Start: 2021-08-23 00:47:47 GMT [stable] Package: gromacs-mpich Source: gromacs Version: 2020.6-2 Installed-Size: 18083 Maintainer: Debichem Team Architecture: amd64 Depends: mpich, libc6 (>= 2.29), libfftw3-double3 (>= 3.3.5), libfftw3-single3 (>= 3.3.5), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libhwloc15 (>= 2.4.1+dfsg), libmpich12 (>= 3.4.1-3), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.0) Recommends: gromacs Suggests: gromacs-data Description: Molecular dynamics sim, binaries for MPICH parallelization Homepage: http://www.gromacs.org/ Description-md5: befd212127fab1c214923ce24592496e Tag: devel::lang:c, devel::library, field::biology, field::chemistry, implemented-in::c, interface::commandline, role::devel-lib, role::program, scope::utility, works-with::software:package Section: science Priority: optional Filename: pool/main/g/gromacs/gromacs-mpich_2020.6-2_amd64.deb Size: 6862540 MD5sum: ec9c30827099a6b9b244a20eb70fa65c SHA256: 809747788427c22d37e72fdc962e9ebc7e764bc9667754e15757603e29278363 [sid] Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt gromacs-mpich=None 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.4 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt gromacs-mpich=None 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp28u_2ws9 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp28u_2ws9 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/proc'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/pts'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/pts'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/console'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/console'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/shm'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/shm'] 0m1.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m1.7s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Created resolv.conf. 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp28u_2ws9/tmp/scripts/ 0m1.8s INFO: Running scripts post_chroot_unpack 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', 'update'] 0m2.8s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [113 kB] Fetched 113 kB in 0s (560 kB/s) Reading package lists... 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', 'update'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.5s DUMP: e5893bf5d89f83f99f0dc7018e11583b - 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.5s INFO: Running scripts post_setup 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.2s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_minimize'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_minimize'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.3s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+b3 install ok installed bsdutils bsdutils 1:2.36.1-8 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.9 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2 install ok installed grep grep 3.6-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13 install ok installed libc6:amd64 libc6 2.31-13 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.36.1-8 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9 install ok installed libpam-runtime libpam-runtime 1.4.0-9 install ok installed libpam0g:amd64 libpam0g 1.4.0-9 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1k-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-6 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2 install ok installed libtirpc-common libtirpc-common 1.3.1-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1 install ok installed libudev1:amd64 libudev1 247.3-6 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8 install ok installed ncurses-base ncurses-base 6.2+20201114-2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021a-1 install ok installed util-linux util-linux 2.36.1-8 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat 0m4.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m4.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m4.5s INFO: Running scripts is_testable 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s INFO: Running scripts pre_test 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_test_root_password'] 0m4.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_test_root_password'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-cache', 'show', '--no-all-versions', 'gromacs-mpich'] 0m4.7s DUMP: Package: gromacs-mpich Source: gromacs Version: 2020.6-2 Installed-Size: 18083 Maintainer: Debichem Team Architecture: amd64 Depends: mpich, libc6 (>= 2.29), libfftw3-double3 (>= 3.3.5), libfftw3-single3 (>= 3.3.5), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libhwloc15 (>= 2.4.1+dfsg), libmpich12 (>= 3.4.1-3), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.0) Recommends: gromacs Suggests: gromacs-data Description-en: Molecular dynamics sim, binaries for MPICH parallelization GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . This package contains only the core simulation engine with parallel support using the MPICH (v3) interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines. Description-md5: befd212127fab1c214923ce24592496e Homepage: http://www.gromacs.org/ Tag: devel::lang:c, devel::library, field::biology, field::chemistry, implemented-in::c, interface::commandline, role::devel-lib, role::program, scope::utility, works-with::software:package Section: science Priority: optional Filename: pool/main/g/gromacs/gromacs-mpich_2020.6-2_amd64.deb Size: 6862540 MD5sum: ec9c30827099a6b9b244a20eb70fa65c SHA256: 809747788427c22d37e72fdc962e9ebc7e764bc9667754e15757603e29278363 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-cache', 'show', '--no-all-versions', 'gromacs-mpich'] 0m4.7s INFO: apt-cache knows about the following packages: gromacs-mpich 0m4.7s INFO: Running scripts pre_install 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-cache', 'policy'] 0m4.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.0,o=Debian,a=stable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-cache', 'policy'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-cache', 'policy', 'gromacs-mpich'] 0m4.9s DUMP: gromacs-mpich: Installed: (none) Candidate: 2020.6-2 Version table: 2020.6-2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-cache', 'policy', 'gromacs-mpich'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', '-y', 'install', 'gromacs-mpich'] 0m6.9s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: hwloc-nox libfftw3-double3 libfftw3-single3 libgfortran5 libgomp1 libhwloc15 libmpich12 libquadmath0 libslurm36 mpich Suggested packages: gromacs-data libfftw3-bin libfftw3-dev libhwloc-contrib-plugins mpich-doc Recommended packages: gromacs libhwloc-plugins libmpich-dev The following NEW packages will be installed: gromacs-mpich hwloc-nox libfftw3-double3 libfftw3-single3 libgfortran5 libgomp1 libhwloc15 libmpich12 libquadmath0 libslurm36 mpich 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. Need to get 12.5 MB of archives. After this operation, 43.3 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 libhwloc15 amd64 2.4.1+dfsg-1 [150 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 hwloc-nox amd64 2.4.1+dfsg-1 [190 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 libmpich12 amd64 3.4.1-4 [1975 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libslurm36 amd64 20.11.7+really20.11.4-2 [666 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 mpich amd64 3.4.1-4 [219 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libfftw3-double3 amd64 3.3.8-2 [733 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libfftw3-single3 amd64 3.3.8-2 [762 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 gromacs-mpich amd64 2020.6-2 [6863 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.5 MB in 0s (84.4 MB/s) Selecting previously unselected package libhwloc15:amd64. (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 ... 6655 files and directories currently installed.) Preparing to unpack .../00-libhwloc15_2.4.1+dfsg-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.4.1+dfsg-1) ... Selecting previously unselected package hwloc-nox. Preparing to unpack .../01-hwloc-nox_2.4.1+dfsg-1_amd64.deb ... Unpacking hwloc-nox (2.4.1+dfsg-1) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../02-libquadmath0_10.2.1-6_amd64.deb ... Unpacking libquadmath0:amd64 (10.2.1-6) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../03-libgfortran5_10.2.1-6_amd64.deb ... Unpacking libgfortran5:amd64 (10.2.1-6) ... Selecting previously unselected package libmpich12:amd64. Preparing to unpack .../04-libmpich12_3.4.1-4_amd64.deb ... Unpacking libmpich12:amd64 (3.4.1-4) ... Selecting previously unselected package libslurm36. Preparing to unpack .../05-libslurm36_20.11.7+really20.11.4-2_amd64.deb ... Unpacking libslurm36 (20.11.7+really20.11.4-2) ... Selecting previously unselected package mpich. Preparing to unpack .../06-mpich_3.4.1-4_amd64.deb ... Unpacking mpich (3.4.1-4) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../07-libgomp1_10.2.1-6_amd64.deb ... Unpacking libgomp1:amd64 (10.2.1-6) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../08-libfftw3-double3_3.3.8-2_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.8-2) ... Selecting previously unselected package libfftw3-single3:amd64. Preparing to unpack .../09-libfftw3-single3_3.3.8-2_amd64.deb ... Unpacking libfftw3-single3:amd64 (3.3.8-2) ... Selecting previously unselected package gromacs-mpich. Preparing to unpack .../10-gromacs-mpich_2020.6-2_amd64.deb ... Unpacking gromacs-mpich (2020.6-2) ... Setting up libslurm36 (20.11.7+really20.11.4-2) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libquadmath0:amd64 (10.2.1-6) ... Setting up libhwloc15:amd64 (2.4.1+dfsg-1) ... Setting up libfftw3-double3:amd64 (3.3.8-2) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libmpich12:amd64 (3.4.1-4) ... Setting up libfftw3-single3:amd64 (3.3.8-2) ... Setting up hwloc-nox (2.4.1+dfsg-1) ... Setting up mpich (3.4.1-4) ... update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode Setting up gromacs-mpich (2020.6-2) ... update-alternatives: using /usr/bin/mdrun_mpi.mpich to provide /usr/bin/mdrun_mpi (mdrun_mpi) in auto mode Processing triggers for libc-bin (2.31-13) ... 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', '-y', 'install', 'gromacs-mpich'] 0m6.9s INFO: Running scripts post_install 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_install_exceptions'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_install_exceptions'] 0m6.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m7.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m7.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp28u_2ws9 to sid 0m7.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m7.3s INFO: Running scripts pre_distupgrade 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', 'update'] 0m10.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [165 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [8727 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6525 kB] Fetched 15.4 MB in 3s (5299 kB/s) Reading package lists... 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', 'update'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', '-yf', 'dist-upgrade'] 0m15.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-11-base The following packages will be upgraded: apt base-files bash bsdutils dash debianutils e2fsprogs gcc-9-base libapt-pkg6.0 libaudit-common libaudit1 libblkid1 libc-bin libc6 libcom-err2 libcrypt1 libext2fs2 libgcc-s1 libgfortran5 libgomp1 libgpg-error0 libidn2-0 libmount1 libmpich12 libquadmath0 libsmartcols1 libss2 libstdc++6 libsystemd0 libtirpc-common libtirpc3 libudev1 libunistring2 libuuid1 logsave mount mpich perl-base util-linux 39 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 18.3 MB of archives. After this operation, 873 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 12 [70.0 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.4-1 [93.3 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.1-3+b1 [1417 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.37.2-1 [149 kB] Get:5 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.11+git20210120+802ebd4-1 [116 kB] Get:6 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.32.1-5 [1629 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-11-base amd64 11.2.0-2 [204 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 11.2.0-2 [42.0 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.31-16 [2817 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.37.2-1 [201 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.37.2-1 [215 kB] Get:12 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.37.2-1 [1193 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 11.2.0-2 [576 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 247.9-1 [376 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 247.9-1 [167 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.3.8 [1020 kB] Get:17 http://deb.debian.org/debian sid/main amd64 apt amd64 2.3.8 [1498 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.31-16 [822 kB] Get:19 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.46.4-1 [75.9 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libext2fs2 amd64 1.46.4-1 [258 kB] Get:21 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.46.4-1 [619 kB] Get:22 http://deb.debian.org/debian sid/main amd64 mount amd64 2.37.2-1 [189 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.0.5-1 [15.7 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.0.5-1 [51.8 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.46.4-1 [75.2 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.25-1 [89.1 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.42-2 [79.1 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libunistring2 amd64 0.9.10-6 [384 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.2-2 [95.3 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.37.2-1 [161 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.2-2 [13.8 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.2-2 [83.9 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.37.2-1 [84.3 kB] Get:34 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.4.0-2 [200 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 11.2.0-2 [144 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 11.2.0-2 [710 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 11.2.0-2 [106 kB] Get:38 http://deb.debian.org/debian sid/main amd64 mpich amd64 3.4.1-5 [219 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libmpich12 amd64 3.4.1-5 [1976 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.46.4-1 [79.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.3 MB in 0s (90.9 MB/s) (Reading database ... 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(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 ... 6784 files and directories currently installed.) Preparing to unpack .../libudev1_247.9-1_amd64.deb ... Unpacking libudev1:amd64 (247.9-1) over (247.3-6) ... Setting up libudev1:amd64 (247.9-1) ... (Reading database ... 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(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 ... 6784 files and directories currently installed.) Preparing to unpack .../archives/apt_2.3.8_amd64.deb ... Unpacking apt (2.3.8) over (2.2.4) ... Setting up apt (2.3.8) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libc-bin_2.31-16_amd64.deb ... Unpacking libc-bin (2.31-16) over (2.31-13) ... Setting up libc-bin (2.31-16) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../logsave_1.46.4-1_amd64.deb ... Unpacking logsave (1.46.4-1) over (1.46.2-2) ... Preparing to unpack .../libext2fs2_1.46.4-1_amd64.deb ... Unpacking libext2fs2:amd64 (1.46.4-1) over (1.46.2-2) ... Setting up libext2fs2:amd64 (1.46.4-1) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.46.4-1_amd64.deb ... Unpacking e2fsprogs (1.46.4-1) over (1.46.2-2) ... Preparing to unpack .../mount_2.37.2-1_amd64.deb ... Unpacking mount (2.37.2-1) over (2.36.1-8) ... Preparing to unpack .../libaudit-common_1%3a3.0.5-1_all.deb ... Unpacking libaudit-common (1:3.0.5-1) over (1:3.0-2) ... Setting up libaudit-common (1:3.0.5-1) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.5-1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.0.5-1) over (1:3.0-2) ... Setting up libaudit1:amd64 (1:3.0.5-1) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libcom-err2_1.46.4-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.46.4-1) over (1.46.2-2) ... Setting up libcom-err2:amd64 (1.46.4-1) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.25-1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.25-1) over (1:4.4.18-4) ... Setting up libcrypt1:amd64 (1:4.4.25-1) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.42-2_amd64.deb ... Unpacking libgpg-error0:amd64 (1.42-2) over (1.38-2) ... Setting up libgpg-error0:amd64 (1.42-2) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-6_amd64.deb ... Unpacking libunistring2:amd64 (0.9.10-6) over (0.9.10-4) ... Setting up libunistring2:amd64 (0.9.10-6) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.2-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.2-2) over (2.3.0-5) ... Setting up libidn2-0:amd64 (2.3.2-2) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.37.2-1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.37.2-1) over (2.36.1-8) ... Setting up libsmartcols1:amd64 (2.37.2-1) ... (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 ... 6784 files and directories currently installed.) Preparing to unpack .../libtirpc-common_1.3.2-2_all.deb ... Unpacking libtirpc-common (1.3.2-2) over (1.3.1-1) ... Setting up libtirpc-common (1.3.2-2) ... (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 ... 6785 files and directories currently installed.) Preparing to unpack .../libtirpc3_1.3.2-2_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.2-2) over (1.3.1-1) ... Setting up libtirpc3:amd64 (1.3.2-2) ... (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 ... 6786 files and directories currently installed.) Preparing to unpack .../libuuid1_2.37.2-1_amd64.deb ... Unpacking libuuid1:amd64 (2.37.2-1) over (2.36.1-8) ... Setting up libuuid1:amd64 (2.37.2-1) ... (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 ... 6786 files and directories currently installed.) Preparing to unpack .../0-gcc-9-base_9.4.0-2_amd64.deb ... Unpacking gcc-9-base:amd64 (9.4.0-2) over (9.3.0-22) ... Preparing to unpack .../1-libquadmath0_11.2.0-2_amd64.deb ... Unpacking libquadmath0:amd64 (11.2.0-2) over (10.2.1-6) ... Preparing to unpack .../2-libgfortran5_11.2.0-2_amd64.deb ... Unpacking libgfortran5:amd64 (11.2.0-2) over (10.2.1-6) ... Preparing to unpack .../3-libgomp1_11.2.0-2_amd64.deb ... Unpacking libgomp1:amd64 (11.2.0-2) over (10.2.1-6) ... Preparing to unpack .../4-mpich_3.4.1-5_amd64.deb ... Unpacking mpich (3.4.1-5) over (3.4.1-4) ... Preparing to unpack .../5-libmpich12_3.4.1-5_amd64.deb ... Unpacking libmpich12:amd64 (3.4.1-5) over (3.4.1-4) ... Preparing to unpack .../6-libss2_1.46.4-1_amd64.deb ... Unpacking libss2:amd64 (1.46.4-1) over (1.46.2-2) ... Setting up libgomp1:amd64 (11.2.0-2) ... Setting up libquadmath0:amd64 (11.2.0-2) ... Setting up libss2:amd64 (1.46.4-1) ... Setting up logsave (1.46.4-1) ... Setting up libgfortran5:amd64 (11.2.0-2) ... Setting up mount (2.37.2-1) ... Setting up libmpich12:amd64 (3.4.1-5) ... Setting up gcc-9-base:amd64 (9.4.0-2) ... Setting up mpich (3.4.1-5) ... Setting up e2fsprogs (1.46.4-1) ... Installing new version of config file /etc/mke2fs.conf ... Processing triggers for libc-bin (2.31-16) ... 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', '-yf', 'dist-upgrade'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.5s DUMP: a5665fec0577b32052ded8a85a9070fc - 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-cache', 'show', '--no-all-versions', 'gromacs-mpich'] 0m16.7s DUMP: Package: gromacs-mpich Status: install ok installed Priority: optional Section: science Installed-Size: 18083 Maintainer: Debichem Team Architecture: amd64 Source: gromacs Version: 2020.6-2 Depends: mpich, libc6 (>= 2.29), libfftw3-double3 (>= 3.3.5), libfftw3-single3 (>= 3.3.5), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libhwloc15 (>= 2.4.1+dfsg), libmpich12 (>= 3.4.1-3), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.0) Recommends: gromacs Suggests: gromacs-data Description: Molecular dynamics sim, binaries for MPICH parallelization GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . This package contains only the core simulation engine with parallel support using the MPICH (v3) interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines. Description-md5: befd212127fab1c214923ce24592496e Homepage: http://www.gromacs.org/ 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-cache', 'show', '--no-all-versions', 'gromacs-mpich'] 0m16.7s INFO: apt-cache does not know about any of the requested packages 0m16.7s INFO: Running scripts post_distupgrade 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m17.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m17.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m17.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m17.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m17.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m17.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', '-ac', '--ignore-obsolete'] 0m18.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', '-ac', '--ignore-obsolete'] 0m18.3s INFO: Running scripts pre_remove 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_exceptions'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/pre_remove_exceptions'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.2s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.3.8 install ok installed base-files base-files 12 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-3+b1 install ok installed bsdutils bsdutils 1:2.37.2-1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20210120+802ebd4-1 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.4-1 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.9 install ok installed e2fsprogs e2fsprogs 1.46.4-1 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-11-base:amd64 gcc-11-base 11.2.0-2 install ok installed gcc-9-base:amd64 gcc-9-base 9.4.0-2 install ok installed gpgv gpgv 2.2.27-2 install ok installed grep grep 3.6-1 install ok installed gromacs-mpich gromacs-mpich 2020.6-2 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed hwloc-nox hwloc-nox 2.4.1+dfsg-1 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.3.8 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0.5-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.5-1 install ok installed libblkid1:amd64 libblkid1 2.37.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-16 install ok installed libc6:amd64 libc6 2.31-16 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.4-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.25-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.4-1 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libfftw3-double3:amd64 libfftw3-double3 3.3.8-2 install ok installed libfftw3-single3:amd64 libfftw3-single3 3.3.8-2 install ok installed libgcc-s1:amd64 libgcc-s1 11.2.0-2 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgfortran5:amd64 libgfortran5 11.2.0-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5 install ok installed libgomp1:amd64 libgomp1 11.2.0-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.42-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libhwloc15:amd64 libhwloc15 2.4.1+dfsg-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.37.2-1 install ok installed libmpich12:amd64 libmpich12 3.4.1-5 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9 install ok installed libpam-runtime libpam-runtime 1.4.0-9 install ok installed libpam0g:amd64 libpam0g 1.4.0-9 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libquadmath0:amd64 libquadmath0 11.2.0-2 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libslurm36 libslurm36 20.11.7+really20.11.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.37.2-1 install ok installed libss2:amd64 libss2 1.46.4-1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1k-1 install ok installed libstdc++6:amd64 libstdc++6 11.2.0-2 install ok installed libsystemd0:amd64 libsystemd0 247.9-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 247.9-1 install ok installed libunistring2:amd64 libunistring2 0.9.10-6 install ok installed libuuid1:amd64 libuuid1 2.37.2-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.4-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.37.2-1 install ok installed mpich mpich 3.4.1-5 install ok installed ncurses-base ncurses-base 6.2+20201114-2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-5 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021a-1 install ok installed util-linux util-linux 2.37.2-1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', 'remove', 'hwloc-nox', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libhwloc15:amd64', 'libmpich12:amd64', 'libquadmath0:amd64', 'libslurm36', 'mpich', 'gromacs-mpich'] 0m19.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: gromacs-mpich hwloc-nox libfftw3-double3 libfftw3-single3 libgfortran5 libgomp1 libhwloc15 libmpich12 libquadmath0 libslurm36 mpich 0 upgraded, 0 newly installed, 11 to remove and 0 not upgraded. After this operation, 43.3 MB disk space will be freed. (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 ... 6786 files and directories currently installed.) Removing gromacs-mpich (2020.6-2) ... Removing mpich (3.4.1-5) ... Removing hwloc-nox (2.4.1+dfsg-1) ... Removing libfftw3-double3:amd64 (3.3.8-2) ... Removing libfftw3-single3:amd64 (3.3.8-2) ... Removing libmpich12:amd64 (3.4.1-5) ... Removing libgfortran5:amd64 (11.2.0-2) ... Removing libgomp1:amd64 (11.2.0-2) ... Removing libhwloc15:amd64 (2.4.1+dfsg-1) ... Removing libquadmath0:amd64 (11.2.0-2) ... Removing libslurm36 (20.11.7+really20.11.4-2) ... Processing triggers for libc-bin (2.31-16) ... 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', 'remove', 'hwloc-nox', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libhwloc15:amd64', 'libmpich12:amd64', 'libquadmath0:amd64', 'libslurm36', 'mpich', 'gromacs-mpich'] 0m19.9s INFO: Running scripts post_remove 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_remove_exceptions'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_remove_exceptions'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg', '--purge', 'hwloc-nox', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libhwloc15:amd64', 'libmpich12:amd64', 'libquadmath0:amd64', 'libslurm36', 'mpich'] 0m19.9s DUMP: dpkg: warning: ignoring request to remove hwloc-nox which isn't installed dpkg: warning: ignoring request to remove libfftw3-double3 which isn't installed dpkg: warning: ignoring request to remove libfftw3-single3 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libhwloc15 which isn't installed dpkg: warning: ignoring request to remove libmpich12 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libslurm36 which isn't installed dpkg: warning: ignoring request to remove mpich which isn't installed 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg', '--purge', 'hwloc-nox', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libhwloc15:amd64', 'libmpich12:amd64', 'libquadmath0:amd64', 'libslurm36', 'mpich'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg', '--purge', 'gromacs-mpich'] 0m20.0s DUMP: dpkg: warning: ignoring request to remove gromacs-mpich which isn't installed 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg', '--purge', 'gromacs-mpich'] 0m20.0s INFO: Running scripts post_purge 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_purge_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_purge_exceptions'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg', '--purge', '--pending'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg', '--purge', '--pending'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg', '--remove', '--pending'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg', '--remove', '--pending'] 0m20.0s INFO: Running scripts post_test 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_test_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'tmp/scripts/post_test_exceptions'] 0m20.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m20.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg-divert', '--list'] 0m20.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'dpkg-divert', '--list'] 0m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', 'clean'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9', 'apt-get', 'clean'] 0m20.4s DEBUG: Recording chroot state 0m21.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/shm'] 0m21.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/shm'] 0m21.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/console'] 0m21.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/console'] 0m21.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/ptmx'] 0m21.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/ptmx'] 0m21.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/pts'] 0m21.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/dev/pts'] 0m21.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/proc'] 0m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9/proc'] 0m21.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m21.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp28u_2ws9'] 0m21.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp28u_2ws9 0m21.2s INFO: PASS: Upgrading between Debian distributions. 0m21.2s INFO: PASS: All tests. 0m21.2s INFO: piuparts run ends. ret=0 End: 2021-08-23 00:48:08 GMT