Mon Jan 10 06:09:27 UTC 2022 I: starting to build relion/bullseye/amd64 on jenkins on '2022-01-10 06:09' Mon Jan 10 06:09:27 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_7/90542/console.log Mon Jan 10 06:09:27 UTC 2022 I: Downloading source for bullseye/relion=3.1.0-4 --2022-01-10 06:09:27-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/relion/relion_3.1.0-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2154 (2.1K) Saving to: ‘relion_3.1.0-4.dsc’ 0K .. 100% 352K=0.006s 2022-01-10 06:09:27 (352 KB/s) - ‘relion_3.1.0-4.dsc’ saved [2154/2154] Mon Jan 10 06:09:27 UTC 2022 I: relion_3.1.0-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: relion Binary: relion, relion-gui Architecture: amd64 i386 Version: 3.1.0-4 Maintainer: Debian Med Packaging Team Uploaders: Roland Fehrenbacher , Andreas Tille , Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/relion Vcs-Git: https://salsa.debian.org/med-team/relion.git Testsuite: autopkgtest Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid Package-List: relion deb science optional arch=amd64,i386 relion-gui deb science optional arch=amd64,i386 Checksums-Sha1: bfc04f255192eb229a41ec565fbaf9ee2193591f 1311280 relion_3.1.0.orig.tar.xz d20d573f50b68d6159a415b06b8511d1a51a2bd6 7004 relion_3.1.0-4.debian.tar.xz Checksums-Sha256: 3958ae5a27a81292f22cf27dc9a4506ea78c29e7580cc088d62f6e6288b4df55 1311280 relion_3.1.0.orig.tar.xz ef35f540b372355d1de7efaf7e533b52e9da242dd9b7e44b21af76f447047802 7004 relion_3.1.0-4.debian.tar.xz Files: e475dbf32c3cd8511be7531f64e90c81 1311280 relion_3.1.0.orig.tar.xz e4318d9322492d0d647e0a6ac4f03ede 7004 relion_3.1.0-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl990nwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEumQ/+P8eLp7M3eVvbeJ9AKdwlcerpatFSaDBG lWnJETZ9siFXMpUDgvEEsJLxjK0DO15m0/c6Knr+j5vm/heWSHsODWxO1a11EX0b Hslz+NdY9l24AaXBdvxkTksylkKpcx2+0OMEDoOExN7Yr0qIjZJokqpn1btWXm4L uAak0M2e+W+wtLi2EzG6LNeF4ObjyJLozV4VsXjbcFtBJ6Mt8YXTQpSGWLCB3J/R KLt3YzQZSQ8Lwl0RIIQlA/bJPuanjYnAnf2gf16yVdEPGe9kUT6mE3wjHI5lxy4l pJWElINMqmBx9wUSCR+U0K/Pf4zpedywdQ76YEQV+AlswzQLWsBfatoWpbJAcB48 4fJW0lDu8Oq5TNOasIUJMs95C4MHGczRYze20Vo2/rN2eV3X5sEHEn6dj6mDckc2 aMJ7rZGFzpGWHdebNa8UNEPk7oAyhmVgkC1EH1qYsGZULbjxk2cLF8ClNhBt/aEk 3pi0hkboLwOph1aNzWn9ebPLMhAEbrcLXiMJke5rbLOgxDmKieVo5gGnOWrbiYuN bHfDS269P4x11n+iKE1AFoeoyRgAwbchyiUrvC/4zbcZR5LIGzWzowIq0WuVwVeM pPUqO5Vj37hbnhzK3SAsKZGKJB3bLHANgD3TbgsxcYIC5lT4Ras+5MVFpEYQ5b8m bIN0s3p4x20= =LZQI -----END PGP SIGNATURE----- Mon Jan 10 06:09:27 UTC 2022 I: Checking whether the package is not for us Mon Jan 10 06:09:27 UTC 2022 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon Jan 10 06:09:27 UTC 2022 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon Jan 10 06:25:36 UTC 2022 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 9 18:09:30 -12 2022 I: pbuilder-time-stamp: 1641794970 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [relion_3.1.0-4.dsc] I: copying [./relion_3.1.0.orig.tar.xz] I: copying [./relion_3.1.0-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.sSaJZeh_/trustedkeys.kbx': General error gpgv: Signature made Wed Oct 7 02:36:44 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./relion_3.1.0-4.dsc dpkg-source: info: extracting relion in relion-3.1.0 dpkg-source: info: unpacking relion_3.1.0.orig.tar.xz dpkg-source: info: unpacking relion_3.1.0-4.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3838652/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='fb33d43e9cd343d5a92a2261ee646bf2' 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='3838652' 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/tmp.QATpWdJhoQ/pbuilderrc_68DQ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.QATpWdJhoQ/b1 --logfile b1/build.log relion_3.1.0-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/3838652/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: amd64 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: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 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 libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libfltk1.3-dev; however: Package libfltk1.3-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libtiff-dev; however: Package libtiff-dev is not installed. pbuilder-satisfydepends-dummy depends on fluid; however: Package fluid 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fluid{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gfortran-10{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0{a} libcurl4{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfltk-cairo1.3{a} libfltk-forms1.3{a} libfltk-gl1.3{a} libfltk-images1.3{a} libfltk1.3{a} libfltk1.3-dev{a} libfontconfig1{a} libfreetype6{a} libgfortran-10-dev{a} libgfortran5{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu67{a} libjbig-dev{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp24{a} libldap-2.4-2{a} libllvm11{a} libltdl-dev{a} libltdl7{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libncurses6{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} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpmix-dev{a} libpmix2{a} libpng16-16{a} libprocps8{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} libpthread-stubs0-dev{a} librdmacm1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtiff-dev{a} libtiff5{a} libtiffxx5{a} libtool{a} libuchardet0{a} libucx0{a} libuv1{a} libvulkan1{a} libwebp6{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxcursor1{a} libxdamage1{a} libxdmcp-dev{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxft2{a} libxinerama1{a} libxml2{a} libxnvctrl0{a} libxrender1{a} libxshmfence1{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} procps{a} sensible-utils{a} ucf{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fltk1.3-doc javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libgl-dev libglu1-mesa-dev libgpm2 libldap-common libmail-sendmail-perl libsasl2-modules lynx mesa-vulkan-drivers psmisc publicsuffix wget xauth 0 packages upgraded, 177 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After unpacking 400 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libfido2-1 amd64 1.6.0-2 [53.3 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 openssh-client amd64 1:8.4p1-5 [929 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [418 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libxcursor1 amd64 1:1.2.0-2 [37.3 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libxinerama1 amd64 2:1.1.4-2 [17.7 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libfltk1.3 amd64 1.3.5-3 [566 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libfltk-forms1.3 amd64 1.3.5-3 [50.0 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libfltk-images1.3 amd64 1.3.5-3 [62.9 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 fluid amd64 1.3.5-3 [234 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libgfortran-10-dev amd64 10.2.1-6 [769 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 gfortran-10 amd64 10.2.1-6 [9447 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libibverbs1 amd64 33.2-1 [59.4 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 ibverbs-providers amd64 33.2-1 [253 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1 [543 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libdeflate-dev amd64 1.7-1 [46.9 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libevent-2.1-7 amd64 2.1.12-stable-1 [188 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-1 [110 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-1 [64.1 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libevent-dev amd64 2.1.12-stable-1 [311 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [169 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 librdmacm1 amd64 33.2-1 [68.9 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libfftw3-double3 amd64 3.3.8-2 [733 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libfftw3-long3 amd64 3.3.8-2 [319 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libfftw3-quad3 amd64 3.3.8-2 [558 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libfftw3-single3 amd64 3.3.8-2 [762 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libfftw3-bin amd64 3.3.8-2 [50.7 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libfftw3-dev amd64 3.3.8-2 [2106 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libfltk-cairo1.3 amd64 1.3.5-3 [43.4 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1 [203 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 libfltk-gl1.3 amd64 1.3.5-3 [76.4 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 x11proto-dev all 2020.1-1 [594 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 145 http://deb.debian.org/debian bullseye/main amd64 libxcb1-dev amd64 1.14-3 [176 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 libx11-dev amd64 2:1.7.2-1 [841 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 libfltk1.3-dev amd64 1.3.5-3 [855 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 libhwloc15 amd64 2.4.1+dfsg-1 [150 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 libnuma-dev amd64 2.0.12-1+b1 [39.3 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 libltdl7 amd64 2.4.6-15 [391 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 libltdl-dev amd64 2.4.6-15 [162 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 libhwloc-dev amd64 2.4.1+dfsg-1 [231 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 libxnvctrl0 amd64 460.91.03-1 [26.9 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 ocl-icd-libopencl1 amd64 2.2.14-2 [42.5 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 libhwloc-plugins amd64 2.4.1+dfsg-1 [21.4 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 libibverbs-dev amd64 33.2-1 [487 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 libjbig-dev amd64 2.1-3.1+b2 [30.5 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo-dev amd64 1:2.0.6-4 [278 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 libjpeg-dev amd64 1:2.0.6-4 [67.8 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2 [229 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 libpmix2 amd64 4.0.0-4.1 [552 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 libucx0 amd64 1.10.1~rc1+really.1.10.0-1 [649 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 libopenmpi3 amd64 4.1.0-10 [2370 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 openmpi-common all 4.1.0-10 [179 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 libpmix-dev amd64 4.0.0-4.1 [655 kB] Get: 172 http://deb.debian.org/debian bullseye/main amd64 openmpi-bin amd64 4.1.0-10 [238 kB] Get: 173 http://deb.debian.org/debian bullseye/main amd64 libopenmpi-dev amd64 4.1.0-10 [1192 kB] Get: 174 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 175 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1 [289 kB] Get: 176 http://deb.debian.org/debian bullseye/main amd64 libtiffxx5 amd64 4.2.0-1 [128 kB] Get: 177 http://deb.debian.org/debian bullseye/main amd64 libtiff-dev amd64 4.2.0-1 [415 kB] Fetched 103 MB in 6s (16.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../001-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_amd64.deb ... 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Setting up cmake-data (3.18.4-2+deb11u1) ... Setting up libtiff5:amd64 (4.2.0-1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libfido2-1:amd64 (1.6.0-2) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libdeflate-dev:amd64 (1.7-1) ... Setting up libdrm-common (2.4.104-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libtiffxx5:amd64 (4.2.0-1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-1) ... Setting up x11proto-dev (2020.1-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-1) ... 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Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libxinerama1:amd64 (2:1.1.4-2) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up libhwloc-dev:amd64 (2.4.1+dfsg-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up librdmacm1:amd64 (33.2-1) ... Setting up libucx0:amd64 (1.10.1~rc1+really.1.10.0-1) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up libglx-mesa0:amd64 (20.3.5-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up libxcursor1:amd64 (1:1.2.0-2) ... Setting up debhelper (13.3.4) ... Setting up libibverbs-dev:amd64 (33.2-1) ... Setting up libhwloc-plugins:amd64 (2.4.1+dfsg-1) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:amd64 (4.0.0-4.1) ... Setting up libopenmpi3:amd64 (4.1.0-10) ... Setting up libfltk1.3:amd64 (1.3.5-3) ... Setting up libfltk-gl1.3:amd64 (1.3.5-3) ... Setting up libfltk-cairo1.3:amd64 (1.3.5-3) ... Setting up libfltk-images1.3:amd64 (1.3.5-3) ... Setting up libfltk-forms1.3:amd64 (1.3.5-3) ... Setting up libpmix-dev:amd64 (4.0.0-4.1) ... Setting up openmpi-bin (4.1.0-10) ... 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 libfltk1.3-dev (1.3.5-3) ... Setting up fluid (1.3.5-3) ... Setting up libopenmpi-dev:amd64 (4.1.0-10) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Processing triggers for libc-bin (2.31-13+deb11u2) ... 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 I: Building the package I: Running cd /build/relion-3.1.0/ && 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 > ../relion_3.1.0-4_source.changes dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/relion-3.1.0' dh_clean rm -rf build make[1]: Leaving directory '/build/relion-3.1.0' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/relion-3.1.0' mkdir /build/relion-3.1.0/build cd /build/relion-3.1.0/build; \ CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /build/relion-3.1.0;\ make -j15; DESTDIR=/build/relion-3.1.0/debian/tmp/cli make install CMake Warning (dev) at /usr/share/cmake-3.18/Modules/CMakeDetermineCompilerId.cmake:72 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Quoted variables like "CUDA" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/CMakeDetermineCCompiler.cmake:116 (CMAKE_DETERMINE_COMPILER_ID) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - 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/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=35 -- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2 -- Setting cpu precision to double -- Setting accelerated code precision to single -- Using non-cuda compilation.... -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include -- MPI_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include -- MPI_CXX_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -- CMAKE_C_COMPILER : /usr/bin/gcc -- CMAKE_CXX_COMPILER : /usr/bin/g++ -- MPI_C_COMPILER : /usr/bin/mpicc -- MPI_CXX_COMPILER : /usr/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- CMAKE_C_COMPILER : /usr/bin/mpicc -- CMAKE_CXX_COMPILER : /usr/bin/mpicxx -- MPI_C_COMPILER : /usr/bin/mpicc -- MPI_CXX_COMPILER : /usr/bin/mpicxx -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Found FLTK: fltk_images;fltk_forms;fltk -- X11 and FLTK were found -- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/x86_64-linux-gnu/libfftw3f.so;/usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.2.0") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) BUILD_SHARED_LIBS = OFF -- Building static libs (larger build size and binaries) Running apps/CMakeLists.txt... -- CMAKE_BINARY_DIR:/build/relion-3.1.0/build -- Git commit ID: GITDIR-NOTFOUND -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: DoublePrec_GPU -- Build files have been written to: /build/relion-3.1.0/build make[2]: Entering directory '/build/relion-3.1.0/build' /usr/bin/cmake -S/build/relion-3.1.0 -B/build/relion-3.1.0/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles /build/relion-3.1.0/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0 /build/relion-3.1.0/build /build/relion-3.1.0/build /build/relion-3.1.0/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= Scanning dependencies of target copy_scripts make[4]: Leaving directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_printtable /build/relion-3.1.0/build/bin/relion_star_printtable /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_plottable /build/relion-3.1.0/build/bin/relion_star_plottable /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_loopheader /build/relion-3.1.0/build/bin/relion_star_loopheader /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_stack /build/relion-3.1.0/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_singlefiles /build/relion-3.1.0/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_ctfdat /build/relion-3.1.0/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/qsub.csh /build/relion-3.1.0/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/relion-3.1.0/build' [ 0%] Built target copy_scripts Scanning dependencies of target relion_lib make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.0/build/macros.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/relion-3.1.0/src/CPlot2D.cpp [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-3.1.0/src/args.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/relion-3.1.0/src/assembly.cpp [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/relion-3.1.0/src/autopicker.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/relion-3.1.0/src/backprojector.cpp [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-3.1.0/src/autopicker_mpi.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /build/relion-3.1.0/src/complex.cpp [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/relion-3.1.0/src/ctffind_runner.cpp [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /build/relion-3.1.0/src/ctf.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /build/relion-3.1.0/src/error.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /build/relion-3.1.0/src/ctffind_runner_mpi.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /build/relion-3.1.0/src/euler.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /build/relion-3.1.0/src/exp_model.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /build/relion-3.1.0/src/fftw.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-3.1.0/src/filename.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/relion-3.1.0/src/flex_analyser.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /build/relion-3.1.0/src/funcs.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /build/relion-3.1.0/src/healpix_sampling.cpp [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/relion-3.1.0/src/helix.cpp [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/relion-3.1.0/src/helix_inimodel2d.cpp [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /build/relion-3.1.0/src/image.cpp [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/relion-3.1.0/src/local_symmetry.cpp [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-3.1.0/src/local_symmetry_mpi.cpp /build/relion-3.1.0/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': /build/relion-3.1.0/src/CPlot2D.cpp:743:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~ /build/relion-3.1.0/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ /build/relion-3.1.0/src/CPlot2D.cpp:743:16: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/relion-3.1.0/src/CPlot2D.cpp:733:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~ /build/relion-3.1.0/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ /build/relion-3.1.0/src/CPlot2D.cpp:733:16: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.0/src/mask.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-3.1.0/src/matrix1d.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/relion-3.1.0/src/matrix2d.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /build/relion-3.1.0/src/memory.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /build/relion-3.1.0/src/metadata_container.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /build/relion-3.1.0/src/metadata_label.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /build/relion-3.1.0/src/metadata_table.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /build/relion-3.1.0/src/micrograph_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /build/relion-3.1.0/src/ml_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /build/relion-3.1.0/src/ml_optimiser.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /build/relion-3.1.0/src/ml_optimiser_mpi.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /build/relion-3.1.0/src/motioncorr_runner.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/relion-3.1.0/src/motioncorr_runner_mpi.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /build/relion-3.1.0/src/mpi.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /build/relion-3.1.0/src/multidim_array.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /build/relion-3.1.0/src/numerical_recipes.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /build/relion-3.1.0/src/parallel.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/relion-3.1.0/src/particle_subtractor.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /build/relion-3.1.0/src/pipeline_control.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/relion-3.1.0/src/pipeline_jobs.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/relion-3.1.0/src/pipeliner.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /build/relion-3.1.0/src/postprocessing.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /build/relion-3.1.0/src/preprocessing.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /build/relion-3.1.0/src/preprocessing_mpi.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /build/relion-3.1.0/src/projector.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/relion-3.1.0/src/reconstructor.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/relion-3.1.0/src/reconstructor_mpi.cpp [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/relion-3.1.0/src/scheduler.cpp [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/relion-3.1.0/src/strings.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /build/relion-3.1.0/src/symmetries.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/relion-3.1.0/src/tabfuncs.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/relion-3.1.0/src/tiff_converter.cpp [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/relion-3.1.0/src/time.cpp [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /build/relion-3.1.0/src/transformations.cpp [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/cxxutils.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/healpix_base.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -c /build/relion-3.1.0/src/jaz/Fourier_helper.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -c /build/relion-3.1.0/src/jaz/Gaussian_pyramid.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /build/relion-3.1.0/src/jaz/aberration_fit.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /build/relion-3.1.0/src/jaz/complex_io.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/relion-3.1.0/src/jaz/convolution_helper.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/relion-3.1.0/src/jaz/ctf_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/relion-3.1.0/src/jaz/damage_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/relion-3.1.0/src/jaz/distribution_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/relion-3.1.0/src/jaz/fftw_helper.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/relion-3.1.0/src/jaz/fsc_helper.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/relion-3.1.0/src/jaz/image_log.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/relion-3.1.0/src/jaz/interpolation.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/relion-3.1.0/src/jaz/jaz_config.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/relion-3.1.0/src/jaz/legacy_obs_model.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /build/relion-3.1.0/src/jaz/local_motion_fit.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/relion-3.1.0/src/jaz/micrograph_handler.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/relion-3.1.0/src/jaz/new_ft.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/relion-3.1.0/src/jaz/noise_helper.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/relion-3.1.0/src/jaz/obs_model.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /build/relion-3.1.0/src/jaz/parallel_ft.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /build/relion-3.1.0/src/jaz/reference_map.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /build/relion-3.1.0/src/jaz/refinement_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /build/relion-3.1.0/src/jaz/resampling_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /build/relion-3.1.0/src/jaz/slice_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/relion-3.1.0/src/jaz/spectral_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/relion-3.1.0/src/jaz/stack_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/relion-3.1.0/src/jaz/structure_tensor.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/relion-3.1.0/src/jaz/svd_helper.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/relion-3.1.0/src/jaz/t_complex.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/relion-3.1.0/src/jaz/volume_converter.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/relion-3.1.0/src/jaz/volume_integration.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/relion-3.1.0/src/jaz/vtk_helper.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/gradient_descent.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/lbfgs.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/nelder_mead.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/optimization.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/aberration_estimator.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/bfactor_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/ctf_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/ctf_refiner_mpi.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/defocus_estimator.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/defocus_helper.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/delocalisation_helper.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/equation2x2.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/magnification_estimator.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/magnification_helper.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/modular_ctf_optimisation.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/tilt_estimator.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/tilt_helper.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/relion-3.1.0/src/jaz/motion/alignment_set.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/relion-3.1.0/src/jaz/motion/frame_recombiner.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/relion-3.1.0/src/jaz/motion/gp_motion_fit.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_estimator.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_helper.cpp [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_param_estimator.cpp [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_refiner.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_refiner_mpi.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /build/relion-3.1.0/src/jaz/motion/three_hyperparameter_fit.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /build/relion-3.1.0/src/jaz/motion/two_hyperparameter_fit.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/relion-3.1.0/src/jaz/math/Zernike.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/relion-3.1.0/src/jaz/img_proc/color_helper.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/relion-3.1.0/src/jaz/img_proc/filter_helper.cpp [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/relion-3.1.0/src/jaz/img_proc/image_op.cpp [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/backprojection_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/imod_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/projection_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/tomo_stack.cpp [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/relion-3.1.0/src/jaz/io/star_converter.cpp [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyev2.c [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevc3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevd3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevh3.c cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevj3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevq3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevv3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsytrd3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/slvsec3.c [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /build/relion-3.1.0/src/jaz/lbfgs/lbfgs.c [ 53%] Linking CXX static library ../../lib/librelion_lib.a cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_lib.dir/cmake_clean_target.cmake cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_lib.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/librelion_lib.a CMakeFiles/relion_lib.dir/__/__/macros.cpp.o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o CMakeFiles/relion_lib.dir/__/args.cpp.o CMakeFiles/relion_lib.dir/__/assembly.cpp.o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o CMakeFiles/relion_lib.dir/__/complex.cpp.o CMakeFiles/relion_lib.dir/__/ctf.cpp.o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/error.cpp.o CMakeFiles/relion_lib.dir/__/euler.cpp.o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o CMakeFiles/relion_lib.dir/__/fftw.cpp.o CMakeFiles/relion_lib.dir/__/filename.cpp.o 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CMakeFiles/relion_lib.dir/__/time.cpp.o CMakeFiles/relion_lib.dir/__/transformations.cpp.o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o 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CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o /usr/bin/ranlib ../../lib/librelion_lib.a make[4]: Leaving directory '/build/relion-3.1.0/build' [ 53%] Built target relion_lib make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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dependencies of target find_tiltpairs make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build Scanning dependencies of target image_handler make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend Scanning dependencies of target helix_inimodel2d make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build Scanning dependencies of target mask_create make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build Scanning dependencies of target flex_analyse_mpi Scanning dependencies of target flex_analyse make[4]: Leaving directory '/build/relion-3.1.0/build' [ 54%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' [ 54%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/relion-3.1.0/src/apps/image_handler.cpp make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /build/relion-3.1.0/src/apps/find_tiltpairs.cpp Scanning dependencies of target external_reconstruct make[4]: Leaving directory '/build/relion-3.1.0/build' [ 55%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /build/relion-3.1.0/src/apps/helix_inimodel2d.cpp Scanning dependencies of target particle_symmetry_expand make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build [ 55%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/relion-3.1.0/src/apps/flex_analyse_mpi.cpp make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' [ 55%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /build/relion-3.1.0/src/apps/flex_analyse.cpp [ 55%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= [ 56%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/relion-3.1.0/src/apps/mask_create.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/relion-3.1.0/src/apps/external_reconstruct.cpp make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= [ 56%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-3.1.0/src/apps/particle_symmetry_expand.cpp make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= Scanning dependencies of target project make[4]: Leaving directory '/build/relion-3.1.0/build' Scanning dependencies of target import make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build Scanning dependencies of target convert_star make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build Scanning dependencies of target refine make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build Scanning dependencies of target helix_toolbox make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' Scanning dependencies of target autopick [ 56%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/import.dir/import.cpp.o -c /build/relion-3.1.0/src/apps/import.cpp [ 57%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o [ 58%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-3.1.0/src/apps/helix_toolbox.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-3.1.0/src/apps/project.cpp make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build [ 58%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /build/relion-3.1.0/src/apps/convert_star.cpp make[4]: Entering directory '/build/relion-3.1.0/build' [ 59%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o Scanning dependencies of target relion_gui_lib cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-3.1.0/src/apps/refine.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 60%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/relion-3.1.0/src/apps/autopick.cpp [ 60%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-3.1.0/src/displayer.cpp [ 60%] Linking CXX executable ../../bin/relion_helix_inimodel2d cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 [ 61%] Linking CXX executable ../../bin/relion_convert_star cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 61%] Linking CXX executable ../../bin/relion_autopick cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 61%] Built target convert_star make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target autopick_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 61%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/relion-3.1.0/src/apps/autopick_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 61%] Built target helix_inimodel2d make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= Scanning dependencies of target convert_to_tiff make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 61%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-3.1.0/src/apps/convert_to_tiff.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 61%] Built target autopick make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= Scanning dependencies of target mrc2vtk make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 61%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /build/relion-3.1.0/src/apps/mrc2vtk.cpp [ 61%] Linking CXX executable ../../bin/relion_flex_analyse_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 62%] Linking CXX executable ../../bin/relion_particle_symmetry_expand cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 62%] Linking CXX executable ../../bin/relion_convert_to_tiff cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 62%] Built target particle_symmetry_expand make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= Scanning dependencies of target ctf_toolbox make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 63%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /build/relion-3.1.0/src/apps/ctf_toolbox.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 63%] Built target convert_to_tiff make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= Scanning dependencies of target align_symmetry make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 63%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/relion-3.1.0/src/apps/align_symmetry.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 63%] Built target flex_analyse_mpi make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= Scanning dependencies of target postprocess make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 64%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/relion-3.1.0/src/apps/postprocess.cpp [ 65%] Linking CXX executable ../../bin/relion_flex_analyse cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 65%] Linking CXX executable ../../bin/relion_refine cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 65%] Linking CXX executable ../../bin/relion_import cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 65%] Built target import make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend [ 66%] Linking CXX executable ../../bin/relion_autopick_mpi make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff Scanning dependencies of target ctf_mask_test make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 66%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-3.1.0/src/apps/ctf_mask_test.cpp [ 66%] Linking CXX executable ../../bin/relion_find_tiltpairs cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 66%] Built target flex_analyse make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= Scanning dependencies of target merge_particles make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 67%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-3.1.0/src/apps/merge_particles.cpp [ 67%] Linking CXX executable ../../bin/relion_external_reconstruct make[4]: Leaving directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 [ 67%] Built target refine make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff Scanning dependencies of target localsym make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 68%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/relion-3.1.0/src/apps/localsym.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 68%] Built target find_tiltpairs make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target run_ctffind_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 69%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/relion-3.1.0/src/apps/run_ctffind_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 69%] Built target external_reconstruct make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= [ 69%] Linking CXX executable ../../bin/relion_mask_create cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 Scanning dependencies of target convert_to_tiff_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 70%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/relion-3.1.0/src/apps/convert_to_tiff_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 70%] Built target autopick_mpi make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target preprocess_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 71%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.0/src/apps/preprocess_mpi.cpp [ 71%] Linking CXX executable ../../bin/relion_mrc2vtk cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 71%] Linking CXX executable ../../bin/relion_postprocess cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 71%] Built target mask_create make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target ctf_refine_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 71%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/ctf_refine_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 71%] Built target mrc2vtk make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target localsym_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 72%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.0/src/apps/localsym_mpi.cpp [ 72%] Linking CXX executable ../../bin/relion_merge_particles cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 72%] Built target postprocess make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= Scanning dependencies of target ctf_refine make[4]: Leaving directory '/build/relion-3.1.0/build' [ 72%] Linking CXX executable ../../bin/relion_localsym make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 make[4]: Entering directory '/build/relion-3.1.0/build' /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 72%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/relion-3.1.0/src/apps/ctf_refine.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 72%] Built target localsym make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' [ 72%] Built target merge_particles make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' Scanning dependencies of target motion_refine cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 72%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/relion-3.1.0/src/apps/motion_refine.cpp Scanning dependencies of target postprocess_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 73%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-3.1.0/src/apps/postprocess_mpi.cpp [ 73%] Linking CXX executable ../../bin/relion_run_ctffind_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 73%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 73%] Linking CXX executable ../../bin/relion_preprocess_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 73%] Built target convert_to_tiff_mpi make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= Scanning dependencies of target particle_FCC make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 74%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-3.1.0/src/apps/particle_FCC.cpp [ 74%] Linking CXX executable ../../bin/relion_localsym_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 74%] Built target run_ctffind_mpi make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= Scanning dependencies of target particle_reposition make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 74%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /build/relion-3.1.0/src/apps/particle_reposition.cpp [ 75%] Linking CXX executable ../../bin/relion_ctf_refine cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 75%] Built target preprocess_mpi make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= Scanning dependencies of target tomo_test make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 75%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/relion-3.1.0/src/apps/tomo_test.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 75%] Built target localsym_mpi make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= Scanning dependencies of target demodulate make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 75%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/relion-3.1.0/src/apps/demodulate.cpp [ 75%] Linking CXX executable ../../bin/relion_ctf_refine_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 75%] Built target ctf_refine make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= Scanning dependencies of target particle_select make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 75%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/relion-3.1.0/src/apps/particle_select.cpp [ 75%] Linking CXX executable ../../bin/relion_ctf_toolbox cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 76%] Linking CXX executable ../../bin/relion_motion_refine cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 [ 76%] Linking CXX executable ../../bin/relion_postprocess_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 76%] Linking CXX executable ../../bin/relion_project cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/relion-3.1.0/build' /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 76%] Built target ctf_refine_mpi make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= Scanning dependencies of target particle_subtract make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 76%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /build/relion-3.1.0/src/apps/particle_subtract.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 76%] Linking CXX executable ../../bin/relion_align_symmetry cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 [ 76%] Built target ctf_toolbox make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' [ 76%] Built target postprocess_mpi make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= Scanning dependencies of target particle_subtract_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 77%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-3.1.0/src/apps/particle_subtract_mpi.cpp Scanning dependencies of target reconstruct make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 77%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-3.1.0/src/apps/reconstruct.cpp [ 77%] Linking CXX executable ../../bin/relion_particle_FCC cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 78%] Linking CXX executable ../../bin/relion_ctf_mask_test cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 78%] Built target align_symmetry make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target motion_refine_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 78%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/motion_refine_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 78%] Built target motion_refine make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' [ 78%] Built target project make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend Scanning dependencies of target plot_delocalisation make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 78%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/relion-3.1.0/src/apps/plot_delocalisation.cpp Scanning dependencies of target reposition make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 78%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-3.1.0/src/apps/reposition.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 78%] Built target particle_FCC make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= Scanning dependencies of target prepare_subtomo make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 78%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.0/src/apps/prepare_subtomo.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 78%] Built target ctf_mask_test make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= Scanning dependencies of target preprocess make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 78%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/relion-3.1.0/src/apps/preprocess.cpp [ 79%] Linking CXX executable ../../bin/relion_particle_select cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 80%] Linking CXX executable ../../bin/relion_tomo_test cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target particle_select make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target reconstruct_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 80%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.0/src/apps/reconstruct_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target tomo_test make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target refine_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 81%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/refine_mpi.cpp [ 81%] Linking CXX executable ../../bin/relion_helix_toolbox cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 82%] Linking CXX executable ../../bin/relion_reconstruct cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 82%] Linking CXX executable ../../bin/relion_preprocess cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 82%] Built target helix_toolbox make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= Scanning dependencies of target run_ctffind make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 82%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-3.1.0/src/apps/run_ctffind.cpp [ 83%] Linking CXX executable ../../bin/relion_image_handler cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 83%] Built target preprocess make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= Scanning dependencies of target run_motioncorr make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 84%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-3.1.0/src/apps/run_motioncorr.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 84%] Built target reconstruct make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= Scanning dependencies of target estimate_gain make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 84%] Linking CXX executable ../../bin/relion_plot_delocalisation cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 [ 84%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /build/relion-3.1.0/src/apps/estimate_gain.cpp /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 85%] Linking CXX executable ../../bin/relion_demodulate cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 85%] Built target image_handler make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target run_motioncorr_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 85%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/relion-3.1.0/src/apps/run_motioncorr_mpi.cpp [ 85%] Linking CXX executable ../../bin/relion_particle_subtract cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 86%] Linking CXX executable ../../bin/relion_motion_refine_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 86%] Built target demodulate make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= Scanning dependencies of target stack_create make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 87%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-3.1.0/src/apps/stack_create.cpp [ 88%] Linking CXX executable ../../bin/relion_reposition cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 [ 89%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.0/src/gui_entries.cpp /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 89%] Built target plot_delocalisation make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= Scanning dependencies of target scheduler make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 89%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/relion-3.1.0/src/apps/scheduler.cpp [ 89%] Linking CXX executable ../../bin/relion_run_ctffind cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 89%] Built target particle_subtract make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= Scanning dependencies of target star_handler make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 90%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/relion-3.1.0/src/apps/star_handler.cpp [ 90%] Linking CXX executable ../../bin/relion_particle_subtract_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 90%] Linking CXX executable ../../bin/relion_run_motioncorr cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 90%] Built target reposition make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' [ 90%] Built target run_ctffind Scanning dependencies of target tiltpair_plot make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' [ 90%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.0/src/gui_jobwindow.cpp [ 90%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/relion-3.1.0/src/apps/tiltpair_plot.cpp [ 90%] Built target motion_refine_mpi [ 91%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.0/src/gui_mainwindow.cpp [ 91%] Linking CXX executable ../../bin/relion_reconstruct_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 91%] Built target run_motioncorr [ 91%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/relion-3.1.0/src/manualpicker.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 91%] Built target particle_subtract_mpi [ 91%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/cxxutils.cc [ 92%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/healpix_base.cc [ 92%] Linking CXX executable ../../bin/relion_refine_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 92%] Built target reconstruct_mpi [ 93%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 94%] Linking CXX executable ../../bin/relion_particle_reposition cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target run_motioncorr_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target refine_mpi [ 95%] Linking CXX executable ../../bin/relion_tiltpair_plot cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target particle_reposition make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target tiltpair_plot [ 95%] Linking CXX executable ../../bin/relion_estimate_gain cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target estimate_gain [ 95%] Linking CXX executable ../../bin/relion_scheduler cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 95%] Linking CXX executable ../../bin/relion_stack_create cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target scheduler make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target stack_create [ 95%] Linking CXX static library ../../lib/librelion_gui_lib.a cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/librelion_gui_lib.a CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o /usr/bin/ranlib ../../lib/librelion_gui_lib.a make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target relion_gui_lib make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/maingui.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= Scanning dependencies of target display make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build Scanning dependencies of target pipeliner make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' Scanning dependencies of target maingui make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/build [ 95%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o Scanning dependencies of target manualpick make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-3.1.0/src/apps/display.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build [ 95%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o [ 95%] Building CXX object src/apps/CMakeFiles/maingui.dir/maingui.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/relion-3.1.0/src/apps/pipeliner.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/maingui.dir/maingui.cpp.o -c /build/relion-3.1.0/src/apps/maingui.cpp make[4]: Entering directory '/build/relion-3.1.0/build' [ 95%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.0/src/apps/manualpick.cpp [ 96%] Linking CXX executable ../../bin/relion_prepare_subtomo cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target prepare_subtomo [ 97%] Linking CXX executable ../../bin/relion_display cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff [ 98%] Linking CXX executable ../../bin/relion_manualpick cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 98%] Built target display [ 98%] Linking CXX executable ../../bin/relion_star_handler cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 99%] Linking CXX executable ../../bin/relion_maingui cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/maingui.dir/link.txt --verbose=1 [ 99%] Built target manualpick /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/maingui.dir/maingui.cpp.o -o ../../bin/relion_maingui ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 99%] Built target star_handler [100%] Linking CXX executable ../../bin/relion_pipeliner cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [100%] Built target pipeliner cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E copy /build/relion-3.1.0/build/bin/relion_maingui /build/relion-3.1.0/build/bin/relion cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E copy /build/relion-3.1.0/build/bin/relion_qsub.csh /build/relion-3.1.0/build/bin/qsub.csh make[4]: Leaving directory '/build/relion-3.1.0/build' [100%] Built target maingui make[3]: Leaving directory '/build/relion-3.1.0/build' /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles 0 make[2]: Leaving directory '/build/relion-3.1.0/build' make[2]: Entering directory '/build/relion-3.1.0/build' /usr/bin/cmake -S/build/relion-3.1.0 -B/build/relion-3.1.0/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles /build/relion-3.1.0/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0 /build/relion-3.1.0/build /build/relion-3.1.0/build /build/relion-3.1.0/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_printtable /build/relion-3.1.0/build/bin/relion_star_printtable /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_plottable /build/relion-3.1.0/build/bin/relion_star_plottable /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_loopheader /build/relion-3.1.0/build/bin/relion_star_loopheader /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_stack /build/relion-3.1.0/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_singlefiles /build/relion-3.1.0/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_ctfdat /build/relion-3.1.0/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/qsub.csh /build/relion-3.1.0/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/relion-3.1.0/build' [ 0%] Built target copy_scripts make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 53%] Built target relion_lib make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 54%] Built target image_handler make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 55%] Built target helix_inimodel2d make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 56%] Built target find_tiltpairs make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 56%] Built target flex_analyse_mpi make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 57%] Built target flex_analyse make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 57%] Built target mask_create make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 58%] Built target external_reconstruct make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_symmetry_expand.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 59%] Built target particle_symmetry_expand make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_gui_lib.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 62%] Built target relion_gui_lib make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/display.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 63%] Built target display make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 64%] Built target pipeliner make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 65%] Built target project make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 66%] Built target convert_star make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 67%] Built target refine make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 67%] Built target import make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/maingui.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/maingui.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 68%] Built target maingui make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 69%] Built target manualpick make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 70%] Built target helix_toolbox make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 71%] Built target autopick make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 72%] Built target autopick_mpi make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 72%] Built target convert_to_tiff make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 72%] Built target mrc2vtk make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_toolbox.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 73%] Built target ctf_toolbox make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 73%] Built target align_symmetry make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 74%] Built target postprocess make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_mask_test.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 75%] Built target ctf_mask_test make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 76%] Built target merge_particles make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 77%] Built target localsym make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 78%] Built target run_ctffind_mpi make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 79%] Built target convert_to_tiff_mpi make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target preprocess_mpi make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target ctf_refine_mpi make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 81%] Built target localsym_mpi make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 82%] Built target ctf_refine make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 83%] Built target motion_refine make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 84%] Built target postprocess_mpi make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 85%] Built target particle_FCC make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 86%] Built target particle_reposition make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 87%] Built target tomo_test make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 88%] Built target demodulate make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 89%] Built target particle_select make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 89%] Built target particle_subtract make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 90%] Built target particle_subtract_mpi make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 91%] Built target reconstruct make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 92%] Built target motion_refine_mpi make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 92%] Built target plot_delocalisation make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reposition.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 93%] Built target reposition make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target prepare_subtomo make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target preprocess make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target reconstruct_mpi make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target refine_mpi make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target run_ctffind make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target run_motioncorr make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/estimate_gain.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target estimate_gain make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 97%] Built target run_motioncorr_mpi make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/stack_create.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 98%] Built target stack_create make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/scheduler.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 98%] Built target scheduler make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 99%] Built target star_handler make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [100%] Built target tiltpair_plot make[3]: Leaving directory '/build/relion-3.1.0/build' /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/relion-3.1.0/build' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/relion-3.1.0/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_printtable -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/qsub.csh -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_maingui -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_manualpick -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_display -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tomo_test -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_project -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_import -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_star -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_demodulate -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_display -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_estimate_gain -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_image_handler -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_import -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_maingui -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_manualpick -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mask_create -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_merge_particles -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_FCC -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_reposition -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_select -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_pipeliner -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_project -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reposition -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_scheduler -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_stack_create -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_handler -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tomo_test make[2]: Leaving directory '/build/relion-3.1.0/build' mkdir -p /build/relion-3.1.0/debian/tmp/gui/usr/bin rm /build/relion-3.1.0/debian/tmp/cli/usr/bin/*.csh # Useless ... for prog in relion relion_display relion_maingui relion_manualpick; do \ mv /build/relion-3.1.0/debian/tmp/cli/usr/bin/$prog \ /build/relion-3.1.0/debian/tmp/gui/usr/bin; done make[1]: Leaving directory '/build/relion-3.1.0' create-stamp debian/debhelper-build-stamp debian/rules override_dh_prep make[1]: Entering directory '/build/relion-3.1.0' # We don't want debian/tmp to be removed again ... dh_prep -X debian/tmp make[1]: Leaving directory '/build/relion-3.1.0' debian/rules override_dh_install-arch make[1]: Entering directory '/build/relion-3.1.0' dh_install -a make[1]: Leaving directory '/build/relion-3.1.0' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'relion' in '../relion_3.1.0-4_amd64.deb'. dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.0-4_amd64.deb'. dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.0-4_amd64.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.0-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../relion_3.1.0-4_amd64.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/3838652 and its subdirectories I: Current time: Sun Jan 9 18:25:31 -12 2022 I: pbuilder-time-stamp: 1641795931 Mon Jan 10 06:25:36 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Mon Jan 10 06:25:36 UTC 2022 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Mon Jan 10 06:35:28 UTC 2022 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Mon Jan 10 06:35:28 UTC 2022 I: relion_3.1.0-4_amd64.changes: Format: 1.8 Date: Wed, 07 Oct 2020 16:03:12 +0200 Source: relion Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym Architecture: amd64 Version: 3.1.0-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: relion - toolkit for 3D reconstructions in cryo-electron microscopy relion-gui - parallel toolkit for 3D reconstructions in cryo-electron microsco Changes: relion (3.1.0-4) unstable; urgency=medium . * Drop useless get-orig-source target (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Build-Depends: fluid Checksums-Sha1: 59a00509c3c064c912223af4c1dba592bc30f926 340978808 relion-dbgsym_3.1.0-4_amd64.deb 126762febae44071d0c0c7a02567a16ce959bdc7 20953760 relion-gui-dbgsym_3.1.0-4_amd64.deb 3d2e6ff4e5cdcf20d326a7e33ac24bbf69606fbc 1126240 relion-gui_3.1.0-4_amd64.deb 23dc0697451223ca9ffcc4b36619962ef899b705 10170 relion_3.1.0-4_amd64.buildinfo 288b6ee0f0b7104338e5889ce884235c6b8d146b 14426380 relion_3.1.0-4_amd64.deb Checksums-Sha256: b830788bc0b411360973d21158b3b594c6d847eaa4d4b996a341d17d05279250 340978808 relion-dbgsym_3.1.0-4_amd64.deb 6fcfe284d0869cc5411ef57e73b0a47241cc8da2310c49a17153632c0141e025 20953760 relion-gui-dbgsym_3.1.0-4_amd64.deb 4433ce8b16d61ffec3689da02549cb46abc4015441c3bf9a912a51b006ba6aa6 1126240 relion-gui_3.1.0-4_amd64.deb 9cb297a0fb7877f8c73d42646f3353c7f3d377b8546a90405abfcb7ed26d9531 10170 relion_3.1.0-4_amd64.buildinfo 3924540ee4e7a8d951ab4f8b6276910d1fdfb0b98be8798b1c7733e15d4d80cc 14426380 relion_3.1.0-4_amd64.deb Files: dd0f6538794c4335681a89eaa9987fbb 340978808 debug optional relion-dbgsym_3.1.0-4_amd64.deb 08f6a668373e1ece99680d5efab4e489 20953760 debug optional relion-gui-dbgsym_3.1.0-4_amd64.deb ee7e5e45f4ce5f6c0489e2ae31b82643 1126240 science optional relion-gui_3.1.0-4_amd64.deb 76d0a5a0fbec9cdec0f00c5f85e54a7e 10170 science optional relion_3.1.0-4_amd64.buildinfo 5e4494c7d25ded23d9e370c5985a0fa4 14426380 science optional relion_3.1.0-4_amd64.deb Mon Jan 10 06:35:30 UTC 2022 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.QATpWdJhoQ/relion_3.1.0-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.QATpWdJhoQ/relion_3.1.0-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.QATpWdJhoQ/relion_3.1.0-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.QATpWdJhoQ/b1/relion_3.1.0-4_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.QATpWdJhoQ/b2/relion_3.1.0-4_amd64.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: 4.494s) 4.494s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 4.190s) 4.190s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jan 10 06:35:40 UTC 2022 I: found no differences in the changes files, and a .buildinfo file also exists. Mon Jan 10 06:35:40 UTC 2022 I: relion from bullseye built successfully and reproducibly on amd64. Mon Jan 10 06:35:41 UTC 2022 I: Submitting .buildinfo files to external archives: Mon Jan 10 06:35:41 UTC 2022 I: Submitting 12K b1/relion_3.1.0-4_amd64.buildinfo.asc Mon Jan 10 06:35:43 UTC 2022 I: Submitting 12K b2/relion_3.1.0-4_amd64.buildinfo.asc Mon Jan 10 06:35:44 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 10 06:35:44 UTC 2022 I: Done submitting .buildinfo files. Mon Jan 10 06:35:44 UTC 2022 I: Removing signed relion_3.1.0-4_amd64.buildinfo.asc files: removed './b1/relion_3.1.0-4_amd64.buildinfo.asc' removed './b2/relion_3.1.0-4_amd64.buildinfo.asc'