0s autopkgtest [15:00:41]: starting date and time: 2025-03-15 15:00:41+0000 0s autopkgtest [15:00:41]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:00:41]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3s8ecysf/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.242 lxd-armhf-10.145.243.242:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [15:01:01]: testbed dpkg architecture: armhf 24s autopkgtest [15:01:03]: testbed apt version: 2.9.33 26s autopkgtest [15:01:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [15:01:08]: testbed release detected to be: None 35s autopkgtest [15:01:16]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 37s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 91s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 94s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 95s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 98s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 98s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 98s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 135s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 136s Fetched 41.0 MB in 1min 39s (413 kB/s) 138s Reading package lists... 143s autopkgtest [15:03:04]: upgrading testbed (apt dist-upgrade and autopurge) 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 146s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 146s Starting 2 pkgProblemResolver with broken count: 0 146s Done 147s Entering ResolveByKeep 147s 147s Calculating upgrade... 148s The following packages will be upgraded: 148s libc-bin libc6 locales python3-jinja2 sos strace 148s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 8642 kB of archives. 148s After this operation, 23.6 kB of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 152s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 152s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 158s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 158s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 159s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 159s Preconfiguring packages ... 160s Fetched 8642 kB in 11s (753 kB/s) 160s (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 ... 64655 files and directories currently installed.) 160s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 160s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Setting up libc6:armhf (2.41-1ubuntu2) ... 160s (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 ... 64655 files and directories currently installed.) 160s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 160s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Setting up libc-bin (2.41-1ubuntu2) ... 161s (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 ... 64655 files and directories currently installed.) 161s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 161s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 161s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 161s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 161s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 161s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 161s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 161s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 161s Setting up sos (4.9.0-5) ... 162s Setting up locales (2.41-1ubuntu2) ... 163s Generating locales (this might take a while)... 164s en_US.UTF-8... done 164s Generation complete. 164s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 165s Setting up strace (6.13+ds-1ubuntu1) ... 165s Processing triggers for man-db (2.13.0-1) ... 166s Processing triggers for systemd (257.3-1ubuntu3) ... 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 169s Starting pkgProblemResolver with broken count: 0 169s Starting 2 pkgProblemResolver with broken count: 0 169s Done 169s Solving dependencies... 170s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s autopkgtest [15:03:33]: rebooting testbed after setup commands that affected boot 212s autopkgtest [15:04:13]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 237s autopkgtest [15:04:38]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 273s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-4build1 (dsc) [2527 B] 273s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-4build1 (tar) [11.5 MB] 273s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-4build1 (diff) [22.2 kB] 273s gpgv: Signature made Tue Mar 4 17:44:28 2025 UTC 273s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 273s gpgv: Can't check signature: No public key 273s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-4build1.dsc: no acceptable signature found 274s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 274s autopkgtest [15:05:15]: testing package openmm version 8.1.2+dfsg-4build1 276s autopkgtest [15:05:17]: build not needed 281s autopkgtest [15:05:22]: test command1: preparing testbed 283s Reading package lists... 284s Building dependency tree... 284s Reading state information... 284s Starting pkgProblemResolver with broken count: 0 284s Starting 2 pkgProblemResolver with broken count: 0 284s Done 285s The following NEW packages will be installed: 285s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 285s python3-iniconfig python3-numpy python3-numpy-dev python3-openmm 285s python3-pluggy python3-pytest 285s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 285s Need to get 15.4 MB of archives. 285s After this operation, 112 MB of additional disk space will be used. 285s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 285s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 286s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 286s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 288s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 293s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libopenmm8.1 armhf 8.1.2+dfsg-4build1 [989 kB] 294s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libopenmm-dev armhf 8.1.2+dfsg-4build1 [338 kB] 294s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 294s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-openmm armhf 8.1.2+dfsg-4build1 [7398 kB] 304s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 304s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.5-1 [252 kB] 304s Fetched 15.4 MB in 18s (839 kB/s) 304s Selecting previously unselected package python3-numpy-dev:armhf. 304s (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 ... 64655 files and directories currently installed.) 304s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 304s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 304s Selecting previously unselected package libblas3:armhf. 304s Preparing to unpack .../01-libblas3_3.12.1-2_armhf.deb ... 304s Unpacking libblas3:armhf (3.12.1-2) ... 304s Selecting previously unselected package libgfortran5:armhf. 304s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 304s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 304s Selecting previously unselected package liblapack3:armhf. 304s Preparing to unpack .../03-liblapack3_3.12.1-2_armhf.deb ... 304s Unpacking liblapack3:armhf (3.12.1-2) ... 304s Selecting previously unselected package python3-numpy. 304s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_armhf.deb ... 304s Unpacking python3-numpy (1:2.2.3+ds-5) ... 304s Selecting previously unselected package libopenmm8.1. 304s Preparing to unpack .../05-libopenmm8.1_8.1.2+dfsg-4build1_armhf.deb ... 304s Unpacking libopenmm8.1 (8.1.2+dfsg-4build1) ... 304s Selecting previously unselected package libopenmm-dev. 304s Preparing to unpack .../06-libopenmm-dev_8.1.2+dfsg-4build1_armhf.deb ... 304s Unpacking libopenmm-dev (8.1.2+dfsg-4build1) ... 305s Selecting previously unselected package python3-iniconfig. 305s Preparing to unpack .../07-python3-iniconfig_1.1.1-2_all.deb ... 305s Unpacking python3-iniconfig (1.1.1-2) ... 305s Selecting previously unselected package python3-openmm. 305s Preparing to unpack .../08-python3-openmm_8.1.2+dfsg-4build1_armhf.deb ... 305s Unpacking python3-openmm (8.1.2+dfsg-4build1) ... 305s Selecting previously unselected package python3-pluggy. 305s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 305s Unpacking python3-pluggy (1.5.0-1) ... 305s Selecting previously unselected package python3-pytest. 305s Preparing to unpack .../10-python3-pytest_8.3.5-1_all.deb ... 305s Unpacking python3-pytest (8.3.5-1) ... 305s Setting up python3-iniconfig (1.1.1-2) ... 305s Setting up libblas3:armhf (3.12.1-2) ... 305s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 305s Setting up python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 305s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 305s Setting up python3-pluggy (1.5.0-1) ... 305s Setting up libopenmm8.1 (8.1.2+dfsg-4build1) ... 305s Setting up liblapack3:armhf (3.12.1-2) ... 305s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 305s Setting up python3-pytest (8.3.5-1) ... 306s Setting up libopenmm-dev (8.1.2+dfsg-4build1) ... 306s Setting up python3-numpy (1:2.2.3+ds-5) ... 308s Setting up python3-openmm (8.1.2+dfsg-4build1) ... 308s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 308s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 308s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 308s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 308s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 308s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 308s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 308s "(?:\s*#.*$)" "|" # comments (dumped) 308s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 308s "(\S+)" # unquoted words 308s Processing triggers for man-db (2.13.0-1) ... 309s Processing triggers for libc-bin (2.41-1ubuntu2) ... 319s autopkgtest [15:06:00]: test command1: cd wrappers/python/tests && pytest-3 319s autopkgtest [15:06:00]: test command1: [----------------------- 322s ============================= test session starts ============================== 322s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 322s rootdir: /tmp/autopkgtest.MmtHRg/build.OCF/src/wrappers/python/tests 322s configfile: pytest.ini 322s plugins: typeguard-4.4.2 322s collected 327 items 322s 322s TestAPIUnits.py .................................. [ 10%] 322s TestATMForce.py . [ 10%] 323s TestAmberInpcrdFile.py .....s [ 12%] 333s TestAmberPrmtopFile.py ....................... [ 19%] 333s TestBytes.py . [ 19%] 361s TestCharmmFiles.py ....s..........s......... [ 27%] 361s TestCheckpointReporter.py . [ 27%] 362s TestDcdFile.py ... [ 28%] 364s TestDesmondDMSFile.py ....... [ 30%] 364s TestElement.py .... [ 32%] 389s TestForceField.py s........................................ss..s.. [ 46%] 389s TestForceGroups.py ... [ 47%] 390s TestGenerators.py .. [ 48%] 390s TestGromacsGroFile.py . [ 48%] 390s TestGromacsTopFile.py sssssssssssss [ 52%] 1014s TestIntegrators.py .s..... [ 54%] 1016s TestMetadynamics.py . [ 55%] 1058s TestModeller.py .............s............. [ 63%] 1058s TestNumpyCompatibility.py ......... [ 66%] 1058s TestPatches.py ..... [ 67%] 1065s TestPdbFile.py ...... [ 69%] 1072s TestPdbReporter.py ........ [ 71%] 1074s TestPdbxFile.py ....... [ 74%] 1075s TestPickle.py ... [ 74%] 1078s TestSimulatedTempering.py .. [ 75%] 1118s TestSimulation.py ....... [ 77%] 1118s TestStateDataReporter.py . [ 77%] 1118s TestSwigWrappers.py . [ 78%] 1118s TestTopology.py ... [ 79%] 1119s TestUnitCell.py .. [ 79%] 1119s TestUnits.py ...................................................... [ 96%] 1119s TestVec3.py ....... [ 98%] 1119s TestXtcFile.py ..... [100%] 1119s 1119s =============================== warnings summary =============================== 1119s :488 1119s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 1119s 1119s :488 1119s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 1119s 1119s :488 1119s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 1119s 1119s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 1119s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1119s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1119s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1119s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 1119s warnings.warn( 1119s 1119s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1119s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1119s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1119s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 1119s warnings.warn( 1119s 1119s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1119s =========== 305 passed, 22 skipped, 10 warnings in 797.36s (0:13:17) =========== 1119s autopkgtest [15:19:20]: test command1: -----------------------] 1124s autopkgtest [15:19:25]: test command1: - - - - - - - - - - results - - - - - - - - - - 1124s command1 PASS 1128s autopkgtest [15:19:29]: @@@@@@@@@@@@@@@@@@@@ summary 1128s command1 PASS