Diff of the two buildlogs: -- --- b1/build.log 2022-01-10 06:25:32.292281097 +0000 +++ b2/build.log 2022-01-10 06:35:24.101922241 +0000 @@ -1,6 +1,6 @@ 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: Current time: Mon Feb 13 02:48:39 +14 2023 +I: pbuilder-time-stamp: 1676206119 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ 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: keyblock resource '/tmp/dpkg-verify-sig.DLjQzcj_/trustedkeys.kbx': General error +gpgv: Signature made Thu Oct 8 04:36:44 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -27,135 +27,169 @@ 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: user script /srv/workspace/pbuilder/3927487/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3927487/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3927487/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + 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='> ' + INVOCATION_ID=6c5e0a69ed7149179bd07666153f4105 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3927487 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.QATpWdJhoQ/pbuilderrc_i079 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.QATpWdJhoQ/b2 --logfile b2/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-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 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 + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) 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 + -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 2021 more + -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount + -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Feb 13 02:48 sh -> bash + lrwxrwxrwx 1 root root 4 Feb 10 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 2021 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/3927487/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -380,7 +414,7 @@ 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) +Fetched 103 MB in 1s (94.3 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.) @@ -1109,7 +1143,8 @@ 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 +hostname: Name or service not known +I: Running cd /build/relion-3.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -1132,7 +1167,7 @@ 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 +make -j16; 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 @@ -1250,33 +1285,33 @@ 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 +[ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o +[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o +[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.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 +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o +[ 2%] 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/__/__/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 +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o +[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o +[ 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/__/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/__/backprojector.cpp.o -c /build/relion-3.1.0/src/backprojector.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.cpp.o -c /build/relion-3.1.0/src/ctffind_runner.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/__/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/__/error.cpp.o -c /build/relion-3.1.0/src/error.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/__/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 @@ -1298,6 +1333,8 @@ 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 +[ 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 /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); @@ -1317,8 +1354,6 @@ /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 @@ -1394,8 +1429,8 @@ [ 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/aberration_fit.cpp.o -c /build/relion-3.1.0/src/jaz/aberration_fit.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/__/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 @@ -1532,8 +1567,8 @@ [ 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 +[ 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/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 @@ -1553,161 +1588,159 @@ 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 -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend +make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend +make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend +make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend +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/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 -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend +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/find_tiltpairs.dir/DependInfo.cmake --color= -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 -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend +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/flex_analyse.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend +make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend +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/mask_create.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend +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/external_reconstruct.dir/DependInfo.cmake --color= -Scanning 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 -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/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 -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/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 -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 find_tiltpairs 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 +Scanning dependencies of target external_reconstruct +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 +Scanning dependencies of target helix_inimodel2d +Scanning dependencies of target import make[4]: Leaving directory '/build/relion-3.1.0/build' +Scanning dependencies of target mask_create +Scanning dependencies of target particle_symmetry_expand 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 -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build +Scanning dependencies of target project +Scanning dependencies of target image_handler +Scanning dependencies of target helix_toolbox +make[4]: Leaving directory '/build/relion-3.1.0/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/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/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 -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build +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]: 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]: Entering 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]: Leaving directory '/build/relion-3.1.0/build' +make[4]: Leaving directory '/build/relion-3.1.0/build' 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 -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/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' +Scanning dependencies of target flex_analyse_mpi +make[4]: Entering directory '/build/relion-3.1.0/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 -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build +make[4]: Leaving directory '/build/relion-3.1.0/build' +make[4]: Entering directory '/build/relion-3.1.0/build' +Scanning dependencies of target flex_analyse +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' +[ 54%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o +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 +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 +[ 55%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o 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 +[ 55%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o +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/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/relion-3.1.0/src/apps/external_reconstruct.cpp +[ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o +[ 55%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o +[ 56%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o +[ 56%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o +[ 57%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.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/convert_star.dir/convert_star.cpp.o -c /build/relion-3.1.0/src/apps/convert_star.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/mask_create.dir/mask_create.cpp.o -c /build/relion-3.1.0/src/apps/mask_create.cpp +make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build +[ 57%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o +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/project.dir/project.cpp.o -c /build/relion-3.1.0/src/apps/project.cpp +Scanning dependencies of target autopick_mpi 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/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-3.1.0/src/apps/particle_symmetry_expand.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/image_handler.dir/image_handler.cpp.o -c /build/relion-3.1.0/src/apps/image_handler.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/import.dir/import.cpp.o -c /build/relion-3.1.0/src/apps/import.cpp +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/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 +[ 58%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o +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' +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 +[ 58%] 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 +[ 59%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o +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/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-3.1.0/src/apps/helix_toolbox.cpp +[ 59%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o [ 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 +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 [ 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%] 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 [ 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 +/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 [ 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' @@ -1719,7 +1752,7 @@ [ 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 +[ 61%] Built target convert_star 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= @@ -1729,17 +1762,8 @@ 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 +[ 61%] Built target autopick 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= @@ -1747,10 +1771,19 @@ 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 +[ 62%] 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 +[ 63%] 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 +[ 64%] Linking CXX executable ../../bin/relion_autopick_mpi +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 +[ 64%] 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' -[ 63%] Built target convert_to_tiff +[ 64%] Built target particle_symmetry_expand 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= @@ -1758,47 +1791,47 @@ 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 +[ 64%] 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 +[ 64%] Built target autopick_mpi make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.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/postprocess.dir/DependInfo.cmake --color= +[ 64%] Built target convert_to_tiff +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= 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 +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' -[ 64%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o +make[4]: Entering directory '/build/relion-3.1.0/build' +[ 64%] 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 +[ 65%] 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 +[ 65%] 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_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 +[ 66%] 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 +[ 66%] 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 +[ 66%] Built target flex_analyse_mpi 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= @@ -1806,16 +1839,13 @@ 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]: Leaving 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 +[ 67%] Built target flex_analyse 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 @@ -1834,21 +1864,18 @@ [ 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 +[ 69%] Built target import 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 +[ 70%] Built target refine 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= @@ -1858,23 +1885,32 @@ 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 +[ 71%] Linking CXX executable ../../bin/relion_external_reconstruct +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_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/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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 71%] Built target mask_create +[ 71%] Built target external_reconstruct 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= +[ 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 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' +/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%] 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 +[ 71%] 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 +/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 +[ 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 +[ 71%] Linking CXX executable ../../bin/relion_localsym +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.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.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 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 @@ -1896,60 +1932,51 @@ 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 +make[4]: Leaving directory '/build/relion-3.1.0/build' [ 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 +[ 72%] Built target mask_create 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 +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 72%] Built target localsym +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= 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 +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%] Built target merge_particles 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= +[ 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 Scanning dependencies of target particle_FCC +/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 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 +[ 74%] 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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 74%] Built target run_ctffind_mpi +[ 74%] Built target convert_to_tiff_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= @@ -1959,11 +1986,11 @@ 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 +[ 74%] 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' -[ 75%] Built target preprocess_mpi +[ 74%] Built target run_ctffind_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= @@ -1971,10 +1998,13 @@ 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 +[ 74%] 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 +[ 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' -[ 75%] Built target localsym_mpi +[ 74%] Built target preprocess_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= @@ -1982,13 +2012,19 @@ 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 +[ 74%] 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 +[ 74%] 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 +[ 74%] 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 +[ 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 ctf_refine +[ 75%] Built target localsym_mpi 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= @@ -1996,22 +2032,10 @@ 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]: Leaving directory '/build/relion-3.1.0/build' +[ 75%] Built target ctf_toolbox [ 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= @@ -2019,85 +2043,94 @@ 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 +[ 75%] 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 +[ 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 +/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 +[ 77%] 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 +[ 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 +[ 77%] 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/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 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 +[ 77%] Built target ctf_refine_mpi 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 +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 78%] 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 +[ 78%] Built target ctf_refine +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 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 +[ 78%] 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 +[ 78%] 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 +/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]: Leaving directory '/build/relion-3.1.0/build' -[ 78%] Built target align_symmetry +[ 78%] Built target postprocess_mpi 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' +[ 78%] Built target ctf_mask_test +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= +Scanning dependencies of target plot_delocalisation +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' Scanning dependencies of target motion_refine_mpi +[ 78%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o 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 +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 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 +[ 78%] Built target align_symmetry 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' +[ 78%] Built target particle_FCC 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 -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' -[ 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 +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 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' +Scanning dependencies of target prepare_subtomo [ 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 +[ 78%] 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 +/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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 78%] Built target ctf_mask_test +[ 78%] Built target motion_refine 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= @@ -2107,59 +2140,56 @@ 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 +[ 78%] Built target project 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= +[ 79%] Linking CXX executable ../../bin/relion_particle_select 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 +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 make[4]: Entering directory '/build/relion-3.1.0/build' -[ 80%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o +/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 +[ 79%] 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 +[ 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' 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= +[ 80%] Built target particle_select +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 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 +Scanning dependencies of target run_ctffind +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/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build +[ 80%] 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 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 +[ 81%] 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 +/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 [ 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 +[ 82%] 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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 83%] Built target preprocess +[ 82%] 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= @@ -2167,44 +2197,47 @@ 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 +[ 83%] 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 +[ 83%] 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= +[ 83%] 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 Scanning dependencies of target estimate_gain 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/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 make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build +make[4]: Leaving directory '/build/relion-3.1.0/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 +[ 83%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o +[ 83%] Built target helix_toolbox 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 +[ 84%] Linking CXX executable ../../bin/relion_motion_refine_mpi 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/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 +[ 84%] 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 +/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 +[ 84%] 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 +[ 85%] 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 +[ 85%] 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' -[ 86%] Built target demodulate +[ 85%] Built target plot_delocalisation 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= @@ -2212,96 +2245,98 @@ 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 +[ 86%] 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 +[ 86%] Built target image_handler 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' 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 +[ 86%] Built target run_ctffind 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= +[ 86%] 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 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 +[ 87%] 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 +[ 88%] 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' +[ 88%] 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 +[ 88%] Built target motion_refine_mpi 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 +/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 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 +[ 88%] Built target particle_subtract +[ 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 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' +[ 89%] 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%] 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 +/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 +[ 90%] 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 +[ 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 demodulate [ 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 +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 90%] Built target reposition [ 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 +[ 91%] Built target particle_subtract_mpi +[ 91%] Built target reconstruct_mpi +[ 92%] 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 +[ 92%] 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 /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 +[ 93%] 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 [ 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 +[ 94%] 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' -[ 94%] Built target refine_mpi +[ 94%] Built target particle_reposition [ 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 +[ 95%] Built target refine_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target tiltpair_plot [ 95%] Linking CXX executable ../../bin/relion_estimate_gain @@ -2312,12 +2347,12 @@ [ 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 +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 95%] Built target scheduler [ 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 @@ -2327,46 +2362,51 @@ 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 -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend +make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/depend +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/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 +Scanning dependencies of target display 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 -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build 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 +Scanning dependencies of target manualpick +Scanning dependencies of target maingui 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]: 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/pipeliner.dir/pipeliner.cpp.o -[ 95%] Building CXX object src/apps/CMakeFiles/maingui.dir/maingui.cpp.o +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/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/display.dir/display.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/display.dir/display.cpp.o -c /build/relion-3.1.0/src/apps/display.cpp [ 95%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.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/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.0/src/apps/manualpick.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 [ 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 +[ 96%] 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' +[ 96%] Built target star_handler [ 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 @@ -2375,16 +2415,11 @@ /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 +[ 99%] Built target manualpick [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 @@ -2978,59 +3013,59 @@ -- 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_star_handler -- 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_refine_mpi -- 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_reconstruct_mpi +-- 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_particle_subtract_mpi +-- 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_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_image_handler -- 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_motion_refine_mpi -- 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_reconstruct +-- 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_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_align_symmetry -- 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_particle_FCC +-- 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_motion_refine -- 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_ctf_refine_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_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_convert_to_tiff_mpi -- 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_localsym -- 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_mrc2vtk -- 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_flex_analyse_mpi -- 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_autopick_mpi -- 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 @@ -3137,12 +3172,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3927487/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3927487/tmp/hooks/B01_cleanup finished 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 +I: removing directory /srv/workspace/pbuilder/3927487 and its subdirectories +I: Current time: Mon Feb 13 02:58:25 +14 2023 +I: pbuilder-time-stamp: 1676206705