0s autopkgtest [18:59:50]: starting date and time: 2024-11-13 18:59:50+0000 0s autopkgtest [18:59:50]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [18:59:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9xw3c9jg/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-1.secgroup --name adt-plucky-ppc64el-openmm-20241113-185950-juju-7f2275-prod-proposed-migration-environment-2-3c6c359a-5775-4841-a34c-12e8a3252a89 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 89s autopkgtest [19:01:19]: testbed dpkg architecture: ppc64el 89s autopkgtest [19:01:19]: testbed apt version: 2.9.8 89s autopkgtest [19:01:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 90s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 90s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [958 kB] 90s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 90s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 90s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [98.3 kB] 90s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [108 kB] 90s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [673 kB] 91s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 91s Fetched 1956 kB in 1s (1706 kB/s) 91s Reading package lists... 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s Calculating upgrade... 95s The following NEW packages will be installed: 95s python3.13-gdbm 95s The following packages will be upgraded: 95s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 95s libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3 95s python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail 95s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 4700 kB of archives. 95s After this operation, 215 kB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 95s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 95s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 96s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 96s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 96s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 96s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 96s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 96s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 96s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 96s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 96s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 96s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 96s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 96s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 96s Fetched 4700 kB in 1s (5377 kB/s) 97s (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 ... 73767 files and directories currently installed.) 97s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 97s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 97s Setting up python3-minimal (3.12.7-1) ... 97s (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 ... 73767 files and directories currently installed.) 97s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 97s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 97s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 97s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 97s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 97s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 97s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 97s (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 ... 73767 files and directories currently installed.) 97s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 98s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 98s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 98s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 98s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 98s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 98s Selecting previously unselected package python3.13-gdbm. 98s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ... 98s Unpacking python3.13-gdbm (3.13.0-2) ... 98s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ... 98s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 98s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 98s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 98s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 98s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 98s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 98s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 98s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 98s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 98s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 98s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 98s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 98s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 98s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 98s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 98s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 98s Setting up libutempter0:ppc64el (1.2.1-4) ... 98s Setting up whiptail (0.52.24-2ubuntu4) ... 98s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 98s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 98s Setting up python3.13-gdbm (3.13.0-2) ... 98s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 98s Setting up bpftrace (0.21.2-2ubuntu2) ... 98s Setting up python3 (3.12.7-1) ... 99s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 99s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 99s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 99s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 99s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 99s Processing triggers for man-db (2.12.1-3) ... 101s Processing triggers for libc-bin (2.40-1ubuntu3) ... 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [19:01:40]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 110s autopkgtest [19:01:40]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 114s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (dsc) [2508 B] 114s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (tar) [11.5 MB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (diff) [18.6 kB] 114s gpgv: Signature made Tue Sep 10 14:07:52 2024 UTC 114s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 114s gpgv: issuer "merkys@debian.org" 114s gpgv: Can't check signature: No public key 114s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-1.dsc: no acceptable signature found 116s autopkgtest [19:01:46]: testing package openmm version 8.1.2+dfsg-1 116s autopkgtest [19:01:46]: build not needed 121s autopkgtest [19:01:51]: test command1: preparing testbed 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s Starting pkgProblemResolver with broken count: 0 123s Starting 2 pkgProblemResolver with broken count: 0 123s Done 123s The following additional packages will be installed: 123s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 123s python3-iniconfig python3-numpy python3-openmm python3-packaging 123s python3-pluggy python3-pytest 123s Suggested packages: 123s gcc gfortran python-numpy-doc python3-dev 123s The following NEW packages will be installed: 123s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libopenmm-dev 123s libopenmm8.1 python3-iniconfig python3-numpy python3-openmm 123s python3-packaging python3-pluggy python3-pytest 123s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 123s Need to get 17.1 MB/17.1 MB of archives. 123s After this operation, 125 MB of additional disk space will be used. 123s Get:1 /tmp/autopkgtest.JKiSLz/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 123s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 124s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 124s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 124s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmm8.1 ppc64el 8.1.2+dfsg-1 [922 kB] 124s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmm-dev ppc64el 8.1.2+dfsg-1 [352 kB] 124s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 124s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 124s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-openmm ppc64el 8.1.2+dfsg-1 [7509 kB] 124s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 124s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 124s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 125s Fetched 17.1 MB in 1s (13.8 MB/s) 125s Selecting previously unselected package libblas3:ppc64el. 125s (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 ... 73775 files and directories currently installed.) 125s Preparing to unpack .../00-libblas3_3.12.0-3build2_ppc64el.deb ... 125s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 125s Selecting previously unselected package libgfortran5:ppc64el. 125s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 125s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 125s Selecting previously unselected package liblapack3:ppc64el. 125s Preparing to unpack .../02-liblapack3_3.12.0-3build2_ppc64el.deb ... 125s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 125s Selecting previously unselected package libopenmm8.1. 125s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-1_ppc64el.deb ... 125s Unpacking libopenmm8.1 (8.1.2+dfsg-1) ... 125s Selecting previously unselected package libopenmm-dev. 125s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-1_ppc64el.deb ... 125s Unpacking libopenmm-dev (8.1.2+dfsg-1) ... 125s Selecting previously unselected package python3-iniconfig. 125s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 125s Unpacking python3-iniconfig (1.1.1-2) ... 125s Selecting previously unselected package python3-numpy. 125s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 125s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 125s Selecting previously unselected package python3-openmm. 125s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-1_ppc64el.deb ... 125s Unpacking python3-openmm (8.1.2+dfsg-1) ... 126s Selecting previously unselected package python3-packaging. 126s Preparing to unpack .../08-python3-packaging_24.1-1_all.deb ... 126s Unpacking python3-packaging (24.1-1) ... 126s Selecting previously unselected package python3-pluggy. 126s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 126s Unpacking python3-pluggy (1.5.0-1) ... 126s Selecting previously unselected package python3-pytest. 126s Preparing to unpack .../10-python3-pytest_8.3.3-1_all.deb ... 126s Unpacking python3-pytest (8.3.3-1) ... 126s Selecting previously unselected package autopkgtest-satdep. 126s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 126s Unpacking autopkgtest-satdep (0) ... 126s Setting up python3-iniconfig (1.1.1-2) ... 126s Setting up libblas3:ppc64el (3.12.0-3build2) ... 126s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 126s Setting up python3-packaging (24.1-1) ... 127s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 127s Setting up python3-pluggy (1.5.0-1) ... 127s Setting up libopenmm8.1 (8.1.2+dfsg-1) ... 127s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 127s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 127s Setting up python3-pytest (8.3.3-1) ... 128s Setting up libopenmm-dev (8.1.2+dfsg-1) ... 128s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 130s Setting up python3-openmm (8.1.2+dfsg-1) ... 131s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 131s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 131s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 131s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 131s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 131s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 131s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 131s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 131s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 131s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 131s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 131s "(?:\s*#.*$)" "|" # comments (dumped) 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 131s "(\S+)" # unquoted words 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 131s """ Tokenizer method for the mmCIF syntax file - 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 131s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 131s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 131s "(?:\s*#.*$)" "|" # comments (dumped) 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 131s "(\S+)" # unquoted words 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 131s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 131s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 131s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 131s "(?:\s*#.*$)" "|" # comments (dumped) 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 131s "(\S+)" # unquoted words 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 131s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 131s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 131s "(?:\s*#.*$)" "|" # comments (dumped) 131s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 131s "(\S+)" # unquoted words 131s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 131s pattern = re.compile('bias_(.*)_(.*)\.npy') 131s /usr/lib/python3/dist-packages/openmm/openmm.py:8376: SyntaxWarning: invalid escape sequence '\S' 131s match = re.search("<([^?]\S*)", inputString) 131s Setting up autopkgtest-satdep (0) ... 131s Processing triggers for man-db (2.12.1-3) ... 132s Processing triggers for libc-bin (2.40-1ubuntu3) ... 135s (Reading database ... 75405 files and directories currently installed.) 135s Removing autopkgtest-satdep (0) ... 136s autopkgtest [19:02:06]: test command1: cd wrappers/python/tests && pytest-3 136s autopkgtest [19:02:06]: test command1: [----------------------- 138s ============================= test session starts ============================== 138s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 138s rootdir: /tmp/autopkgtest.JKiSLz/build.MUj/src/wrappers/python/tests 138s configfile: pytest.ini 138s plugins: typeguard-4.4.1 138s collected 327 items 138s 138s TestAPIUnits.py .................................. [ 10%] 138s TestATMForce.py . [ 10%] 138s TestAmberInpcrdFile.py .....s [ 12%] 154s TestAmberPrmtopFile.py ....................... [ 19%] 154s TestBytes.py . [ 19%] 196s TestCharmmFiles.py ....s..........s......... [ 27%] 197s TestCheckpointReporter.py . [ 27%] 197s TestDcdFile.py ... [ 28%] 201s TestDesmondDMSFile.py ....... [ 30%] 201s TestElement.py .... [ 32%] 233s TestForceField.py s........................................ss..s.. [ 46%] 233s TestForceGroups.py ... [ 47%] 234s TestGenerators.py .. [ 48%] 234s TestGromacsGroFile.py . [ 48%] 234s TestGromacsTopFile.py sssssssssssss [ 52%] 935s TestIntegrators.py .s..... [ 54%] 938s TestMetadynamics.py . [ 55%] 998s TestModeller.py .............s............. [ 63%] 998s TestNumpyCompatibility.py ......... [ 66%] 998s TestPatches.py ..... [ 67%] 1009s TestPdbFile.py ...... [ 69%] 1018s TestPdbReporter.py ........ [ 71%] 1021s TestPdbxFile.py ....... [ 74%] 1023s TestPickle.py ... [ 74%] 1028s TestSimulatedTempering.py .. [ 75%] 1071s TestSimulation.py ....... [ 77%] 1071s TestStateDataReporter.py . [ 77%] 1071s TestSwigWrappers.py . [ 78%] 1071s TestTopology.py ... [ 79%] 1071s TestUnitCell.py .. [ 79%] 1071s TestUnits.py ...................................................... [ 96%] 1071s TestVec3.py ....... [ 98%] 1071s TestXtcFile.py ..... [100%] 1071s 1071s =============================== warnings summary =============================== 1071s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 1071s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1071s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1071s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1071s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 1071s warnings.warn( 1071s 1071s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1071s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1071s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1071s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 1071s warnings.warn( 1071s 1071s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1071s =========== 305 passed, 22 skipped, 7 warnings in 934.83s (0:15:34) ============ 1072s autopkgtest [19:17:42]: test command1: -----------------------] 1072s command1 PASS 1072s autopkgtest [19:17:42]: test command1: - - - - - - - - - - results - - - - - - - - - - 1073s autopkgtest [19:17:43]: @@@@@@@@@@@@@@@@@@@@ summary 1073s command1 PASS 1077s virt: nova [W] Using flock in prodstack6-ppc64el 1077s virt: Creating nova instance adt-plucky-ppc64el-openmm-20241113-185950-juju-7f2275-prod-proposed-migration-environment-2-3c6c359a-5775-4841-a34c-12e8a3252a89 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...