Start: 2025-03-12 22:30:18 GMT
[testing]
Package: gromacs
Version: 2025.0-2
Installed-Size: 461
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Architecture: amd64
Replaces: gromacs-mpi (<< 2022~), gromacs-mpich (<< 2021.1-2), gromacs-openmpi (<< 2021.1-2)
Depends: gromacs-data (= 2025.0-2), sse4.2-support, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgromacs10 (>= 2025.0), libopenmpi40 (>= 5.0.6), libstdc++6 (>= 11)
Recommends: cpp, mpi-default-bin
Suggests: pymol
Breaks: gromacs-mpi (<< 2022~), gromacs-mpich (<< 2021.1-2), gromacs-openmpi (<< 2021.1-2)
Description: Molecular dynamics simulator, with building and analysis tools
Homepage: https://www.gromacs.org/
Description-md5: b2bae23de6e584a47799dd4899a2c30a
Tag: field::biology, field::biology:structural, field::chemistry,
implemented-in::c, interface::commandline, interface::graphical,
interface::x11, role::program, uitoolkit::xlib, x11::application
Section: science
Priority: optional
Filename: pool/main/g/gromacs/gromacs_2025.0-2_amd64.deb
Size: 60800
MD5sum: 5a568714f012b44e68f8c947a1e93dc7
SHA256: e55d4ccfb76afa17620b3de08d736fcceb6c28261238fd3ce574aef49be50ede
[sid]
Package: gromacs
Version: 2025.1-1
Installed-Size: 461
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Architecture: amd64
Replaces: gromacs-mpi (<< 2022~), gromacs-mpich (<< 2021.1-2), gromacs-openmpi (<< 2021.1-2)
Depends: gromacs-data (= 2025.1-1), sse4.2-support, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgromacs10 (>= 2025.1), libopenmpi40 (>= 5.0.7), libstdc++6 (>= 11)
Recommends: cpp, mpi-default-bin
Suggests: pymol
Breaks: gromacs-mpi (<< 2022~), gromacs-mpich (<< 2021.1-2), gromacs-openmpi (<< 2021.1-2)
Description: Molecular dynamics simulator, with building and analysis tools
Homepage: https://www.gromacs.org/
Description-md5: b2bae23de6e584a47799dd4899a2c30a
Tag: field::biology, field::biology:structural, field::chemistry,
implemented-in::c, interface::commandline, interface::graphical,
interface::x11, role::program, uitoolkit::xlib, x11::application
Section: science
Priority: optional
Filename: pool/main/g/gromacs/gromacs_2025.1-1_amd64.deb
Size: 60604
MD5sum: eff6000bdf1e680ba73071b9279b28b9
SHA256: 82f847d8cde496860756ad0fe7c1e1fd1b56089e030829316b0dfd0ebff81f18
Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt gromacs=2025.1-1
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 1.5.2~202503032318~1.5.1-8-g1db83cba starting up.
0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt gromacs=2025.1-1
0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64
0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp1u7heu7i
0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp1u7heu7i
0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz']
0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz']
0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/proc']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/proc']
0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/pts']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/pts']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/ptmx']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/ptmx']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/console']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/console']
0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/shm']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/shm']
0m0.4s DEBUG: sources.list:
deb http://deb.debian.org/debian/ trixie main
0m0.5s DEBUG: Created policy-rc.d and chmodded it.
0m0.5s DEBUG: Created resolv.conf.
0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp1u7heu7i/tmp/scripts/
0m0.5s INFO: Running scripts post_chroot_unpack
0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', 'update']
0m3.0s DUMP:
Get:1 http://deb.debian.org/debian trixie InRelease [175 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9529 kB]
Get:3 http://deb.debian.org/debian trixie/main Translation-en [6390 kB]
Fetched 16.1 MB in 2s (9495 kB/s)
Reading package lists...
0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', 'update']
0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-yf', 'dist-upgrade']
0m5.3s DUMP:
Reading package lists...
Building dependency tree...
Calculating upgrade...
The following packages will be upgraded:
apt base-files libapt-pkg7.0 libc-bin libc6 libsystemd0 libtinfo6 libudev1
ncurses-base ncurses-bin
10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 7757 kB of archives.
After this operation, 89.1 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.41-4 [2843 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.41-4 [635 kB]
Get:3 http://deb.debian.org/debian trixie/main amd64 base-files amd64 13.7 [73.0 kB]
Get:4 http://deb.debian.org/debian trixie/main amd64 ncurses-bin amd64 6.5+20250216-2 [438 kB]
Get:5 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 257.4-1 [451 kB]
Get:6 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 257.4-1 [149 kB]
Get:7 http://deb.debian.org/debian trixie/main amd64 libapt-pkg7.0 amd64 2.9.31 [1105 kB]
Get:8 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.31 [1441 kB]
Get:9 http://deb.debian.org/debian trixie/main amd64 ncurses-base all 6.5+20250216-2 [273 kB]
Get:10 http://deb.debian.org/debian trixie/main amd64 libtinfo6 amd64 6.5+20250216-2 [348 kB]
Preconfiguring packages ...
Fetched 7757 kB in 0s (92.7 MB/s)
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Preparing to unpack .../libc6_2.41-4_amd64.deb ...
Unpacking libc6:amd64 (2.41-4) over (2.40-7) ...
Setting up libc6:amd64 (2.41-4) ...
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Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ...
Setting up ncurses-base (6.5+20250216-2) ...
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Preparing to unpack .../libtinfo6_6.5+20250216-2_amd64.deb ...
Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ...
Setting up libtinfo6:amd64 (6.5+20250216-2) ...
Processing triggers for libc-bin (2.41-4) ...
0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-yf', 'dist-upgrade']
0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m6.4s DUMP:
c2592d2267999fac018763d04a49a513 -
0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m6.4s INFO: Running scripts post_setup
0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_dummy_users']
0m7.1s DUMP:
useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999
useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999
useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999
useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999
useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999
useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999
useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999
useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999
useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999
useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999
useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999
0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_dummy_users']
0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_forbid_home']
0m7.1s DUMP:
Disabling /home
Adding 'local diversion of /home to /home.distrib'
0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_forbid_home']
0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_force-unsafe-io']
0m7.1s DUMP:
Enabling dpkg --force-unsafe-io.
Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib'
Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged'
'/bin/sync' -> 'true'
0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_force-unsafe-io']
0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_minimize']
0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_minimize']
0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_squeeze-backports']
0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_squeeze-backports']
0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_zz_backports']
0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_setup_zz_backports']
0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m7.2s DUMP:
install ok installed apt apt 2.9.31
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.6
install ok installed bash bash 5.2.37-1.1
install ok installed bsdutils bsdutils 1:2.40.4-5
install ok installed coreutils coreutils 9.5-1+b1
install ok installed dash dash 0.5.12-12
install ok installed debconf debconf 1.5.89
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-2
install ok installed dpkg dpkg 1.22.15
install ok installed findutils findutils 4.10.0-3
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-17
install ok installed grep grep 3.11-4
install ok installed gzip gzip 1.13-1
install ok installed hostname hostname 3.25
install ok installed init-system-helpers init-system-helpers 1.68
install ok installed libacl1:amd64 libacl1 2.3.2-2+b1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.31
install ok installed libattr1:amd64 libattr1 1:2.5.2-3
install ok installed libaudit-common libaudit-common 1:4.0.2-2
install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2
install ok installed libblkid1:amd64 libblkid1 2.40.4-5
install ok installed libbsd0:amd64 libbsd0 0.12.2-2
install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6
install ok installed libc-bin libc-bin 2.41-4
install ok installed libc6:amd64 libc6 2.41-4
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.66-5+b1
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-17
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3
install ok installed liblzma5:amd64 liblzma5 5.6.4-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.40.4-5
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3
install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3
install ok installed libpam-runtime libpam-runtime 1.7.0-3
install ok installed libpam0g:amd64 libpam0g 1.7.0-3
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1
install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2+b1
install ok installed libselinux1:amd64 libselinux1 3.8-4
install ok installed libsemanage-common libsemanage-common 3.8-1
install ok installed libsemanage2:amd64 libsemanage2 3.8-1+b1
install ok installed libsepol2:amd64 libsepol2 3.8-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5
install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-17
install ok installed libsystemd0:amd64 libsystemd0 257.4-1
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libudev1:amd64 libudev1 257.4-1
install ok installed libuuid1:amd64 libuuid1 2.40.4-5
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2
install ok installed login login 1:4.16.0-2+really2.40.4-5
install ok installed login.defs login.defs 1:4.17.3-1
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed mount mount 2.40.4-5
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1
install ok installed passwd passwd 1:4.17.3-1
install ok installed perl-base perl-base 5.40.1-2
install ok installed sed sed 4.9-2
install ok installed sqv sqv 1.2.1-6+b1
install ok installed sysvinit-utils sysvinit-utils 3.14-3
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025a-2
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.40.4-5
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m7.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat
0m7.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m7.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m7.7s INFO: Running scripts is_testable
0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/is_testable_uninstallable']
0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/is_testable_uninstallable']
0m7.7s INFO: Running scripts pre_test
0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_test_exceptions']
0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_test_exceptions']
0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_test_root_password']
0m7.7s DUMP:
New password: Retype new password: passwd: password updated successfully
0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_test_root_password']
0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'show', '--no-all-versions', 'gromacs']
0m7.9s DUMP:
Package: gromacs
Version: 2025.0-2
Installed-Size: 461
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Architecture: amd64
Replaces: gromacs-mpi (<< 2022~), gromacs-mpich (<< 2021.1-2), gromacs-openmpi (<< 2021.1-2)
Depends: gromacs-data (= 2025.0-2), sse4.2-support, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgromacs10 (>= 2025.0), libopenmpi40 (>= 5.0.6), libstdc++6 (>= 11)
Recommends: cpp, mpi-default-bin
Suggests: pymol
Breaks: gromacs-mpi (<< 2022~), gromacs-mpich (<< 2021.1-2), gromacs-openmpi (<< 2021.1-2)
Description-en: Molecular dynamics simulator, with building and analysis tools
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 variants both for execution on a single machine, and
using the MPI interface across multiple machines.
Description-md5: b2bae23de6e584a47799dd4899a2c30a
Homepage: https://www.gromacs.org/
Tag: field::biology, field::biology:structural, field::chemistry,
implemented-in::c, interface::commandline, interface::graphical,
interface::x11, role::program, uitoolkit::xlib, x11::application
Section: science
Priority: optional
Filename: pool/main/g/gromacs/gromacs_2025.0-2_amd64.deb
Size: 60800
MD5sum: 5a568714f012b44e68f8c947a1e93dc7
SHA256: e55d4ccfb76afa17620b3de08d736fcceb6c28261238fd3ce574aef49be50ede
0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'show', '--no-all-versions', 'gromacs']
0m7.9s INFO: apt-cache knows about the following packages: gromacs
0m7.9s INFO: Running scripts pre_install
0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_database-server']
0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_database-server']
0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_exceptions']
0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_exceptions']
0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_extras']
0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_extras']
0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture']
0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture']
0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy']
0m8.0s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian trixie/main amd64 Packages
release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy']
0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy', 'gromacs']
0m8.1s DUMP:
gromacs:
Installed: (none)
Candidate: 2025.0-2
Version table:
2025.0-2 500
500 http://deb.debian.org/debian trixie/main amd64 Packages
0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy', 'gromacs']
0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-y', 'install', 'gromacs']
0m21.7s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
adduser fonts-mathjax gromacs-data ibverbs-providers isa-support
libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libdrm-amdgpu1 libdrm-common
libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64
libevent-pthreads-2.1-7t64 libfabric1 libffi8 libfftw3-double3
libfftw3-single3 libfuse3-3 libgfortran5 libgomp1 libgromacs10
libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5
libibumad3 libibverbs1 libicu72 libjs-mathjax liblapack3 libllvm17t64
libmunge2 libmuparser2v5 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi40
libpciaccess0 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libucx0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0
libz3-4 ocl-icd-libopencl1 sse4.2-support
Suggested packages:
liblocale-gettext-perl perl cron quota pymol libfftw3-bin libfftw3-dev fuse3
libhwloc-contrib-plugins fonts-mathjax-extras fonts-stix libjs-mathjax-doc
pciutils opencl-icd
Recommended packages:
cpp mpi-default-bin
The following NEW packages will be installed:
adduser fonts-mathjax gromacs gromacs-data ibverbs-providers isa-support
libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libdrm-amdgpu1 libdrm-common
libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64
libevent-pthreads-2.1-7t64 libfabric1 libffi8 libfftw3-double3
libfftw3-single3 libfuse3-3 libgfortran5 libgomp1 libgromacs10
libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5
libibumad3 libibverbs1 libicu72 libjs-mathjax liblapack3 libllvm17t64
libmunge2 libmuparser2v5 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi40
libpciaccess0 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libucx0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0
libz3-4 ocl-icd-libopencl1 sse4.2-support
0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded.
Need to get 166 MB of archives.
After this operation, 813 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian trixie/main amd64 isa-support amd64 26 [15.0 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 sse4.2-support amd64 26 [3492 B]
Get:3 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB]
Get:4 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get:5 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get:6 http://deb.debian.org/debian trixie/main amd64 gromacs-data all 2025.0-2 [46.0 MB]
Get:7 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get:8 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-17 [137 kB]
Get:9 http://deb.debian.org/debian trixie/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB]
Get:10 http://deb.debian.org/debian trixie/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB]
Get:11 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB]
Get:12 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get:13 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get:14 http://deb.debian.org/debian trixie/main amd64 libmuparser2v5 amd64 2.3.4-1+b1 [149 kB]
Get:15 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB]
Get:16 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB]
Get:17 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB]
Get:18 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB]
Get:19 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 55.0-1 [62.2 kB]
Get:20 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 55.0-1 [351 kB]
Get:21 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-17 [9316 B]
Get:22 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB]
Get:23 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB]
Get:24 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB]
Get:25 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 55.0-1 [70.2 kB]
Get:26 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB]
Get:27 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB]
Get:28 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB]
Get:29 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get:30 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get:31 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get:32 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get:33 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get:34 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get:35 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get:36 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get:37 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB]
Get:38 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB]
Get:39 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.12.0-1 [18.1 kB]
Get:40 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.6-5 [651 kB]
Get:41 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB]
Get:42 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get:43 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get:44 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-21 [23.6 MB]
Get:45 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB]
Get:46 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.124-1 [8180 B]
Get:47 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.124-1 [38.9 kB]
Get:48 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.124-1 [22.4 kB]
Get:49 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get:50 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB]
Get:51 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB]
Get:52 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-5+b1 [8882 kB]
Get:53 http://deb.debian.org/debian trixie/main amd64 libfuse3-3 amd64 3.14.0-10 [89.7 kB]
Get:54 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 55.0-1 [28.5 kB]
Get:55 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 55.0-1 [43.3 kB]
Get:56 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.18.1+ds-1 [1197 kB]
Get:57 http://deb.debian.org/debian trixie/main amd64 libopenmpi40 amd64 5.0.7-1 [2365 kB]
Get:58 http://deb.debian.org/debian trixie/main amd64 libgromacs10 amd64 2025.0-2 [33.1 MB]
Get:59 http://deb.debian.org/debian trixie/main amd64 gromacs amd64 2025.0-2 [60.8 kB]
Preconfiguring packages ...
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Unpacking libgfortran5:amd64 (14.2.0-17) ...
Selecting previously unselected package liblapack3:amd64.
Preparing to unpack .../09-liblapack3_3.12.1-2_amd64.deb ...
Unpacking liblapack3:amd64 (3.12.1-2) ...
Selecting previously unselected package libmuparser2v5:amd64.
Preparing to unpack .../10-libmuparser2v5_2.3.4-1+b1_amd64.deb ...
Unpacking libmuparser2v5:amd64 (2.3.4-1+b1) ...
Selecting previously unselected package libevent-core-2.1-7t64:amd64.
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Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64.
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Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Selecting previously unselected package libnl-3-200:amd64.
Preparing to unpack .../13-libnl-3-200_3.7.0-0.3+b1_amd64.deb ...
Unpacking libnl-3-200:amd64 (3.7.0-0.3+b1) ...
Selecting previously unselected package libnl-route-3-200:amd64.
Preparing to unpack .../14-libnl-route-3-200_3.7.0-0.3+b1_amd64.deb ...
Unpacking libnl-route-3-200:amd64 (3.7.0-0.3+b1) ...
Selecting previously unselected package libibverbs1:amd64.
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Unpacking libibverbs1:amd64 (55.0-1) ...
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Unpacking ibverbs-providers:amd64 (55.0-1) ...
Selecting previously unselected package libatomic1:amd64.
Preparing to unpack .../17-libatomic1_14.2.0-17_amd64.deb ...
Unpacking libatomic1:amd64 (14.2.0-17) ...
Selecting previously unselected package libpsm-infinipath1.
Preparing to unpack .../18-libpsm-infinipath1_3.3+20.604758e7-6.3_amd64.deb ...
Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) ...
Selecting previously unselected package libnuma1:amd64.
Preparing to unpack .../19-libnuma1_2.0.18-1+b1_amd64.deb ...
Unpacking libnuma1:amd64 (2.0.18-1+b1) ...
Selecting previously unselected package libpsm2-2.
Preparing to unpack .../20-libpsm2-2_11.2.185-2.1_amd64.deb ...
Unpacking libpsm2-2 (11.2.185-2.1) ...
Selecting previously unselected package librdmacm1t64:amd64.
Preparing to unpack .../21-librdmacm1t64_55.0-1_amd64.deb ...
Unpacking librdmacm1t64:amd64 (55.0-1) ...
Selecting previously unselected package libfabric1:amd64.
Preparing to unpack .../22-libfabric1_1.17.0-3.1_amd64.deb ...
Unpacking libfabric1:amd64 (1.17.0-3.1) ...
Selecting previously unselected package libmunge2:amd64.
Preparing to unpack .../23-libmunge2_0.5.16-1_amd64.deb ...
Unpacking libmunge2:amd64 (0.5.16-1) ...
Selecting previously unselected package libpciaccess0:amd64.
Preparing to unpack .../24-libpciaccess0_0.17-3+b3_amd64.deb ...
Unpacking libpciaccess0:amd64 (0.17-3+b3) ...
Selecting previously unselected package libxau6:amd64.
Preparing to unpack .../25-libxau6_1%3a1.0.11-1_amd64.deb ...
Unpacking libxau6:amd64 (1:1.0.11-1) ...
Selecting previously unselected package libxdmcp6:amd64.
Preparing to unpack .../26-libxdmcp6_1%3a1.1.5-1_amd64.deb ...
Unpacking libxdmcp6:amd64 (1:1.1.5-1) ...
Selecting previously unselected package libxcb1:amd64.
Preparing to unpack .../27-libxcb1_1.17.0-2+b1_amd64.deb ...
Unpacking libxcb1:amd64 (1.17.0-2+b1) ...
Selecting previously unselected package libx11-data.
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Unpacking libx11-data (2:1.8.10-2) ...
Selecting previously unselected package libx11-6:amd64.
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Unpacking libx11-6:amd64 (2:1.8.10-2) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../30-libicu72_72.1-6_amd64.deb ...
Unpacking libicu72:amd64 (72.1-6) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../31-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_amd64.deb ...
Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Selecting previously unselected package libxext6:amd64.
Preparing to unpack .../32-libxext6_2%3a1.3.4-1+b3_amd64.deb ...
Unpacking libxext6:amd64 (2:1.3.4-1+b3) ...
Selecting previously unselected package libxnvctrl0:amd64.
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Unpacking libxnvctrl0:amd64 (535.171.04-1+b2) ...
Selecting previously unselected package ocl-icd-libopencl1:amd64.
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Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ...
Selecting previously unselected package libhwloc-plugins:amd64.
Preparing to unpack .../35-libhwloc-plugins_2.12.0-1_amd64.deb ...
Unpacking libhwloc-plugins:amd64 (2.12.0-1) ...
Selecting previously unselected package libpmix2t64:amd64.
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Unpacking libpmix2t64:amd64 (5.0.6-5) ...
Selecting previously unselected package libedit2:amd64.
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Unpacking libedit2:amd64 (3.1-20250104-1) ...
Selecting previously unselected package libffi8:amd64.
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Unpacking libffi8:amd64 (3.4.7-1) ...
Selecting previously unselected package libz3-4:amd64.
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Unpacking libz3-4:amd64 (4.13.3-1) ...
Selecting previously unselected package libllvm17t64:amd64.
Preparing to unpack .../40-libllvm17t64_1%3a17.0.6-21_amd64.deb ...
Unpacking libllvm17t64:amd64 (1:17.0.6-21) ...
Selecting previously unselected package libamd-comgr2:amd64.
Preparing to unpack .../41-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2_amd64.deb ...
Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ...
Selecting previously unselected package libdrm-common.
Preparing to unpack .../42-libdrm-common_2.4.124-1_all.deb ...
Unpacking libdrm-common (2.4.124-1) ...
Selecting previously unselected package libdrm2:amd64.
Preparing to unpack .../43-libdrm2_2.4.124-1_amd64.deb ...
Unpacking libdrm2:amd64 (2.4.124-1) ...
Selecting previously unselected package libdrm-amdgpu1:amd64.
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Unpacking libdrm-amdgpu1:amd64 (2.4.124-1) ...
Selecting previously unselected package libelf1t64:amd64.
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Unpacking libelf1t64:amd64 (0.192-4) ...
Selecting previously unselected package libhsakmt1:amd64.
Preparing to unpack .../46-libhsakmt1_6.2.4+ds-1_amd64.deb ...
Unpacking libhsakmt1:amd64 (6.2.4+ds-1) ...
Selecting previously unselected package libhsa-runtime64-1:amd64.
Preparing to unpack .../47-libhsa-runtime64-1_6.1.2-3_amd64.deb ...
Unpacking libhsa-runtime64-1:amd64 (6.1.2-3) ...
Selecting previously unselected package libamdhip64-5.
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Unpacking libamdhip64-5 (5.7.1-5+b1) ...
Selecting previously unselected package libfuse3-3:amd64.
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Unpacking libfuse3-3:amd64 (3.14.0-10) ...
Selecting previously unselected package libibumad3:amd64.
Preparing to unpack .../50-libibumad3_55.0-1_amd64.deb ...
Unpacking libibumad3:amd64 (55.0-1) ...
Selecting previously unselected package libibmad5:amd64.
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Unpacking libibmad5:amd64 (55.0-1) ...
Selecting previously unselected package libucx0:amd64.
Preparing to unpack .../52-libucx0_1.18.1+ds-1_amd64.deb ...
Unpacking libucx0:amd64 (1.18.1+ds-1) ...
Selecting previously unselected package libopenmpi40:amd64.
Preparing to unpack .../53-libopenmpi40_5.0.7-1_amd64.deb ...
Unpacking libopenmpi40:amd64 (5.0.7-1) ...
Selecting previously unselected package libgromacs10:amd64.
Preparing to unpack .../54-libgromacs10_2025.0-2_amd64.deb ...
Unpacking libgromacs10:amd64 (2025.0-2) ...
Selecting previously unselected package gromacs.
Preparing to unpack .../55-gromacs_2025.0-2_amd64.deb ...
Unpacking gromacs (2025.0-2) ...
Setting up libpciaccess0:amd64 (0.17-3+b3) ...
Setting up libxau6:amd64 (1:1.0.11-1) ...
Setting up libxdmcp6:amd64 (1:1.1.5-1) ...
Setting up libxcb1:amd64 (1.17.0-2+b1) ...
Setting up fonts-mathjax (2.7.9+dfsg-1) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up libjs-mathjax (2.7.9+dfsg-1) ...
Setting up libedit2:amd64 (3.1-20250104-1) ...
Setting up libibumad3:amd64 (55.0-1) ...
Setting up libibmad5:amd64 (55.0-1) ...
Setting up libgomp1:amd64 (14.2.0-17) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up libz3-4:amd64 (4.13.3-1) ...
Setting up libblas3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libmunge2:amd64 (0.5.16-1) ...
Setting up libx11-data (2:1.8.10-2) ...
Setting up libhwloc15:amd64 (2.12.0-1) ...
Setting up libatomic1:amd64 (14.2.0-17) ...
Setting up libfuse3-3:amd64 (3.14.0-10) ...
Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ...
Setting up libgfortran5:amd64 (14.2.0-17) ...
Setting up libffi8:amd64 (3.4.7-1) ...
Setting up libnuma1:amd64 (2.0.18-1+b1) ...
Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ...
Setting up sse4.2-support (26) ...
Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ...
Setting up libpsm2-2 (11.2.185-2.1) ...
Setting up libx11-6:amd64 (2:1.8.10-2) ...
Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ...
update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode
Setting up libmuparser2v5:amd64 (2.3.4-1+b1) ...
Setting up libdrm-common (2.4.124-1) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up gromacs-data (2025.0-2) ...
Setting up liblapack3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up libfftw3-single3:amd64 (3.3.10-2+b1) ...
Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b3) ...
Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ...
Setting up libxnvctrl0:amd64 (535.171.04-1+b2) ...
Setting up libllvm17t64:amd64 (1:17.0.6-21) ...
Setting up libdrm2:amd64 (2.4.124-1) ...
Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ...
Setting up libdrm-amdgpu1:amd64 (2.4.124-1) ...
Setting up libibverbs1:amd64 (55.0-1) ...
Setting up ibverbs-providers:amd64 (55.0-1) ...
Setting up libhwloc-plugins:amd64 (2.12.0-1) ...
Setting up libpmix2t64:amd64 (5.0.6-5) ...
Setting up librdmacm1t64:amd64 (55.0-1) ...
Setting up libhsakmt1:amd64 (6.2.4+ds-1) ...
Setting up libfabric1:amd64 (1.17.0-3.1) ...
Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ...
Setting up libamdhip64-5 (5.7.1-5+b1) ...
Setting up libucx0:amd64 (1.18.1+ds-1) ...
Setting up libopenmpi40:amd64 (5.0.7-1) ...
Setting up libgromacs10:amd64 (2025.0-2) ...
Setting up gromacs (2025.0-2) ...
Processing triggers for libc-bin (2.41-4) ...
0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-y', 'install', 'gromacs']
0m21.7s INFO: Running scripts post_install
0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_install_exceptions']
0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_install_exceptions']
0m21.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m23.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m23.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp1u7heu7i to sid
0m23.6s DEBUG: sources.list:
deb http://deb.debian.org/debian/ sid main
0m23.6s INFO: Running scripts pre_distupgrade
0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_exceptions']
0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_exceptions']
0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', 'update']
0m26.7s DUMP:
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7380 kB]
Fetched 17.7 MB in 2s (7590 kB/s)
Reading package lists...
0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', 'update']
0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-yf', 'dist-upgrade']
0m36.8s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
adduser apt debconf dpkg gcc-14-base gromacs gromacs-data ibverbs-providers
libapt-pkg7.0 libatomic1 libcap2 libgcc-s1 libgfortran5 libgomp1
libgromacs10 libibmad5 libibumad3 libibverbs1 libllvm17t64 liblz4-1
libnl-3-200 libnl-route-3-200 librdmacm1t64 libstdc++6 libucx0
sysvinit-utils
26 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 111 MB of archives.
After this operation, 692 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-18 [9300 B]
Get:2 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-18 [137 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-18 [836 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-18 [49.4 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-18 [72.8 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-18 [713 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.10.0-4 [63.9 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 2.9.33 [1109 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.18 [1545 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 adduser all 3.145 [109 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.33 [1447 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.14-4 [34.1 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.91 [121 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.75-1 [27.5 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 gromacs amd64 2025.1-1 [60.6 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 gromacs-data all 2025.1-1 [46.1 MB]
Get:17 http://deb.debian.org/debian sid/main amd64 libgromacs10 amd64 2025.1-1 [33.2 MB]
Get:18 http://deb.debian.org/debian sid/main amd64 libnl-route-3-200 amd64 3.7.0-1 [182 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 libnl-3-200 amd64 3.7.0-1 [59.4 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 libibverbs1 amd64 56.0-2 [62.2 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 ibverbs-providers amd64 56.0-2 [357 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 libibumad3 amd64 56.0-2 [29.8 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libibmad5 amd64 56.0-2 [44.3 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 libllvm17t64 amd64 1:17.0.6-21+b1 [23.6 MB]
Get:25 http://deb.debian.org/debian sid/main amd64 librdmacm1t64 amd64 56.0-2 [70.2 kB]
Get:26 http://deb.debian.org/debian sid/main amd64 libucx0 amd64 1.18.1+ds-2 [1196 kB]
Preconfiguring packages ...
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Unpacking libatomic1:amd64 (14.2.0-18) over (14.2.0-17) ...
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Unpacking gcc-14-base:amd64 (14.2.0-18) over (14.2.0-17) ...
Setting up gcc-14-base:amd64 (14.2.0-18) ...
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Setting up libgcc-s1:amd64 (14.2.0-18) ...
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Setting up libstdc++6:amd64 (14.2.0-18) ...
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Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ...
Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ...
Setting up liblz4-1:amd64 (1.10.0-4) ...
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Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31) ...
Setting up libapt-pkg7.0:amd64 (2.9.33) ...
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Preparing to unpack .../dpkg_1.22.18_amd64.deb ...
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Setting up dpkg (1.22.18) ...
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Preparing to unpack .../archives/adduser_3.145_all.deb ...
Unpacking adduser (3.145) over (3.137) ...
Setting up adduser (3.145) ...
Installing new version of config file /etc/adduser.conf ...
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Preparing to unpack .../archives/apt_2.9.33_amd64.deb ...
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Setting up apt (2.9.33) ...
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Preparing to unpack .../sysvinit-utils_3.14-4_amd64.deb ...
Unpacking sysvinit-utils (3.14-4) over (3.14-3) ...
Setting up sysvinit-utils (3.14-4) ...
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Setting up debconf (1.5.91) ...
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Setting up libcap2:amd64 (1:2.75-1) ...
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Preparing to unpack .../00-gromacs_2025.1-1_amd64.deb ...
Unpacking gromacs (2025.1-1) over (2025.0-2) ...
Preparing to unpack .../01-gromacs-data_2025.1-1_all.deb ...
Unpacking gromacs-data (2025.1-1) over (2025.0-2) ...
Preparing to unpack .../02-libgromacs10_2025.1-1_amd64.deb ...
Unpacking libgromacs10:amd64 (2025.1-1) over (2025.0-2) ...
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Unpacking libnl-3-200:amd64 (3.7.0-1) over (3.7.0-0.3+b1) ...
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Unpacking libibverbs1:amd64 (56.0-2) over (55.0-1) ...
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Unpacking ibverbs-providers:amd64 (56.0-2) over (55.0-1) ...
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Unpacking libibmad5:amd64 (56.0-2) over (55.0-1) ...
Preparing to unpack .../09-libllvm17t64_1%3a17.0.6-21+b1_amd64.deb ...
Unpacking libllvm17t64:amd64 (1:17.0.6-21+b1) over (1:17.0.6-21) ...
Preparing to unpack .../10-librdmacm1t64_56.0-2_amd64.deb ...
Unpacking librdmacm1t64:amd64 (56.0-2) over (55.0-1) ...
Preparing to unpack .../11-libucx0_1.18.1+ds-2_amd64.deb ...
Unpacking libucx0:amd64 (1.18.1+ds-2) over (1.18.1+ds-1) ...
Setting up gromacs-data (2025.1-1) ...
Setting up libibumad3:amd64 (56.0-2) ...
Setting up libibmad5:amd64 (56.0-2) ...
Setting up libgomp1:amd64 (14.2.0-18) ...
Setting up libllvm17t64:amd64 (1:17.0.6-21+b1) ...
Setting up libatomic1:amd64 (14.2.0-18) ...
Setting up libgfortran5:amd64 (14.2.0-18) ...
Setting up libgromacs10:amd64 (2025.1-1) ...
Setting up libnl-3-200:amd64 (3.7.0-1) ...
Setting up gromacs (2025.1-1) ...
Setting up libnl-route-3-200:amd64 (3.7.0-1) ...
Setting up libibverbs1:amd64 (56.0-2) ...
Setting up ibverbs-providers:amd64 (56.0-2) ...
Setting up librdmacm1t64:amd64 (56.0-2) ...
Setting up libucx0:amd64 (1.18.1+ds-2) ...
Processing triggers for libc-bin (2.41-4) ...
0m36.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-yf', 'dist-upgrade']
0m36.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m38.2s DUMP:
ca2fd84f7060b310d83740510cdd7a14 -
0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'show', '--no-all-versions', 'gromacs']
0m38.5s DUMP:
Package: gromacs
Version: 2025.1-1
Installed-Size: 461
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Architecture: amd64
Replaces: gromacs-mpi (<< 2022~), gromacs-mpich (<< 2021.1-2), gromacs-openmpi (<< 2021.1-2)
Depends: gromacs-data (= 2025.1-1), sse4.2-support, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgromacs10 (>= 2025.1), libopenmpi40 (>= 5.0.7), libstdc++6 (>= 11)
Recommends: cpp, mpi-default-bin
Suggests: pymol
Breaks: gromacs-mpi (<< 2022~), gromacs-mpich (<< 2021.1-2), gromacs-openmpi (<< 2021.1-2)
Description-en: Molecular dynamics simulator, with building and analysis tools
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 variants both for execution on a single machine, and
using the MPI interface across multiple machines.
Description-md5: b2bae23de6e584a47799dd4899a2c30a
Homepage: https://www.gromacs.org/
Tag: field::biology, field::biology:structural, field::chemistry,
implemented-in::c, interface::commandline, interface::graphical,
interface::x11, role::program, uitoolkit::xlib, x11::application
Section: science
Priority: optional
Filename: pool/main/g/gromacs/gromacs_2025.1-1_amd64.deb
Size: 60604
MD5sum: eff6000bdf1e680ba73071b9279b28b9
SHA256: 82f847d8cde496860756ad0fe7c1e1fd1b56089e030829316b0dfd0ebff81f18
0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'show', '--no-all-versions', 'gromacs']
0m38.5s INFO: apt-cache knows about the following packages: gromacs
0m38.5s INFO: Running scripts pre_install
0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_database-server']
0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_database-server']
0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_exceptions']
0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_exceptions']
0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_extras']
0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_extras']
0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture']
0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture']
0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m38.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m38.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy']
0m38.6s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian sid/main amd64 Packages
release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy']
0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy', 'gromacs']
0m38.7s DUMP:
gromacs:
Installed: 2025.1-1
Candidate: 2025.1-1
Version table:
*** 2025.1-1 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy', 'gromacs']
0m38.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-y', 'install', 'gromacs']
0m39.5s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
gromacs is already the newest version (2025.1-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-y', 'install', 'gromacs']
0m39.5s INFO: Running scripts post_install
0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_install_exceptions']
0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_install_exceptions']
0m39.5s INFO: Running scripts post_distupgrade
0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_base_cleanup']
0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_base_cleanup']
0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_exceptions']
0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_exceptions']
0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_zz_backports']
0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_distupgrade_zz_backports']
0m39.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m41.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m41.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m43.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m43.0s INFO: Running scripts pre_install
0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_database-server']
0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_database-server']
0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_exceptions']
0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_exceptions']
0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_extras']
0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_extras']
0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture']
0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture']
0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy']
0m43.1s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian sid/main amd64 Packages
release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy']
0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy', 'gromacs']
0m43.1s DUMP:
gromacs:
Installed: 2025.1-1
Candidate: 2025.1-1
Version table:
*** 2025.1-1 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-cache', 'policy', 'gromacs']
0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-y', 'install', 'gromacs=2025.1-1']
0m43.8s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
gromacs is already the newest version (2025.1-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', '-y', 'install', 'gromacs=2025.1-1']
0m43.8s INFO: Running scripts post_install
0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_install_exceptions']
0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_install_exceptions']
0m43.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m45.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m48.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', '-ac', '--ignore-obsolete']
0m52.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', '-ac', '--ignore-obsolete']
0m52.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m52.1s DUMP:
0.15.6
0m52.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m52.1s INFO: Running adequate version 0.15.6 now.
0m52.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'gromacs']
0m52.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'gromacs']
0m52.3s INFO: Running scripts pre_remove
0m52.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m55.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m55.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m55.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m55.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m55.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m55.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_exceptions']
0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/pre_remove_exceptions']
0m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m55.9s DUMP:
install ok installed adduser adduser 3.145
install ok installed apt apt 2.9.33
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.6
install ok installed bash bash 5.2.37-1.1
install ok installed bsdutils bsdutils 1:2.40.4-5
install ok installed coreutils coreutils 9.5-1+b1
install ok installed dash dash 0.5.12-12
install ok installed debconf debconf 1.5.91
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-2
install ok installed dpkg dpkg 1.22.18
install ok installed findutils findutils 4.10.0-3
install ok installed fonts-mathjax fonts-mathjax 2.7.9+dfsg-1
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-18
install ok installed grep grep 3.11-4
install ok installed gromacs gromacs 2025.1-1
install ok installed gromacs-data gromacs-data 2025.1-1
install ok installed gzip gzip 1.13-1
install ok installed hostname hostname 3.25
install ok installed ibverbs-providers:amd64 ibverbs-providers 56.0-2
install ok installed init-system-helpers init-system-helpers 1.68
install ok installed isa-support:amd64 isa-support 26
install ok installed libacl1:amd64 libacl1 2.3.2-2+b1
install ok installed libamd-comgr2:amd64 libamd-comgr2 6.0+git20231212.4510c28+dfsg-3+b2
install ok installed libamdhip64-5 libamdhip64-5 5.7.1-5+b1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.33
install ok installed libatomic1:amd64 libatomic1 14.2.0-18
install ok installed libattr1:amd64 libattr1 1:2.5.2-3
install ok installed libaudit-common libaudit-common 1:4.0.2-2
install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2
install ok installed libblas3:amd64 libblas3 3.12.1-2
install ok installed libblkid1:amd64 libblkid1 2.40.4-5
install ok installed libbsd0:amd64 libbsd0 0.12.2-2
install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6
install ok installed libc-bin libc-bin 2.41-4
install ok installed libc6:amd64 libc6 2.41-4
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.75-1
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277
install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.124-1
install ok installed libdrm-common libdrm-common 2.4.124-1
install ok installed libdrm2:amd64 libdrm2 2.4.124-1
install ok installed libedit2:amd64 libedit2 3.1-20250104-1
install ok installed libelf1t64:amd64 libelf1t64 0.192-4
install ok installed libevent-core-2.1-7t64:amd64 libevent-core-2.1-7t64 2.1.12-stable-10+b1
install ok installed libevent-pthreads-2.1-7t64:amd64 libevent-pthreads-2.1-7t64 2.1.12-stable-10+b1
install ok installed libfabric1:amd64 libfabric1 1.17.0-3.1
install ok installed libffi8:amd64 libffi8 3.4.7-1
install ok installed libfftw3-double3:amd64 libfftw3-double3 3.3.10-2+b1
install ok installed libfftw3-single3:amd64 libfftw3-single3 3.3.10-2+b1
install ok installed libfuse3-3:amd64 libfuse3-3 3.14.0-10
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-18
install ok installed libgfortran5:amd64 libgfortran5 14.2.0-18
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libgomp1:amd64 libgomp1 14.2.0-18
install ok installed libgromacs10:amd64 libgromacs10 2025.1-1
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed libhsa-runtime64-1:amd64 libhsa-runtime64-1 6.1.2-3
install ok installed libhsakmt1:amd64 libhsakmt1 6.2.4+ds-1
install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.12.0-1
install ok installed libhwloc15:amd64 libhwloc15 2.12.0-1
install ok installed libibmad5:amd64 libibmad5 56.0-2
install ok installed libibumad3:amd64 libibumad3 56.0-2
install ok installed libibverbs1:amd64 libibverbs1 56.0-2
install ok installed libicu72:amd64 libicu72 72.1-6
install ok installed libjs-mathjax libjs-mathjax 2.7.9+dfsg-1
install ok installed liblapack3:amd64 liblapack3 3.12.1-2
install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-21+b1
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4
install ok installed liblzma5:amd64 liblzma5 5.6.4-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.40.4-5
install ok installed libmunge2:amd64 libmunge2 0.5.16-1
install ok installed libmuparser2v5:amd64 libmuparser2v5 2.3.4-1+b1
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-1
install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-1
install ok installed libnuma1:amd64 libnuma1 2.0.18-1+b1
install ok installed libopenmpi40:amd64 libopenmpi40 5.0.7-1
install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3
install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3
install ok installed libpam-runtime libpam-runtime 1.7.0-3
install ok installed libpam0g:amd64 libpam0g 1.7.0-3
install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b3
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1
install ok installed libpmix2t64:amd64 libpmix2t64 5.0.6-5
install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.3
install ok installed libpsm2-2 libpsm2-2 11.2.185-2.1
install ok installed librdmacm1t64:amd64 librdmacm1t64 56.0-2
install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2+b1
install ok installed libselinux1:amd64 libselinux1 3.8-4
install ok installed libsemanage-common libsemanage-common 3.8-1
install ok installed libsemanage2:amd64 libsemanage2 3.8-1+b1
install ok installed libsepol2:amd64 libsepol2 3.8-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5
install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-18
install ok installed libsystemd0:amd64 libsystemd0 257.4-1
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libucx0:amd64 libucx0 1.18.1+ds-2
install ok installed libudev1:amd64 libudev1 257.4-1
install ok installed libuuid1:amd64 libuuid1 2.40.4-5
install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2
install ok installed libx11-data libx11-data 2:1.8.10-2
install ok installed libxau6:amd64 libxau6 1:1.0.11-1
install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1
install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1
install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3
install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b2
install ok installed libxnvctrl0:amd64 libxnvctrl0 535.171.04-1+b2
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libz3-4:amd64 libz3-4 4.13.3-1
install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2
install ok installed login login 1:4.16.0-2+really2.40.4-5
install ok installed login.defs login.defs 1:4.17.3-1
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed mount mount 2.40.4-5
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.2-1+b2
install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1
install ok installed passwd passwd 1:4.17.3-1
install ok installed perl-base perl-base 5.40.1-2
install ok installed sed sed 4.9-2
install ok installed sqv sqv 1.2.1-6+b1
install ok installed sse4.2-support sse4.2-support 26
install ok installed sysvinit-utils sysvinit-utils 3.14-4
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025a-2
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.40.4-5
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', 'remove', '--allow-remove-essential', 'adduser', 'fonts-mathjax', 'gromacs-data', 'ibverbs-providers:amd64', 'isa-support:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libblas3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libfuse3-3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgromacs10:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjs-mathjax', 'liblapack3:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libmuparser2v5:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libpciaccess0:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'ocl-icd-libopencl1:amd64', 'sse4.2-support', 'gromacs']
0m57.8s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
adduser fonts-mathjax gromacs gromacs-data ibverbs-providers isa-support
libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libdrm-amdgpu1 libdrm-common
libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64
libevent-pthreads-2.1-7t64 libfabric1 libffi8 libfftw3-double3
libfftw3-single3 libfuse3-3 libgfortran5 libgomp1 libgromacs10
libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5
libibumad3 libibverbs1 libicu72 libjs-mathjax liblapack3 libllvm17t64
libmunge2 libmuparser2v5 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi40
libpciaccess0 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libucx0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0
libz3-4 ocl-icd-libopencl1 sse4.2-support
0 upgraded, 0 newly installed, 59 to remove and 0 not upgraded.
After this operation, 814 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 ... 35507 files and directories currently installed.)
Removing gromacs (2025.1-1) ...
Removing libgromacs10:amd64 (2025.1-1) ...
Removing libopenmpi40:amd64 (5.0.7-1) ...
Removing libucx0:amd64 (1.18.1+ds-2) ...
Removing libfabric1:amd64 (1.17.0-3.1) ...
Removing ibverbs-providers:amd64 (56.0-2) ...
Removing librdmacm1t64:amd64 (56.0-2) ...
Removing libibverbs1:amd64 (56.0-2) ...
Removing adduser (3.145) ...
Removing gromacs-data (2025.1-1) ...
Removing libjs-mathjax (2.7.9+dfsg-1) ...
Removing fonts-mathjax (2.7.9+dfsg-1) ...
Removing sse4.2-support (26) ...
Removing isa-support:amd64 (26) ...
Removing libamdhip64-5 (5.7.1-5+b1) ...
Removing libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ...
Removing libatomic1:amd64 (14.2.0-18) ...
Removing liblapack3:amd64 (3.12.1-2) ...
Removing libblas3:amd64 (3.12.1-2) ...
Removing libhsa-runtime64-1:amd64 (6.1.2-3) ...
Removing libhsakmt1:amd64 (6.2.4+ds-1) ...
Removing libdrm-amdgpu1:amd64 (2.4.124-1) ...
Removing libdrm2:amd64 (2.4.124-1) ...
Removing libdrm-common (2.4.124-1) ...
Removing libllvm17t64:amd64 (1:17.0.6-21+b1) ...
Removing libedit2:amd64 (3.1-20250104-1) ...
Removing libelf1t64:amd64 (0.192-4) ...
Removing libpmix2t64:amd64 (5.0.6-5) ...
Removing libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Removing libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Removing libffi8:amd64 (3.4.7-1) ...
Removing libfftw3-double3:amd64 (3.3.10-2+b1) ...
Removing libfftw3-single3:amd64 (3.3.10-2+b1) ...
Removing libfuse3-3:amd64 (3.14.0-10) ...
Removing libgfortran5:amd64 (14.2.0-18) ...
Removing libmuparser2v5:amd64 (2.3.4-1+b1) ...
Removing libgomp1:amd64 (14.2.0-18) ...
Removing libhwloc-plugins:amd64 (2.12.0-1) ...
Removing libhwloc15:amd64 (2.12.0-1) ...
Removing libibmad5:amd64 (56.0-2) ...
Removing libibumad3:amd64 (56.0-2) ...
Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Removing libicu72:amd64 (72.1-6) ...
Removing libmunge2:amd64 (0.5.16-1) ...
Removing libnl-route-3-200:amd64 (3.7.0-1) ...
Removing libnl-3-200:amd64 (3.7.0-1) ...
Removing libpsm2-2 (11.2.185-2.1) ...
Removing libnuma1:amd64 (2.0.18-1+b1) ...
Removing libpciaccess0:amd64 (0.17-3+b3) ...
Removing libpsm-infinipath1 (3.3+20.604758e7-6.3) ...
update-alternatives: warning: alternative /usr/lib/libpsm1/libpsm_infinipath.so.1.16 (part of link group libpsm_infinipath.so.1) doesn't exist; removing from list of alternatives
update-alternatives: warning: /etc/alternatives/libpsm_infinipath.so.1 is dangling; it will be updated with best choice
Removing libxnvctrl0:amd64 (535.171.04-1+b2) ...
Removing libxext6:amd64 (2:1.3.4-1+b3) ...
Removing libx11-6:amd64 (2:1.8.10-2) ...
Removing libx11-data (2:1.8.10-2) ...
Removing libxcb1:amd64 (1.17.0-2+b1) ...
Removing libxau6:amd64 (1:1.0.11-1) ...
Removing libxdmcp6:amd64 (1:1.1.5-1) ...
Removing libz3-4:amd64 (4.13.3-1) ...
Removing ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ...
Processing triggers for libc-bin (2.41-4) ...
0m57.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', 'remove', '--allow-remove-essential', 'adduser', 'fonts-mathjax', 'gromacs-data', 'ibverbs-providers:amd64', 'isa-support:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libblas3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libfuse3-3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgromacs10:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjs-mathjax', 'liblapack3:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libmuparser2v5:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libpciaccess0:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'ocl-icd-libopencl1:amd64', 'sse4.2-support', 'gromacs']
0m57.8s INFO: Running scripts post_remove
0m57.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_remove_exceptions']
0m57.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_remove_exceptions']
0m57.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg', '--purge', 'adduser', 'fonts-mathjax', 'gromacs-data', 'ibverbs-providers:amd64', 'isa-support:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libblas3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libfuse3-3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgromacs10:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjs-mathjax', 'liblapack3:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libmuparser2v5:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libpciaccess0:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'ocl-icd-libopencl1:amd64', 'sse4.2-support']
0m58.0s DUMP:
(Reading database ... 4934 files and directories currently installed.)
Purging configuration files for adduser (3.145) ...
dpkg: warning: ignoring request to remove fonts-mathjax which isn't installed
dpkg: warning: ignoring request to remove gromacs-data which isn't installed
Purging configuration files for ibverbs-providers:amd64 (56.0-2) ...
dpkg: warning: ignoring request to remove isa-support which isn't installed
dpkg: warning: ignoring request to remove libamd-comgr2 which isn't installed
dpkg: warning: ignoring request to remove libamdhip64-5 which isn't installed
dpkg: warning: ignoring request to remove libatomic1 which isn't installed
dpkg: warning: ignoring request to remove libblas3 which isn't installed
dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed
dpkg: warning: ignoring request to remove libdrm-common which isn't installed
dpkg: warning: ignoring request to remove libdrm2 which isn't installed
dpkg: warning: ignoring request to remove libedit2 which isn't installed
dpkg: warning: ignoring request to remove libelf1t64 which isn't installed
dpkg: warning: ignoring request to remove libevent-core-2.1-7t64 which isn't installed
dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7t64 which isn't installed
dpkg: warning: ignoring request to remove libfabric1 which isn't installed
dpkg: warning: ignoring request to remove libffi8 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 libfuse3-3 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 libgromacs10 which isn't installed
dpkg: warning: ignoring request to remove libhsa-runtime64-1 which isn't installed
dpkg: warning: ignoring request to remove libhsakmt1 which isn't installed
dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed
dpkg: warning: ignoring request to remove libhwloc15 which isn't installed
dpkg: warning: ignoring request to remove libibmad5 which isn't installed
dpkg: warning: ignoring request to remove libibumad3 which isn't installed
dpkg: warning: ignoring request to remove libibverbs1 which isn't installed
dpkg: warning: ignoring request to remove libicu72 which isn't installed
dpkg: warning: ignoring request to remove libjs-mathjax which isn't installed
dpkg: warning: ignoring request to remove liblapack3 which isn't installed
dpkg: warning: ignoring request to remove libllvm17t64 which isn't installed
dpkg: warning: ignoring request to remove libmunge2 which isn't installed
dpkg: warning: ignoring request to remove libmuparser2v5 which isn't installed
Purging configuration files for libnl-3-200:amd64 (3.7.0-1) ...
dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed
dpkg: warning: ignoring request to remove libnuma1 which isn't installed
dpkg: warning: ignoring request to remove libopenmpi40 which isn't installed
dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed
dpkg: warning: ignoring request to remove libpmix2t64 which isn't installed
Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.3) ...
dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed
dpkg: warning: ignoring request to remove librdmacm1t64 which isn't installed
dpkg: warning: ignoring request to remove libucx0 which isn't installed
dpkg: warning: ignoring request to remove libx11-6 which isn't installed
dpkg: warning: ignoring request to remove libx11-data which isn't installed
dpkg: warning: ignoring request to remove libxau6 which isn't installed
dpkg: warning: ignoring request to remove libxcb1 which isn't installed
dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed
dpkg: warning: ignoring request to remove libxext6 which isn't installed
dpkg: warning: ignoring request to remove libxml2 which isn't installed
dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed
dpkg: warning: ignoring request to remove libz3-4 which isn't installed
dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed
Purging configuration files for sse4.2-support (26) ...
0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg', '--purge', 'adduser', 'fonts-mathjax', 'gromacs-data', 'ibverbs-providers:amd64', 'isa-support:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libblas3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libffi8:amd64', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libfuse3-3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgromacs10:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjs-mathjax', 'liblapack3:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libmuparser2v5:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libpciaccess0:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'ocl-icd-libopencl1:amd64', 'sse4.2-support']
0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg', '--purge', 'gromacs']
0m58.0s DUMP:
dpkg: warning: ignoring request to remove gromacs which isn't installed
0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg', '--purge', 'gromacs']
0m58.0s INFO: Running scripts post_purge
0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_purge_exceptions']
0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_purge_exceptions']
0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg', '--purge', '--pending']
0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg', '--purge', '--pending']
0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg', '--remove', '--pending']
0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg', '--remove', '--pending']
0m58.0s INFO: Running scripts post_test
0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_test_exceptions']
0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'tmp/scripts/post_test_exceptions']
0m58.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m58.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m58.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg-divert', '--list']
0m58.3s DUMP:
local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged
local diversion of /home to /home.distrib
diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6
diversion of /libx32 to /.libx32.usr-is-merged by base-files
local diversion of /usr/bin/sync to /usr/bin/sync.distrib
diversion of /lib32 to /.lib32.usr-is-merged by base-files
diversion of /libo32 to /.libo32.usr-is-merged by base-files
0m58.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'dpkg-divert', '--list']
0m58.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', 'clean']
0m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i', 'apt-get', 'clean']
0m58.4s DEBUG: Recording chroot state
0m59.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/shm']
0m59.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/shm']
0m59.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/console']
0m59.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/console']
0m59.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/ptmx']
0m59.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/ptmx']
0m59.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/pts']
0m59.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/dev/pts']
0m59.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/proc']
0m59.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i/proc']
0m59.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m59.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1u7heu7i']
0m59.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp1u7heu7i
0m59.7s INFO: PASS: Upgrading between Debian distributions.
0m59.7s INFO: PASS: All tests.
0m59.7s INFO: piuparts run ends.
ret=0
End: 2025-03-12 22:31:18 GMT