0s autopkgtest [21:19:27]: starting date and time: 2025-02-15 21:19:27+0000 0s autopkgtest [21:19:27]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:19:27]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b6klu20h/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-15.secgroup --name adt-plucky-amd64-openmm-20250215-211927-juju-7f2275-prod-proposed-migration-environment-15-2604170e-efab-4548-bbfb-3996bc9b89fc --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 55s autopkgtest [21:20:22]: testbed dpkg architecture: amd64 55s autopkgtest [21:20:22]: testbed apt version: 2.9.28 56s autopkgtest [21:20:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 56s autopkgtest [21:20:23]: testbed release detected to be: None 57s autopkgtest [21:20:24]: updating testbed package index (apt update) 57s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 58s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 58s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [62.8 kB] 58s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 58s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 58s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [820 kB] 58s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.0 kB] 58s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [82.9 kB] 58s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 58s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 58s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [844 kB] 58s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [303 kB] 58s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B] 58s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.3 kB] 58s Fetched 2329 kB in 1s (1856 kB/s) 59s Reading package lists... 60s + lsb_release --codename --short 60s + RELEASE=plucky 60s + cat 60s + [ plucky != trusty ] 60s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s The following packages will be upgraded: 60s libtasn1-6 60s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 51.2 kB of archives. 60s After this operation, 22.5 kB of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB] 61s Fetched 51.2 kB in 0s (180 kB/s) 61s (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 ... 108914 files and directories currently installed.) 61s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ... 61s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ... 61s Setting up libtasn1-6:amd64 (4.20.0-2) ... 61s Processing triggers for libc-bin (2.40-4ubuntu1) ... 61s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 61s + /usr/lib/apt/apt-helper analyze-pattern ?true 61s + uname -r 61s + sed s/\./\\./g 61s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 61s + + tail -n+2 61s + grep -v ^linux-.*6\.12\.0-15-generic.* 61s + cut -d/ -f1 61s apt list ?obsolete 61s + true 61s + obsolete_pkgs= 61s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 61s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 62s + grep -q trusty /etc/lsb-release 62s + [ ! -d /usr/share/doc/unattended-upgrades ] 62s + [ ! -d /usr/share/doc/lxd ] 62s + [ ! -d /usr/share/doc/lxd-client ] 62s + [ ! -d /usr/share/doc/snapd ] 62s + type iptables 62s + cat 62s + chmod 755 /etc/rc.local 62s + . /etc/rc.local 62s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 62s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 62s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 62s + uname -m 62s + [ x86_64 = ppc64le ] 62s + [ -d /run/systemd/system ] 62s + systemd-detect-virt --quiet --vm 62s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 62s + cat 62s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 62s + echo COMPRESS=lz4 62s autopkgtest [21:20:29]: upgrading testbed (apt dist-upgrade and autopurge) 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 63s Starting 2 pkgProblemResolver with broken count: 0 63s Done 63s Entering ResolveByKeep 63s 63s The following packages will be upgraded: 63s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 63s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 11.8 MB of archives. 63s After this operation, 746 kB of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 64s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 65s Preconfiguring packages ... 65s Fetched 11.8 MB in 2s (7822 kB/s) 65s (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 ... 108914 files and directories currently installed.) 65s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 65s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 65s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 65s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 65s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 65s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 65s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 65s Checking for services that may need to be restarted... 65s Checking init scripts... 65s Checking for services that may need to be restarted... 65s Checking init scripts... 66s Stopping some services possibly affected by the upgrade (will be restarted later): 66s cron: stopping...done. 66s 66s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 66s Setting up libc6:amd64 (2.41-1ubuntu1) ... 66s Checking for services that may need to be restarted... 66s Checking init scripts... 66s Restarting services possibly affected by the upgrade: 66s cron: restarting...done. 66s 66s Services restarted successfully. 66s (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 ... 108915 files and directories currently installed.) 66s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 66s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 66s Setting up libc-bin (2.41-1ubuntu1) ... 66s (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 ... 108915 files and directories currently installed.) 66s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ... 66s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 66s Setting up iproute2 (6.13.0-1ubuntu1) ... 67s Setting up locales (2.41-1ubuntu1) ... 67s Installing new version of config file /etc/locale.alias ... 67s Generating locales (this might take a while)... 68s en_US.UTF-8... done 68s Generation complete. 68s Setting up libc-dev-bin (2.41-1ubuntu1) ... 68s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 68s Processing triggers for man-db (2.13.0-1) ... 70s Processing triggers for systemd (257.2-3ubuntu1) ... 70s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Starting pkgProblemResolver with broken count: 0 71s Starting 2 pkgProblemResolver with broken count: 0 71s Done 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [21:20:41]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 74s autopkgtest [21:20:41]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 79s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (dsc) [2508 B] 79s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (tar) [11.5 MB] 79s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (diff) [20.6 kB] 79s gpgv: Signature made Tue Feb 4 09:57:44 2025 UTC 79s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 79s gpgv: issuer "merkys@debian.org" 79s gpgv: Can't check signature: No public key 79s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-3.dsc: no acceptable signature found 80s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 80s autopkgtest [21:20:47]: testing package openmm version 8.1.2+dfsg-3 80s autopkgtest [21:20:47]: build not needed 86s autopkgtest [21:20:53]: test command1: preparing testbed 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s Starting pkgProblemResolver with broken count: 0 87s Starting 2 pkgProblemResolver with broken count: 0 87s Done 87s The following NEW packages will be installed: 87s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 87s python3-iniconfig python3-numpy python3-openmm python3-packaging 87s python3-pluggy python3-pytest 87s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 87s Need to get 19.5 MB of archives. 87s After this operation, 146 MB of additional disk space will be used. 87s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 87s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-17ubuntu1 [910 kB] 88s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 88s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-3 [1120 kB] 88s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm-dev amd64 8.1.2+dfsg-3 [349 kB] 88s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 88s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 88s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-openmm amd64 8.1.2+dfsg-3 [7948 kB] 88s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 88s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 88s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 89s Fetched 19.5 MB in 1s (14.3 MB/s) 89s Selecting previously unselected package libblas3:amd64. 89s (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 ... 108916 files and directories currently installed.) 89s Preparing to unpack .../00-libblas3_3.12.1-2_amd64.deb ... 89s Unpacking libblas3:amd64 (3.12.1-2) ... 89s Selecting previously unselected package libgfortran5:amd64. 89s Preparing to unpack .../01-libgfortran5_14.2.0-17ubuntu1_amd64.deb ... 89s Unpacking libgfortran5:amd64 (14.2.0-17ubuntu1) ... 89s Selecting previously unselected package liblapack3:amd64. 89s Preparing to unpack .../02-liblapack3_3.12.1-2_amd64.deb ... 89s Unpacking liblapack3:amd64 (3.12.1-2) ... 89s Selecting previously unselected package libopenmm8.1. 89s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-3_amd64.deb ... 89s Unpacking libopenmm8.1 (8.1.2+dfsg-3) ... 89s Selecting previously unselected package libopenmm-dev. 89s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-3_amd64.deb ... 89s Unpacking libopenmm-dev (8.1.2+dfsg-3) ... 89s Selecting previously unselected package python3-iniconfig. 89s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 89s Unpacking python3-iniconfig (1.1.1-2) ... 89s Selecting previously unselected package python3-numpy. 89s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 89s Unpacking python3-numpy (1:1.26.4+ds-13) ... 89s Selecting previously unselected package python3-openmm. 89s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-3_amd64.deb ... 89s Unpacking python3-openmm (8.1.2+dfsg-3) ... 89s Selecting previously unselected package python3-packaging. 89s Preparing to unpack .../08-python3-packaging_24.2-1_all.deb ... 89s Unpacking python3-packaging (24.2-1) ... 89s Selecting previously unselected package python3-pluggy. 89s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 89s Unpacking python3-pluggy (1.5.0-1) ... 89s Selecting previously unselected package python3-pytest. 89s Preparing to unpack .../10-python3-pytest_8.3.4-1_all.deb ... 89s Unpacking python3-pytest (8.3.4-1) ... 90s Setting up python3-iniconfig (1.1.1-2) ... 90s Setting up libblas3:amd64 (3.12.1-2) ... 90s 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 90s Setting up python3-packaging (24.2-1) ... 90s Setting up libgfortran5:amd64 (14.2.0-17ubuntu1) ... 90s Setting up python3-pluggy (1.5.0-1) ... 90s Setting up libopenmm8.1 (8.1.2+dfsg-3) ... 90s Setting up liblapack3:amd64 (3.12.1-2) ... 90s 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 90s Setting up python3-pytest (8.3.4-1) ... 90s Setting up libopenmm-dev (8.1.2+dfsg-3) ... 90s Setting up python3-numpy (1:1.26.4+ds-13) ... 91s Setting up python3-openmm (8.1.2+dfsg-3) ... 91s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 91s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 91s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 91s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 91s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 91s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 91s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 91s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 91s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 91s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 91s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 91s "(?:\s*#.*$)" "|" # comments (dumped) 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 91s "(\S+)" # unquoted words 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 91s """ Tokenizer method for the mmCIF syntax file - 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 91s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 91s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 91s "(?:\s*#.*$)" "|" # comments (dumped) 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 91s "(\S+)" # unquoted words 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 91s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 91s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 91s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 91s "(?:\s*#.*$)" "|" # comments (dumped) 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 91s "(\S+)" # unquoted words 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 91s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 91s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 91s "(?:\s*#.*$)" "|" # comments (dumped) 91s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 91s "(\S+)" # unquoted words 91s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 91s pattern = re.compile('bias_(.*)_(.*)\.npy') 91s /usr/lib/python3/dist-packages/openmm/openmm.py:6170: SyntaxWarning: invalid escape sequence '\S' 91s match = re.search("<([^?]\S*)", inputString) 92s Processing triggers for man-db (2.13.0-1) ... 92s Processing triggers for libc-bin (2.41-1ubuntu1) ... 93s autopkgtest [21:21:00]: test command1: cd wrappers/python/tests && pytest-3 93s autopkgtest [21:21:00]: test command1: [----------------------- 94s ============================= test session starts ============================== 94s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 94s rootdir: /tmp/autopkgtest.QLjIq9/build.XZM/src/wrappers/python/tests 94s configfile: pytest.ini 94s plugins: typeguard-4.4.1 94s collected 327 items 94s 94s TestAPIUnits.py .................................. [ 10%] 94s TestATMForce.py . [ 10%] 94s TestAmberInpcrdFile.py .....s [ 12%] 101s TestAmberPrmtopFile.py ....................... [ 19%] 101s TestBytes.py . [ 19%] 125s TestCharmmFiles.py ....s..........s......... [ 27%] 125s TestCheckpointReporter.py . [ 27%] 125s TestDcdFile.py ... [ 28%] 126s TestDesmondDMSFile.py ....... [ 30%] 127s TestElement.py .... [ 32%] 143s TestForceField.py s........................................ss..s.. [ 46%] 143s TestForceGroups.py ... [ 47%] 143s TestGenerators.py .. [ 48%] 143s TestGromacsGroFile.py . [ 48%] 143s TestGromacsTopFile.py sssssssssssss [ 52%] 650s TestIntegrators.py .s..... [ 54%] 651s TestMetadynamics.py . [ 55%] 678s TestModeller.py .............s............. [ 63%] 678s TestNumpyCompatibility.py ......... [ 66%] 678s TestPatches.py ..... [ 67%] 683s TestPdbFile.py ...... [ 69%] 688s TestPdbReporter.py ........ [ 71%] 689s TestPdbxFile.py ....... [ 74%] 690s TestPickle.py ... [ 74%] 693s TestSimulatedTempering.py .. [ 75%] 727s TestSimulation.py ....... [ 77%] 728s TestStateDataReporter.py . [ 77%] 728s TestSwigWrappers.py . [ 78%] 728s TestTopology.py ... [ 79%] 728s TestUnitCell.py .. [ 79%] 728s TestUnits.py ...................................................... [ 96%] 728s TestVec3.py ....... [ 98%] 728s TestXtcFile.py ..... [100%] 728s 728s =============================== warnings summary =============================== 728s :488 728s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 728s 728s :488 728s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 728s 728s :488 728s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 728s 728s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 728s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 728s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 728s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 728s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 728s warnings.warn( 728s 728s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 728s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 728s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 728s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 728s warnings.warn( 728s 728s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 728s =========== 305 passed, 22 skipped, 10 warnings in 634.12s (0:10:34) =========== 728s autopkgtest [21:31:35]: test command1: -----------------------] 729s autopkgtest [21:31:36]: test command1: - - - - - - - - - - results - - - - - - - - - - 729s command1 PASS 729s autopkgtest [21:31:36]: @@@@@@@@@@@@@@@@@@@@ summary 729s command1 PASS 746s nova [W] Skipping flock for amd64 746s Creating nova instance adt-plucky-amd64-openmm-20250215-211927-juju-7f2275-prod-proposed-migration-environment-15-2604170e-efab-4548-bbfb-3996bc9b89fc from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID d1f7bb98-7df8-4026-816e-9f6798166d8b)... 746s nova [W] Timed out waiting for 21f1d017-2244-4309-80bf-6c209dc28af6 to get deleted.