4880 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function 'sprintf', inlined from 'writedataFE' at /build/reproducible-path/apbs-3.4.1/src/routines.c:4880:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 88%] Linking C shared library libapbs_routines.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.3 -o libapbs_routines.so.3 CMakeFiles/apbs_routines.dir/routines.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp mg/libapbs_mg.so.3 fem/libapbs_fem.so.3 pmgc/libapbs_pmgc.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libapbs_routines.so.3 libapbs_routines.so.3 libapbs_routines.so make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 88%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake "--color=" make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/mergedx2.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build [ 88%] Building C object src/CMakeFiles/apbs.dir/main.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs.dir/main.c.o -MF CMakeFiles/apbs.dir/main.c.o.d -o CMakeFiles/apbs.dir/main.c.o -c /build/reproducible-path/apbs-3.4.1/src/main.c make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/build [ 89%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o -MF CMakeFiles/mgmesh.dir/mgmesh.c.o.d -o CMakeFiles/mgmesh.dir/mgmesh.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/mgmesh.c [ 89%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o [ 89%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/multivalue.dir/DependInfo.cmake "--color=" [ 90%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base 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/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh 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tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o -MF CMakeFiles/multivalue.dir/multivalue.c.o.d -o CMakeFiles/multivalue.dir/multivalue.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/multivalue.c [ 91%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o [ 91%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o [ 91%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o -MF CMakeFiles/benchmark.dir/benchmark.c.o.d -o CMakeFiles/benchmark.dir/benchmark.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/benchmark.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/similarity.dir/similarity.c.o -MF CMakeFiles/similarity.dir/similarity.c.o.d -o CMakeFiles/similarity.dir/similarity.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/similarity.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/analysis.dir/analysis.c.o -MF CMakeFiles/analysis.dir/analysis.c.o.d -o CMakeFiles/analysis.dir/analysis.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/analysis.c [ 91%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o -MF CMakeFiles/dx2mol.dir/dx2mol.c.o.d -o CMakeFiles/dx2mol.dir/dx2mol.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/dx2mol.c /build/reproducible-path/apbs-3.4.1/src/main.c: In function 'main': /build/reproducible-path/apbs-3.4.1/src/main.c:319:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /build/reproducible-path/apbs-3.4.1/src/main.c:319:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ [ 91%] Linking C executable ../bin/mgmesh cd 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../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 91%] Linking C executable ../bin/value cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/value.dir/link.txt --verbose=1 [ 92%] Linking C executable ../bin/multivalue cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/multivalue.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/value.dir/value.c.o -o ../bin/value ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -MF CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o.d -o CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/dx2uhbd.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 95%] Linking C executable ../bin/similarity cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/similarity.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 95%] Linking C executable apbs make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 95%] Built target multivalue [ 95%] Linking C executable ../bin/mergedx /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/similarity.dir/similarity.c.o -o ../bin/similarity ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 [ 95%] Built target dx2mol make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 95%] Built target smooth /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/apbs.dir/main.c.o -o apbs -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp libapbs_routines.so.3 mg/libapbs_mg.so.3 pmgc/libapbs_pmgc.so.3 fem/libapbs_fem.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/del2dx.dir/DependInfo.cmake "--color=" [ 95%] Built target value make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend [ 95%] Linking C executable ../bin/mergedx2 cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 95%] Built target dxmath cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 95%] Built target benchmark cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/manip /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/manip /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake "--color=" /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx2.dir/mergedx2.c.o -o ../bin/mergedx2 ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 95%] Built target analysis make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/build [ 95%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o -MF CMakeFiles/del2dx.dir/del2dx.c.o.d -o CMakeFiles/del2dx.dir/del2dx.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python-pybind /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind/CMakeFiles/apbs_pybind.dir/DependInfo.cmake "--color=" [ 96%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build [ 96%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o -MF CMakeFiles/tensor2dx.dir/tensor2dx.c.o.d -o CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 97%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o.d -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c [ 97%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/born.dir/born.c.o -MF CMakeFiles/born.dir/born.c.o.d -o CMakeFiles/born.dir/born.c.o -c /build/reproducible-path/apbs-3.4.1/tools/manip/born.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o -MF CMakeFiles/coulomb.dir/coulomb.c.o.d -o CMakeFiles/coulomb.dir/coulomb.c.o -c /build/reproducible-path/apbs-3.4.1/tools/manip/coulomb.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 97%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o [ 98%] Linking C executable ../bin/dx2uhbd cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cc -D_apbslib_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/python3.11 -I/build/reproducible-path/apbs-3.4.1/tools/python -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -MF CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o.d -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2uhbd.dir/link.txt --verbose=1 [ 98%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o -MF CMakeFiles/apbs_pybind.dir/module.cpp.o.d -o CMakeFiles/apbs_pybind.dir/module.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/module.cpp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 98%] Built target apbs /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c: In function 'main': /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:76:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:89:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:97:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:103:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c:106:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_nosh.cpp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c: In function 'main': /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c: In function 'main': /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Built target similarity [ 98%] Built target mergedx2 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_vatom.cpp [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o [ 99%] Built target mergedx cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_valist.cpp [100%] Linking C executable ../bin/del2dx cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 [100%] Linking C executable ../bin/tensor2dx cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 [100%] Linking C executable ../bin/uhbd_asc2bin cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/del2dx.dir/del2dx.c.o -o ../bin/del2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [100%] Linking C executable ../bin/coulomb cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/coulomb.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -o ../bin/uhbd_asc2bin ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/coulomb.dir/coulomb.c.o -o ../bin/coulomb ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [100%] Linking C executable ../bin/born cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/born.dir/born.c.o -o ../bin/born ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [100%] Built target dx2uhbd make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target del2dx make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target tensor2dx make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target uhbd_asc2bin [100%] Built target born make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target coulomb [100%] Linking C shared library _apbslib.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,_apbslib.so -o _apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target _apbslib [100%] Linking CXX shared module apbs.cpython-311-aarch64-linux-gnu.so cd /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pybind.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o apbs.cpython-311-aarch64-linux-gnu.so CMakeFiles/apbs_pybind.dir/module.cpp.o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' [100%] Built target apbs_pybind make[2]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' PYTHONPATH=/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/tools/python sphinx-build -b html docs /build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu/docs/_build/html # HTML generator Running Sphinx v7.2.6 WARNING: html_static_path entry '_static' does not exist [autosummary] generating autosummary for: api/index.rst, background.rst, formats/apbs-xml-parm.rst, formats/flat-parm.rst, formats/harwell.rst, formats/index.rst, formats/mcsf.rst, formats/opendx.rst, formats/pdb.rst, formats/pqr.rst, ..., using/input/old/generic/sdens.rst, using/input/old/generic/srad.rst, using/input/old/generic/swin.rst, using/input/old/generic/temp.rst, using/input/old/index.rst, using/input/old/print.rst, using/input/old/read.rst, using/tests.rst, using/tools.rst, using/units.rst WARNING: Failed to import apbs.input_file.calculate.finite_element. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.boundary_element. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.generic. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.nonpolar.Nonpolar. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.read. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.process. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.finite_difference. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' loading intersphinx inventory from https://docs.python.org/3/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 127 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 1%] api/index reading sources... [ 2%] background reading sources... [ 2%] formats/apbs-xml-parm reading sources... [ 3%] formats/flat-parm reading sources... [ 4%] formats/harwell reading sources... [ 5%] formats/index reading sources... [ 6%] formats/mcsf reading sources... [ 6%] formats/opendx reading sources... [ 7%] formats/pdb reading sources... [ 8%] formats/pqr reading sources... [ 9%] formats/uhbd reading sources... [ 9%] formats/xml-struct reading sources... [ 10%] getting/index reading sources... [ 11%] getting/source reading sources... [ 12%] help reading sources... [ 13%] index reading sources... [ 13%] reading reading sources... [ 14%] releases reading sources... [ 15%] supporting reading sources... [ 16%] todo reading sources... [ 17%] using/examples/binding-energies reading sources... [ 17%] using/examples/salt-linkage reading sources... [ 18%] using/examples/solvation-energies reading sources... [ 19%] using/examples/visualization-pymol reading sources... [ 20%] using/examples/visualization-unitymol reading sources... [ 20%] using/index reading sources... [ 21%] using/input/new/calculate/boundary_element reading sources... [ 22%] using/input/new/calculate/finite_difference reading sources... [ 23%] using/input/new/calculate/finite_element reading sources... [ 24%] using/input/new/calculate/index reading sources... 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WARNING: autodoc: failed to import module 'input_file.calculate.boundary_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_difference' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.generic' from module 'apbs'; the following exception was raised: No module named 'pyparsing' /build/reproducible-path/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document or section may not begin with a transition. /build/reproducible-path/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document may not end with a transition. WARNING: autodoc: failed to import module 'input_file.calculate.nonpolar.Nonpolar' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.process' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.read' from module 'apbs'; the following exception was raised: No module named 'pyparsing' looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/apbs-3.4.1/docs/using/input/old/elec/pygbe.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [ 1%] api/index writing output... 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[ 80%] media/1fas_VR.png copying images... [ 90%] media/UI.png copying images... [100%] media/AChE.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 28 warnings. The HTML pages are in obj-aarch64-linux-gnu/docs/_build/html. make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=cmake dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_installdirs -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/apbs-3.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/apbs-3.4.1 -B/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RELWITHDEBINFO" -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindUMFPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuperLU.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuiteSparse.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindLAPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindARPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindAMD.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/punc.h -- Installing: 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/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/vpmg.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/vf2c.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libvf2c.so -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libcgcode.so -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/gamer/gamer.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/gamer/gamer_base.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/gamer/triangle.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/gamer/tetgen.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/gamer/biom.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgamer.so.1.9.3 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgamer.so.1.9 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgamer.so -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/mc/mc_base.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/mc/mc.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/mc/bam.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/mc/bmat.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/mc/bvec.h -- Installing: 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/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/weiner86-param.dat -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber2uhbd.sh -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/amber2charmm.sh -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/WHATIF2AMBER.sed -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/README.md -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/CMakeLists.txt -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/born -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/coulomb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/tensor2dx -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/similarity -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/value -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mgmesh make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-aarch64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' (cd tests; PATH=/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/aarch64-linux-gnu:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/build/reproducible-path/apbs-3.4.1/tools/manip python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__) TESTING WITH BINARY_NAME:apbs START_DIR:/build/reproducible-path/apbs-3.4.1/build -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.024231 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in CHECKING:/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs NOTE: Using apbs binary:/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs Testing all sections The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv ================================================================================ Running tests for born section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential-PE0.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) *** PASSED *** Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) *** PASSED *** Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) *** PASSED *** Elapsed time: 14.986623 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] COMPUTED RESULT 960.7073836227 COMPUTED RESULT 2200.266567971 COMPUTED RESULT 4732.245131587 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.7735526282 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) *** PASSED *** Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) *** PASSED *** Elapsed time: 12.745306 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 2201.243880085 COMPUTED RESULT 4733.006258977 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.0124252387 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE0.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.401768459022e+02 8.142935592471e+02 1.485255308186e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.761864094552e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE0.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE1.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.401768459022e+02 8.142778312125e+02 1.485246667424e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.762728170718e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE1.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE2.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605695E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.401768459091e+02 8.142935605695e+02 1.485255306569e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.761864257239e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE2.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE3.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344953E+01 kJ/mol Global net ELEC energy = -5.762728344953E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.401768459091e+02 8.142778325440e+02 1.485246665692e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.762728344953e+01 Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) *** PASSED *** Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) *** PASSED *** Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) *** PASSED *** Elapsed time: 66.389139 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-mol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] COMPUTED RESULT 960.7073836226 COMPUTED RESULT 3257.1427835730997 COMPUTED RESULT 5941.0039478710005 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867462003 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE0.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.383232191816e+02 8.145369591602e+02 1.485524998001e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734895113069e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE0.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE1.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.383232191816e+02 8.145419898332e+02 1.485529328612e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734462051928e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE1.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE2.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.383232191909e+02 8.145369593489e+02 1.485524997676e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734895146550e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE2.out BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE3.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.383232191909e+02 8.145419900310e+02 1.485529328301e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734462084052e+01 Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) *** PASSED *** Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) *** PASSED *** Elapsed time: 60.294653 seconds -------------------------------------------------------------------------------- Total elapsed time: 154.439952 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in Checking for intermediate energies in input file apbs-smol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 3258.1578983732998 COMPUTED RESULT 5942.108652589999 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -229.38714395599 Running tests for actin-dimer-auto section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058621E+02 kJ/mol Global net ELEC energy = 1.048683058621E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) *** PASSED *** Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) *** PASSED *** Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) *** PASSED *** Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) *** PASSED *** Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) *** PASSED *** Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) *** PASSED *** Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02) *** PASSED *** Elapsed time: 201.987765 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058621] EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] COMPUTED RESULT 152761.7850342 COMPUTED RESULT 291951.0754196 COMPUTED RESULT 152767.184488 COMPUTED RESULT 291546.8859278 COMPUTED RESULT 305631.7807611 COMPUTED RESULT 583602.8296532 COMPUTED RESULT 104.8683058621 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077688E+02 kJ/mol Global net ELEC energy = 1.095841077688E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) *** PASSED *** Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) *** PASSED *** Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) *** PASSED *** Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) *** PASSED *** Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) *** PASSED *** Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) *** PASSED *** Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 131.844864 seconds -------------------------------------------------------------------------------- Total elapsed time: 333.832629 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file alkanes.in Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077688] EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] COMPUTED RESULT 152863.2421825 COMPUTED RESULT 292061.866232 COMPUTED RESULT 152929.7900572 COMPUTED RESULT 291659.2202835 COMPUTED RESULT 305924.4262535 COMPUTED RESULT 583830.6706232 COMPUTED RESULT 109.5841077688 Running tests for alkanes section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: alkanes.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'alkanes.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) *** PASSED *** Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) *** PASSED *** Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) *** PASSED *** Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) *** PASSED *** Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) *** PASSED *** Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) *** PASSED *** Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) *** PASSED *** Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) *** PASSED *** Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) *** PASSED *** Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) *** PASSED *** Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) *** PASSED *** Elapsed time: 11.166323 seconds -------------------------------------------------------------------------------- Total elapsed time: 11.166323 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in Checking for intermediate energies in input file alkanes.out EXPECTED COMPUTED: 11 EXPECTED EXPECTED: 11 COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] EXPECTED: ['1.439739455792E+01', '1.208346456826E+01', '1.354016672221E+01', '9.363673200142E+00', '9.422717598546E+00', '1.640068943201E+01', '1.323144287435E+01', '7.894367190329E+00', '1.449633815052E+01', '1.447900211546E+01', '1.192358496286E+01'] COMPUTED RESULT 14.39739455792 COMPUTED RESULT 12.08346456826 COMPUTED RESULT 13.54016672221 COMPUTED RESULT 9.363673200142 COMPUTED RESULT 9.422717598546 COMPUTED RESULT 16.40068943201 COMPUTED RESULT 13.23144287435 COMPUTED RESULT 7.894367190329 COMPUTED RESULT 14.49633815052 COMPUTED RESULT 14.47900211546 COMPUTED RESULT 11.92358496286 Running tests for FKBP section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7h-dmso-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086373E+01 kJ/mol Global net ELEC energy = 1.500810086373E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) *** PASSED *** Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) *** PASSED *** Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) *** PASSED *** Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 40.905937 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in Checking for intermediate energies in input file 1d7h-dmso-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086373] EXPECTED: ['1.060899690259E+04', '4.276523673491E+04', '1.399234956777E+04', '4.610066575192E+04', '3.961107503213E+01', '7.121048606059E+02', '6.751571424823E+01', '7.339101343121E+02', '1.058410584089E+04', '4.205385249581E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.500810086371E+01'] COMPUTED RESULT 10608.99690259 COMPUTED RESULT 42765.23673491 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 39.61107503213 COMPUTED RESULT 712.1048606059 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10584.10584089 COMPUTED RESULT 42053.85249581 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3335.429017008 COMPUTED RESULT -21.80527370616 COMPUTED RESULT -3328.631844166 COMPUTED RESULT 15.00810086373 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7h-dmso-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192074E+01 kJ/mol Global net ELEC energy = 1.624454192074E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) *** PASSED *** Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) *** PASSED *** Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) *** PASSED *** Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 29.879338 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in Checking for intermediate energies in input file 1d7h-dmso-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192074] EXPECTED: ['1.074948704824E+04', '4.289487256481E+04', '1.399234956777E+04', '4.610066575192E+04', '3.719709905887E+01', '7.125747080979E+02', '6.751571424823E+01', '7.339101343121E+02', '1.071654753674E+04', '4.218178203716E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.624454192072E+01'] COMPUTED RESULT 10749.48704824 COMPUTED RESULT 42894.87256481 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 37.19709905887 COMPUTED RESULT 712.5747080979 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10716.54753674 COMPUTED RESULT 42181.78203716 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3205.793187109 COMPUTED RESULT -21.33542621421 COMPUTED RESULT -3200.702302816 COMPUTED RESULT 16.24454192074 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7i-dss-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933664E+01 kJ/mol Global net ELEC energy = 1.442499933664E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) *** PASSED *** Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) *** PASSED *** Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) *** PASSED *** Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 38.943921 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in Checking for intermediate energies in input file 1d7i-dss-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933664] EXPECTED: ['9.160578033846E+03', '3.955701871716E+04', '1.264965939588E+04', '4.301801664829E+04', '9.431133325426E+01', '1.677348113184E+03', '1.171079106781E+02', '1.697869784185E+03', '9.040108332204E+03', '3.787747796627E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.442500529301E+01'] COMPUTED RESULT 9160.578033846 COMPUTED RESULT 39557.01871716 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 94.31133325426 COMPUTED RESULT 1677.348113184 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9040.108332204 COMPUTED RESULT 37877.47796627 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -3460.997931137 COMPUTED RESULT -20.52167100108 COMPUTED RESULT -3454.901259473 COMPUTED RESULT 14.42499933664 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7i-dss-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742843E+01 kJ/mol Global net ELEC energy = 1.545150742843E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) *** PASSED *** Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) *** PASSED *** Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) *** PASSED *** Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 25.754602 seconds -------------------------------------------------------------------------------- Total elapsed time: 135.483798 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file 1d7i-dss-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742843] EXPECTED: ['9.634884642408E+03', '4.003177540425E+04', '1.264965939588E+04', '4.301801664829E+04', '7.942232645345E+01', '1.677798535473E+03', '1.171079106781E+02', '1.697869784185E+03', '9.507068451372E+03', '3.835075772299E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.545150009785E+01'] COMPUTED RESULT 9634.884642408 COMPUTED RESULT 40031.77540425 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 79.42232645345 COMPUTED RESULT 1677.798535473 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9507.068451372 COMPUTED RESULT 38350.75772299 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -2986.24124404 COMPUTED RESULT -20.07124871262 COMPUTED RESULT -2981.621502756 COMPUTED RESULT 15.45150742843 Running tests for hca-bind section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812684E+01 kJ/mol Global net ELEC energy = -5.246475812684E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) *** PASSED *** Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) *** PASSED *** Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) *** PASSED *** Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) *** PASSED *** Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) *** PASSED *** Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) *** PASSED *** Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) *** PASSED *** Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) *** PASSED *** Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) *** PASSED *** Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 36.300594 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812684] EXPECTED: ['2.213600726771E+02', '1.825764811255E+03', '6.458471211905E+03', '2.093606095527E+04', '1.515433544464E+05', '1.786369323561E+05', '2.105322784838E+04', '1.533304996252E+05', '1.850429388099E+05', '-5.246475812665E+01'] COMPUTED RESULT 221.3600726771 COMPUTED RESULT 1825.764811255 COMPUTED RESULT 6458.471211905 COMPUTED RESULT 20936.06095527 COMPUTED RESULT 151543.3544464 COMPUTED RESULT 178636.9323561 COMPUTED RESULT 21053.22784838 COMPUTED RESULT 153330.4996252 COMPUTED RESULT 185042.9388099 COMPUTED RESULT -52.46475812684 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017059E+01 kJ/mol Global net ELEC energy = -5.405979017059E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) *** PASSED *** Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) *** PASSED *** Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) *** PASSED *** Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) *** PASSED *** Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) *** PASSED *** Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) *** PASSED *** Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) *** PASSED *** Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) *** PASSED *** Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) *** PASSED *** Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 23.650809 seconds -------------------------------------------------------------------------------- Total elapsed time: 59.951403 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017059] EXPECTED: ['1.884888131017E+02', '1.820045922544E+03', '6.460002606908E+03', '2.189161497021E+04', '1.520000494925E+05', '1.790436191580E+05', '2.195842512312E+04', '1.537771604355E+05', '1.854495619747E+05', '-5.405977880082E+01'] COMPUTED RESULT 188.4888131017 COMPUTED RESULT 1820.045922544 COMPUTED RESULT 6460.002606908 COMPUTED RESULT 21891.61497021 COMPUTED RESULT 152000.0494925 COMPUTED RESULT 179043.619158 COMPUTED RESULT 21958.42512312 COMPUTED RESULT 153777.1604355 COMPUTED RESULT 185449.5619747 COMPUTED RESULT -54.05979017059 Running tests for ionize section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) *** PASSED *** Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) *** PASSED *** Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) *** PASSED *** Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) *** PASSED *** Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) *** PASSED *** Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) *** PASSED *** Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) *** PASSED *** Elapsed time: 28.005164 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5823.898055191, 9793.274462353, 5846.917564309, 9815.953282539, 8219.846763777, 13927.41988698, 8420.373979905, 14127.16615065, 3862.359524598, 6288.15625161, 4162.533113906, 6585.616091973, -22.67882018629, -199.7462636633, -297.4598403628, -474.5272838398] EXPECTED: ['5.823898055191E+03', '9.793274462353E+03', '5.846917564309E+03', '9.815953282539E+03', '8.219846763777E+03', '1.392741988698E+04', '8.420373979905E+03', '1.412716615065E+04', '3.862359524598E+03', '6.288156251610E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.267881997628E+01', '-1.997462580204E+02', '-2.974598331751E+02', '-4.745272868358E+02'] COMPUTED RESULT 5823.898055191 COMPUTED RESULT 9793.274462353 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8219.846763777 COMPUTED RESULT 13927.41988698 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3862.359524598 COMPUTED RESULT 6288.15625161 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.67882018629 COMPUTED RESULT -199.7462636633 COMPUTED RESULT -297.4598403628 COMPUTED RESULT -474.5272838398 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) *** PASSED *** Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) *** PASSED *** Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) *** PASSED *** Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) *** PASSED *** Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) *** PASSED *** Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) *** PASSED *** Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) *** PASSED *** Elapsed time: 23.534164 seconds -------------------------------------------------------------------------------- Total elapsed time: 51.539328 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file ion-pmf.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5824.172730822, 9793.622759239, 5846.917564309, 9815.953282539, 8221.328580569, 13928.67783119, 8420.373979905, 14127.16615065, 3863.066835285, 6289.649216644, 4162.533113906, 6585.616091973, -22.33052329981, -198.4883194538, -295.9668753288, -472.1246714828] EXPECTED: ['5.824172730822E+03', '9.793622759239E+03', '5.846917564309E+03', '9.815953282539E+03', '8.221328580569E+03', '1.392867783119E+04', '8.420373979905E+03', '1.412716615065E+04', '3.863066835285E+03', '6.289649216644E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.233050451129E+01', '-1.984883191396E+02', '-2.959668653531E+02', '-4.721247084138E+02'] COMPUTED RESULT 5824.172730822 COMPUTED RESULT 9793.622759239 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8221.328580569 COMPUTED RESULT 13928.67783119 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3863.066835285 COMPUTED RESULT 6289.649216644 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.33052329981 COMPUTED RESULT -198.4883194538 COMPUTED RESULT -295.9668753288 COMPUTED RESULT -472.1246714828 Running tests for ion-pmf section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: ion-pmf.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'ion-pmf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.128e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.766e-05 tot 1 -2.723e-02 9.131e-07 9.134e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.768e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718345777E+00 WCA energy for atom 1: -6.909411348230E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365306965532E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365306965532E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) *** PASSED *** Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) *** PASSED *** Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) *** PASSED *** Elapsed time: 10.146894 seconds -------------------------------------------------------------------------------- Total elapsed time: 10.146894 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in Checking for intermediate energies in input file ion-pmf.out EXPECTED COMPUTED: 4 EXPECTED EXPECTED: 4 COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65306965532 Running tests for pka-lig section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-vdw.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648803E+00 kJ/mol Global net ELEC energy = 8.083515648803E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) *** PASSED *** Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) *** PASSED *** Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) *** PASSED *** Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) *** PASSED *** Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) *** PASSED *** Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) *** PASSED *** Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 36.402867 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in Checking for intermediate energies in input file apbs-mol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.083515648803] EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] COMPUTED RESULT 2224.988750664 COMPUTED RESULT 10496.95084686 COMPUTED RESULT 181845.0789522 COMPUTED RESULT 300825.4338259 COMPUTED RESULT 184091.8409896 COMPUTED RESULT 311330.4681884 COMPUTED RESULT 8.083515648803 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255720E+01 kJ/mol Global net ELEC energy = 2.096300255720E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) *** PASSED *** Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) *** PASSED *** Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) *** PASSED *** Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) *** PASSED *** Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) *** PASSED *** Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) *** PASSED *** Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 22.105418 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in Checking for intermediate energies in input file apbs-smol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.9630025572] EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] COMPUTED RESULT 2226.793167046 COMPUTED RESULT 10505.04485887 COMPUTED RESULT 182797.6621645 COMPUTED RESULT 301722.8546773 COMPUTED RESULT 185081.9075387 COMPUTED RESULT 312248.8625388 COMPUTED RESULT 20.9630025572 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-surf.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686582E+02 kJ/mol Global net ELEC energy = 1.192607686582E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) *** PASSED *** Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) *** PASSED *** Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) *** PASSED *** Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) *** PASSED *** Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) *** PASSED *** Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) *** PASSED *** Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 27.138642 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in Checking for intermediate energies in input file apbs-mol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686582] EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] COMPUTED RESULT 2244.350164274 COMPUTED RESULT 10521.49475373 COMPUTED RESULT 186261.5690066 COMPUTED RESULT 305181.0884053 COMPUTED RESULT 188662.5455219 COMPUTED RESULT 315821.8439277 COMPUTED RESULT 119.2607686582 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-surf.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) *** PASSED *** Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) *** PASSED *** Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) *** PASSED *** Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) *** PASSED *** Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) *** PASSED *** Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) *** PASSED *** Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) *** PASSED *** Elapsed time: 22.663617 seconds -------------------------------------------------------------------------------- Total elapsed time: 108.310544 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_1.in Checking for intermediate energies in input file apbs-smol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] COMPUTED RESULT 2251.46678942 COMPUTED RESULT 10528.14502873 COMPUTED RESULT 186407.1689626 COMPUTED RESULT 305331.9953673 COMPUTED RESULT 188802.7142979 COMPUTED RESULT 315969.0177241 COMPUTED RESULT 108.8773280806 Running tests for point-pmf section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_1.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) *** PASSED *** Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) *** PASSED *** Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) *** PASSED *** Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) *** PASSED *** Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) *** PASSED *** Elapsed time: 5.468862 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in Checking for intermediate energies in input file complex-0_1.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 89.75920687031, 205.8277719334, 0.0, 0.0, 0.0, 97.7604, 89.7592, 205.828, 96.5336, 88.6151, 201.106, 18.30820799027] EXPECTED: ['9.776035707281E+01', '8.975920687031E+01', '2.058277719334E+02', '*', '*', '*', '97.7604', '89.7592', '205.828', '96.5336', '88.6151', '201.106', '1.830820799027E+01'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 89.75920687031 COMPUTED RESULT 205.8277719334 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 89.7592 COMPUTED RESULT 205.828 COMPUTED RESULT 96.5336 COMPUTED RESULT 88.6151 COMPUTED RESULT 201.106 COMPUTED RESULT 18.30820799027 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_2.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086751E+00 kJ/mol Global net ELEC energy = 8.906694086751E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) *** PASSED *** Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) *** PASSED *** Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00) *** PASSED *** Elapsed time: 5.559118 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in Checking for intermediate energies in input file complex-0_2.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.906694086751] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.084282010393E+02', '*', '*', '*', '97.7604', '101.761', '208.428', '96.5336', '100.656', '203.83', '8.906694086750E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 208.4282010393 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 208.428 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.656 COMPUTED RESULT 203.83 COMPUTED RESULT 8.906694086751 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_3.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) *** PASSED *** Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) *** PASSED *** Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) *** PASSED *** Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) *** PASSED *** Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) *** PASSED *** Elapsed time: 5.616526 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in Checking for intermediate energies in input file complex-0_3.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 133.7661883222, 237.436145212, 0.0, 0.0, 0.0, 97.7604, 133.766, 237.436, 96.5336, 132.672, 232.924, 5.909599816984] EXPECTED: ['9.776035707281E+01', '1.337661883222E+02', '2.374361452120E+02', '*', '*', '*', '97.7604', '133.766', '237.436', '96.5336', '132.672', '232.924', '5.909599816984E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 133.7661883222 COMPUTED RESULT 237.436145212 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 133.766 COMPUTED RESULT 237.436 COMPUTED RESULT 96.5336 COMPUTED RESULT 132.672 COMPUTED RESULT 232.924 COMPUTED RESULT 5.909599816984 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_4.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_4.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) *** PASSED *** Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) *** PASSED *** Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) *** PASSED *** Elapsed time: 5.763066 seconds -------------------------------------------------------------------------------- Total elapsed time: 22.407572 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file complex-0_4.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 203.9516519, 0.0, 0.0, 0.0, 97.7604, 101.761, 203.952, 96.5336, 100.654, 199.493, 4.430144947418] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.039516519000E+02', '*', '*', '*', '97.7604', '101.761', '203.952', '96.5336', '100.654', '199.493', '4.430144947418E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 203.9516519 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 203.952 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.654 COMPUTED RESULT 199.493 COMPUTED RESULT 4.430144947418 Running tests for solv section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488075E+01 kJ/mol Global net ELEC energy = -3.624863488075E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) *** PASSED *** Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) *** PASSED *** Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) *** PASSED *** Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) *** PASSED *** Testing computed result against expected result (-3.624863488075e+01, -3.624863445503e+01) *** PASSED *** Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) *** PASSED *** Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) *** PASSED *** Elapsed time: 7.677696 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488075, -390.4121708125, -354.1635359318] EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] COMPUTED RESULT 1847.663548071 COMPUTED RESULT 1883.912182952 COMPUTED RESULT 2732.623683321 COMPUTED RESULT 3123.035854133 COMPUTED RESULT -36.24863488075 COMPUTED RESULT -390.4121708125 COMPUTED RESULT -354.1635359318 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Feb 28 2024 at 01:04:53 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772492E+01 kJ/mol Global net ELEC energy = -3.757593772492E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) *** PASSED *** Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) *** PASSED *** Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) *** PASSED *** Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) *** PASSED *** Testing computed result against expected result (-3.757593772492e+01, -3.757593797629e+01) *** PASSED *** Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) *** PASSED *** Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) *** PASSED *** Elapsed time: 7.618297 seconds -------------------------------------------------------------------------------- Total elapsed time: 15.295993 seconds Test results have been logged -------------------------------------------------------------------------------- Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772492, -391.2388603848, -353.6629226599] EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] COMPUTED RESULT 1847.86044002 COMPUTED RESULT 1885.436377745 COMPUTED RESULT 2734.040568569 COMPUTED RESULT 3125.279428954 COMPUTED RESULT -37.57593772492 COMPUTED RESULT -391.2388603848 COMPUTED RESULT -353.6629226599 make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_sphinxdoc -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_python3 -O--buildsystem=cmake I: dh_python3 fs:418: renaming _apbslib.so to _apbslib.cpython-311-aarch64-linux-gnu.so dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' dh_fixperms for example in FKBP/1d7h-dmso/UHBD/pqr2qcd \ ion-pmf/runme.sh \ point-pmf/runme.sh \ protein-rna/postprocess.sh \ protein-rna/test.sh \ helix/Run_membrane-helix.sh \ protein-rna/run_apdx_files.sh; \ do \ chmod +x debian/apbs-data/usr/share/apbs/examples/${example}; \ done for script in amber2charmm.sh \ param/pdb2pqr/amber2uhbd.sh \ qcd2pqr.awk; \ do \ chmod a+x debian/apbs-data/usr/share/apbs/tools/conversion/${script}; \ done for example in bem-pKa/test_proteins \ pbsam-barn_bars; \ do \ chmod a-x debian/apbs-data/usr/share/apbs/examples/${example}/*.pqr; \ done make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' dh_fixperms -O--buildsystem=cmake -Napbs-data -Napbs-doc dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3: DWARF compression not beneficial - old size 90449 new size 92959 dwz: debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libmc.so.1.9.3: DWARF compression not beneficial - old size 454851 new size 461553 dwz: debian/libapbs3t64/usr/lib/aarch64-linux-gnu/libapbs_pmgc.so.3: DWARF compression not beneficial - old size 156081 new size 156709 dwz: debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libgamer.so.1.9.3: DWARF compression not beneficial - old size 918211 new size 921070 dwz: debian/python3-apbslib/usr/lib/python3/dist-packages/apbs.cpython-311-aarch64-linux-gnu.so: DWARF compression not beneficial - old size 6193169 new size 6205875 dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol e_wsfe used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol ddot_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sdot_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol saxpy_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sqrt used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol daxpy_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol s_stop used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol scopy_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol snrm2_ used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol sinh used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol erf used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sincos used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sin used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol tanh used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol tan used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol acos used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow used by debian/libfetk1.9t64/usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libcholmod.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libcamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libstdc++.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libcgcode.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libspqr.so.4 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libccolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libcolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libsuperlu.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libumfpack.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libapbs_pmgc.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libsuitesparseconfig.so.7 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libarpack.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libpunc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libgomp.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libvf2c.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libmc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libapbs_fem.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libmpi.so.40 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis were not linked against libblas.so.3 (they use none of the library's symbols) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package libapbs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libfetk-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: package apbs-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'apbs-doc' in '../apbs-doc_3.4.1-5.1_all.deb'. dpkg-deb: building package 'apbs' in '../apbs_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libapbs3t64' in '../libapbs3t64_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'apbs-data' in '../apbs-data_3.4.1-5.1_all.deb'. dpkg-deb: building package 'libfetk-dev' in '../libfetk-dev_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'apbs-dbgsym' in '../apbs-dbgsym_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libapbs3t64-dbgsym' in '../libapbs3t64-dbgsym_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'python3-apbslib-dbgsym' in '../python3-apbslib-dbgsym_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libfetk1.9t64-dbgsym' in '../libfetk1.9t64-dbgsym_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'libfetk1.9t64' in '../libfetk1.9t64_3.4.1-5.1_arm64.deb'. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-5.1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../apbs_3.4.1-5.1_arm64.buildinfo dpkg-genchanges --build=binary -O../apbs_3.4.1-5.1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2355443 and its subdirectories I: Current time: Thu Jun 19 16:25:05 -12 2025 I: pbuilder-time-stamp: 1750393505 Fri May 17 22:02:09 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_15-43435.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/apbs_3.4.1-5.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/apbs_3.4.1-5.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/apbs_3.4.1-5.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/b1/apbs_3.4.1-5.1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bLtafaTe/b2/apbs_3.4.1-5.1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.528s) 0.528s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.171s) 0.171s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 881ms CPU time consumed: 881ms Fri May 17 22:02:10 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Fri May 17 22:02:10 UTC 2024 I: apbs from unstable built successfully and reproducibly on arm64. Fri May 17 22:02:11 UTC 2024 I: Submitting .buildinfo files to external archives: Fri May 17 22:02:11 UTC 2024 I: Submitting 16K b1/apbs_3.4.1-5.1_arm64.buildinfo.asc Fri May 17 22:02:12 UTC 2024 I: Submitting 16K b2/apbs_3.4.1-5.1_arm64.buildinfo.asc Fri May 17 22:02:13 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 17 22:02:13 UTC 2024 I: Done submitting .buildinfo files. Fri May 17 22:02:13 UTC 2024 I: Removing signed apbs_3.4.1-5.1_arm64.buildinfo.asc files: removed './b1/apbs_3.4.1-5.1_arm64.buildinfo.asc' removed './b2/apbs_3.4.1-5.1_arm64.buildinfo.asc'