0s autopkgtest [20:24:04]: starting date and time: 2025-10-20 20:24:04+0000 0s autopkgtest [20:24:04]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:24:04]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bnfn_lsr/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-20.secgroup --name adt-resolute-arm64-openmm-20251020-202404-juju-7f2275-prod-proposed-migration-environment-15-596fa449-9878-4e31-a8c7-8e6496adcb23 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-openmm-20251020-202404-juju-7f2275-prod-proposed-migration-environment-15-596fa449-9878-4e31-a8c7-8e6496adcb23 from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 61s autopkgtest [20:25:05]: testbed dpkg architecture: arm64 61s autopkgtest [20:25:05]: testbed apt version: 3.1.8ubuntu1 62s autopkgtest [20:25:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [20:25:06]: testbed release detected to be: None 63s autopkgtest [20:25:07]: updating testbed package index (apt update) 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 64s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 64s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 64s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 64s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 64s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 64s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 64s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 64s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 64s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 65s Fetched 1382 kB in 1s (1286 kB/s) 66s Reading package lists... 67s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 69s Reading package lists... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 70s Calculating upgrade... 70s The following packages will be upgraded: 70s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 70s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 512 kB of archives. 70s After this operation, 31.7 kB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 71s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 71s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 71s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 71s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 72s dpkg-preconfigure: unable to re-open stdin: No such file or directory 72s Fetched 512 kB in 1s (886 kB/s) 72s (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 ... 83364 files and directories currently installed.) 72s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 72s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 73s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 73s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 73s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 73s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 73s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 73s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 74s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 74s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 74s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 74s Setting up python3-zipp (3.23.0-1) ... 74s Setting up python3-inflect (7.5.0-1) ... 75s Setting up python3-oauthlib (3.3.1-1) ... 75s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 75s Processing triggers for libc-bin (2.42-0ubuntu3) ... 76s autopkgtest [20:25:20]: upgrading testbed (apt dist-upgrade and autopurge) 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s Calculating upgrade... 77s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 77s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Solving dependencies... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s autopkgtest [20:25:26]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 82s autopkgtest [20:25:26]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 87s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11 (dsc) [2584 B] 87s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11 (tar) [11.5 MB] 87s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11 (diff) [23.3 kB] 87s gpgv: Signature made Fri Mar 21 00:11:20 2025 UTC 87s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 87s gpgv: issuer "dparsons@debian.org" 87s gpgv: Can't check signature: No public key 87s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-11.dsc: no acceptable signature found 89s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 89s autopkgtest [20:25:33]: testing package openmm version 8.1.2+dfsg-11 90s autopkgtest [20:25:34]: build not needed 94s autopkgtest [20:25:38]: test test-python: preparing testbed 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Solving dependencies... 96s The following NEW packages will be installed: 96s cpp cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu gcc gcc-15 96s gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libblas3 libcc1-0 96s libgcc-15-dev libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 liblapack3 96s liblsan0 libmpc3 libopenmm-dev libopenmm8.1 libtsan2 libubsan1 python3-all 96s python3-iniconfig python3-numpy python3-numpy-dev python3-openmm 96s python3-packaging python3-pluggy python3-pytest 96s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 64.9 MB of archives. 96s After this operation, 281 MB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 97s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 97s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 97s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 97s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 98s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1 [676 kB] 98s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-1build3 [58.9 kB] 98s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-5ubuntu1 [11.7 MB] 98s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-5ubuntu1 [1028 B] 98s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 98s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 98s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-5ubuntu1 [49.2 kB] 98s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 98s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-5ubuntu1 [28.1 kB] 98s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-5ubuntu1 [2922 kB] 99s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-5ubuntu1 [1316 kB] 99s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-5ubuntu1 [2689 kB] 99s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-5ubuntu1 [1176 kB] 99s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-5ubuntu1 [1639 kB] 99s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-5ubuntu1 [2601 kB] 99s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-5ubuntu1 [23.1 MB] 100s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-5ubuntu1 [512 kB] 100s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 100s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 100s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmm8.1 arm64 8.1.2+dfsg-11 [987 kB] 100s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmm-dev arm64 8.1.2+dfsg-11 [333 kB] 100s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.7-1 [884 B] 100s Get:28 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 100s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-openmm arm64 8.1.2+dfsg-11 [7449 kB] 100s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 100s Get:31 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 100s Get:32 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pytest all 8.4.2-1 [268 kB] 101s Fetched 64.9 MB in 4s (16.2 MB/s) 101s Selecting previously unselected package python3-numpy-dev:arm64. 101s (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 ... 83374 files and directories currently installed.) 101s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 101s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 101s Selecting previously unselected package libblas3:arm64. 101s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 101s Unpacking libblas3:arm64 (3.12.1-6build1) ... 101s Selecting previously unselected package libgfortran5:arm64. 101s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 101s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 101s Selecting previously unselected package liblapack3:arm64. 101s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 101s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 101s Selecting previously unselected package python3-numpy. 101s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 101s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 102s Selecting previously unselected package libisl23:arm64. 102s Preparing to unpack .../05-libisl23_0.27-1_arm64.deb ... 102s Unpacking libisl23:arm64 (0.27-1) ... 102s Selecting previously unselected package libmpc3:arm64. 102s Preparing to unpack .../06-libmpc3_1.3.1-1build3_arm64.deb ... 102s Unpacking libmpc3:arm64 (1.3.1-1build3) ... 102s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 102s Preparing to unpack .../07-cpp-15-aarch64-linux-gnu_15.2.0-5ubuntu1_arm64.deb ... 102s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-5ubuntu1) ... 102s Selecting previously unselected package cpp-15. 102s Preparing to unpack .../08-cpp-15_15.2.0-5ubuntu1_arm64.deb ... 102s Unpacking cpp-15 (15.2.0-5ubuntu1) ... 102s Selecting previously unselected package cpp-aarch64-linux-gnu. 102s Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 102s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 103s Selecting previously unselected package cpp. 103s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 103s Unpacking cpp (4:15.2.0-4ubuntu1) ... 103s Selecting previously unselected package libcc1-0:arm64. 103s Preparing to unpack .../11-libcc1-0_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking libcc1-0:arm64 (15.2.0-5ubuntu1) ... 103s Selecting previously unselected package libgomp1:arm64. 103s Preparing to unpack .../12-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 103s Selecting previously unselected package libitm1:arm64. 103s Preparing to unpack .../13-libitm1_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking libitm1:arm64 (15.2.0-5ubuntu1) ... 103s Selecting previously unselected package libasan8:arm64. 103s Preparing to unpack .../14-libasan8_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking libasan8:arm64 (15.2.0-5ubuntu1) ... 103s Selecting previously unselected package liblsan0:arm64. 103s Preparing to unpack .../15-liblsan0_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking liblsan0:arm64 (15.2.0-5ubuntu1) ... 103s Selecting previously unselected package libtsan2:arm64. 103s Preparing to unpack .../16-libtsan2_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking libtsan2:arm64 (15.2.0-5ubuntu1) ... 103s Selecting previously unselected package libubsan1:arm64. 103s Preparing to unpack .../17-libubsan1_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking libubsan1:arm64 (15.2.0-5ubuntu1) ... 103s Selecting previously unselected package libhwasan0:arm64. 103s Preparing to unpack .../18-libhwasan0_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking libhwasan0:arm64 (15.2.0-5ubuntu1) ... 103s Selecting previously unselected package libgcc-15-dev:arm64. 103s Preparing to unpack .../19-libgcc-15-dev_15.2.0-5ubuntu1_arm64.deb ... 103s Unpacking libgcc-15-dev:arm64 (15.2.0-5ubuntu1) ... 104s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 104s Preparing to unpack .../20-gcc-15-aarch64-linux-gnu_15.2.0-5ubuntu1_arm64.deb ... 104s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-5ubuntu1) ... 105s Selecting previously unselected package gcc-15. 105s Preparing to unpack .../21-gcc-15_15.2.0-5ubuntu1_arm64.deb ... 105s Unpacking gcc-15 (15.2.0-5ubuntu1) ... 105s Selecting previously unselected package gcc-aarch64-linux-gnu. 105s Preparing to unpack .../22-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 105s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 105s Selecting previously unselected package gcc. 105s Preparing to unpack .../23-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 105s Unpacking gcc (4:15.2.0-4ubuntu1) ... 105s Selecting previously unselected package libopenmm8.1. 105s Preparing to unpack .../24-libopenmm8.1_8.1.2+dfsg-11_arm64.deb ... 105s Unpacking libopenmm8.1 (8.1.2+dfsg-11) ... 105s Selecting previously unselected package libopenmm-dev. 105s Preparing to unpack .../25-libopenmm-dev_8.1.2+dfsg-11_arm64.deb ... 105s Unpacking libopenmm-dev (8.1.2+dfsg-11) ... 105s Selecting previously unselected package python3-all. 105s Preparing to unpack .../26-python3-all_3.13.7-1_arm64.deb ... 105s Unpacking python3-all (3.13.7-1) ... 105s Selecting previously unselected package python3-iniconfig. 105s Preparing to unpack .../27-python3-iniconfig_1.1.1-2_all.deb ... 105s Unpacking python3-iniconfig (1.1.1-2) ... 105s Selecting previously unselected package python3-openmm. 105s Preparing to unpack .../28-python3-openmm_8.1.2+dfsg-11_arm64.deb ... 105s Unpacking python3-openmm (8.1.2+dfsg-11) ... 106s Selecting previously unselected package python3-packaging. 106s Preparing to unpack .../29-python3-packaging_25.0-1_all.deb ... 106s Unpacking python3-packaging (25.0-1) ... 106s Selecting previously unselected package python3-pluggy. 106s Preparing to unpack .../30-python3-pluggy_1.6.0-1_all.deb ... 106s Unpacking python3-pluggy (1.6.0-1) ... 106s Selecting previously unselected package python3-pytest. 106s Preparing to unpack .../31-python3-pytest_8.4.2-1_all.deb ... 106s Unpacking python3-pytest (8.4.2-1) ... 106s Setting up python3-iniconfig (1.1.1-2) ... 106s Setting up python3-all (3.13.7-1) ... 106s Setting up libgomp1:arm64 (15.2.0-5ubuntu1) ... 106s Setting up libblas3:arm64 (3.12.1-6build1) ... 106s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 106s Setting up python3-packaging (25.0-1) ... 107s Setting up libmpc3:arm64 (1.3.1-1build3) ... 107s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 107s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 107s Setting up python3-pluggy (1.6.0-1) ... 107s Setting up libubsan1:arm64 (15.2.0-5ubuntu1) ... 107s Setting up libhwasan0:arm64 (15.2.0-5ubuntu1) ... 107s Setting up libasan8:arm64 (15.2.0-5ubuntu1) ... 107s Setting up libtsan2:arm64 (15.2.0-5ubuntu1) ... 107s Setting up libisl23:arm64 (0.27-1) ... 107s Setting up libopenmm8.1 (8.1.2+dfsg-11) ... 107s Setting up libcc1-0:arm64 (15.2.0-5ubuntu1) ... 107s Setting up liblsan0:arm64 (15.2.0-5ubuntu1) ... 107s Setting up libitm1:arm64 (15.2.0-5ubuntu1) ... 107s Setting up cpp-15-aarch64-linux-gnu (15.2.0-5ubuntu1) ... 107s Setting up liblapack3:arm64 (3.12.1-6build1) ... 107s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 107s Setting up libgcc-15-dev:arm64 (15.2.0-5ubuntu1) ... 107s Setting up python3-pytest (8.4.2-1) ... 108s Setting up libopenmm-dev (8.1.2+dfsg-11) ... 108s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 108s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 111s Setting up python3-openmm (8.1.2+dfsg-11) ... 112s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 112s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 112s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 112s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 112s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 112s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 112s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 112s "(?:\s*#.*$)" "|" # comments (dumped) 112s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 112s "(\S+)" # unquoted words 112s Setting up cpp-15 (15.2.0-5ubuntu1) ... 112s Setting up cpp (4:15.2.0-4ubuntu1) ... 112s Setting up gcc-15-aarch64-linux-gnu (15.2.0-5ubuntu1) ... 112s Setting up gcc-15 (15.2.0-5ubuntu1) ... 112s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 112s Setting up gcc (4:15.2.0-4ubuntu1) ... 112s Processing triggers for man-db (2.13.1-1) ... 114s Processing triggers for libc-bin (2.42-0ubuntu3) ... 115s autopkgtest [20:25:59]: test test-python: [----------------------- 118s ============================= test session starts ============================== 118s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 118s rootdir: /tmp/autopkgtest.W5u6Od/build.vTv/src/wrappers/python/tests 118s configfile: pytest.ini 118s plugins: typeguard-4.4.2 118s collected 327 items 118s 119s TestAPIUnits.py .................................. [ 10%] 119s TestATMForce.py . [ 10%] 119s TestAmberInpcrdFile.py .....s [ 12%] 132s TestAmberPrmtopFile.py ....................... [ 19%] 132s TestBytes.py . [ 19%] 183s TestCharmmFiles.py ....s..........s......... [ 27%] 184s TestCheckpointReporter.py . [ 27%] 184s TestDcdFile.py ... [ 28%] 188s TestDesmondDMSFile.py ....... [ 30%] 189s TestElement.py .... [ 32%] 234s TestForceField.py s........................................ss..s.. [ 46%] 234s TestForceGroups.py ... [ 47%] 234s TestGenerators.py .. [ 48%] 234s TestGromacsGroFile.py . [ 48%] 234s TestGromacsTopFile.py sssssssssssss [ 52%] 1159s TestIntegrators.py .s..... [ 54%] 1162s TestMetadynamics.py . [ 55%] 1240s TestModeller.py .............s............. [ 63%] 1240s TestNumpyCompatibility.py ......... [ 66%] 1240s TestPatches.py ..... [ 67%] 1253s TestPdbFile.py ...... [ 69%] 1266s TestPdbReporter.py ........ [ 71%] 1270s TestPdbxFile.py ....... [ 74%] 1272s TestPickle.py ... [ 74%] 1278s TestSimulatedTempering.py .. [ 75%] 1339s TestSimulation.py ....... [ 77%] 1339s TestStateDataReporter.py . [ 77%] 1339s TestSwigWrappers.py . [ 78%] 1340s TestTopology.py ... [ 79%] 1340s TestUnitCell.py .. [ 79%] 1340s TestUnits.py ...................................................... [ 96%] 1340s TestVec3.py ....... [ 98%] 1340s TestXtcFile.py ..... [100%] 1340s 1340s =============================== warnings summary =============================== 1340s :488 1340s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 1340s 1340s :488 1340s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 1340s 1340s :488 1340s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 1340s 1340s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 1340s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1340s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1340s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1340s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 1340s warnings.warn( 1340s 1340s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1340s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1340s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1340s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 1340s warnings.warn( 1340s 1340s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1340s ========== 305 passed, 22 skipped, 10 warnings in 1223.25s (0:20:23) =========== 1341s autopkgtest [20:46:25]: test test-python: -----------------------] 1342s autopkgtest [20:46:26]: test test-python: - - - - - - - - - - results - - - - - - - - - - 1342s test-python PASS 1342s autopkgtest [20:46:26]: @@@@@@@@@@@@@@@@@@@@ summary 1342s test-python PASS