0s autopkgtest [04:46:23]: starting date and time: 2026-02-05 04:46:23+0000 0s autopkgtest [04:46:23]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [04:46:23]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n1az7gfa/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:chiark-tcl --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 chiark-tcl/1.3.7build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-17.secgroup --name adt-resolute-arm64-openmm-20260205-044623-juju-7f2275-prod-proposed-migration-environment-20-0db08cde-b2c3-4433-ae34-8a72b8b89244 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-openmm-20260205-044623-juju-7f2275-prod-proposed-migration-environment-20-0db08cde-b2c3-4433-ae34-8a72b8b89244 from image adt/ubuntu-resolute-arm64-server-20260204.img (UUID f58d981d-b271-4157-b9b1-fd704695563c)... 68s autopkgtest [04:47:31]: testbed dpkg architecture: arm64 68s autopkgtest [04:47:31]: testbed apt version: 3.1.14 68s autopkgtest [04:47:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s autopkgtest [04:47:31]: testbed release detected to be: None 69s autopkgtest [04:47:32]: updating testbed package index (apt update) 70s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 70s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 70s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 70s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 70s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 70s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [265 kB] 70s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7328 B] 70s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 70s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 70s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1481 kB] 70s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [40.2 kB] 70s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [26.0 kB] 70s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 74s Fetched 3984 kB in 1s (4649 kB/s) 75s Reading package lists... 75s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 75s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 75s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 75s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 76s Reading package lists... 76s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Calculating upgrade... 77s The following packages will be upgraded: 77s libc-bin libc-gconv-modules-extra libc6 locales pollinate python3-linkify-it 77s python3-referencing sed 77s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 8110 kB of archives. 77s After this operation, 0 B of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 sed arm64 4.9-2build3 [193 kB] 77s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-gconv-modules-extra arm64 2.42-2ubuntu5 [1413 kB] 77s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6 arm64 2.42-2ubuntu5 [1594 kB] 78s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-bin arm64 2.42-2ubuntu5 [599 kB] 78s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 locales all 2.42-2ubuntu5 [4255 kB] 78s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 78s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 pollinate all 4.33-4ubuntu5 [14.0 kB] 78s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 78s dpkg-preconfigure: unable to re-open stdin: No such file or directory 78s Fetched 8110 kB in 0s (17.2 MB/s) 78s (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 ... 89360 files and directories currently installed.) 78s Preparing to unpack .../sed_4.9-2build3_arm64.deb ... 78s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 78s Setting up sed (4.9-2build3) ... 79s (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 ... 89360 files and directories currently installed.) 79s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_arm64.deb ... 79s Unpacking libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 79s Setting up libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) ... 79s (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 ... 89360 files and directories currently installed.) 79s Preparing to unpack .../libc6_2.42-2ubuntu5_arm64.deb ... 79s Unpacking libc6:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 79s Setting up libc6:arm64 (2.42-2ubuntu5) ... 79s (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 ... 89360 files and directories currently installed.) 79s Preparing to unpack .../libc-bin_2.42-2ubuntu5_arm64.deb ... 79s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 80s Setting up libc-bin (2.42-2ubuntu5) ... 80s (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 ... 89360 files and directories currently installed.) 80s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 80s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 80s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 80s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 80s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 80s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 80s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 80s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 80s Setting up locales (2.42-2ubuntu5) ... 81s Generating locales (this might take a while)... 83s en_US.UTF-8... done 83s Generation complete. 83s Setting up pollinate (4.33-4ubuntu5) ... 93s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 93s Setting up python3-referencing (0.36.2-1ubuntu2) ... 94s Processing triggers for man-db (2.13.1-1) ... 95s Processing triggers for install-info (7.2-5) ... 95s Processing triggers for systemd (259-1ubuntu3) ... 98s autopkgtest [04:47:59]: upgrading testbed (apt dist-upgrade and autopurge) 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Calculating upgrade... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Solving dependencies... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s autopkgtest [04:48:01]: rebooting testbed after setup commands that affected boot 136s autopkgtest [04:48:39]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 139s autopkgtest [04:48:42]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 144s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (dsc) [2579 B] 144s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (tar) [11.5 MB] 144s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (diff) [23.7 kB] 144s gpgv: Signature made Mon Sep 29 08:59:53 2025 UTC 144s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 144s gpgv: issuer "merkys@debian.org" 144s gpgv: Can't check signature: No public key 144s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-12.dsc: no acceptable signature found 145s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 145s autopkgtest [04:48:48]: testing package openmm version 8.1.2+dfsg-12 145s autopkgtest [04:48:48]: build not needed 151s autopkgtest [04:48:54]: test test-python: preparing testbed 151s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Solving dependencies... 152s The following NEW packages will be installed: 152s cpp cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu gcc gcc-15 152s gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libblas3 libcc1-0 152s libgcc-15-dev libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 liblapack3 152s liblsan0 libmpc3 libopenmm-dev libopenmm8.1 libpython3.14-minimal 152s libpython3.14-stdlib libtsan2 libubsan1 python3-all python3-iniconfig 152s python3-numpy python3-numpy-dev python3-openmm python3-pluggy python3-pytest 152s python3.14 python3.14-minimal 153s 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 72.5 MB of archives. 153s After this operation, 319 MB of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 153s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 153s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 153s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 153s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 153s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 153s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 153s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 153s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 153s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 153s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 153s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 153s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 153s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 153s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 153s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 153s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 153s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 153s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 153s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 153s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 153s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 154s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 154s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 154s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 154s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 154s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmm8.1 arm64 8.1.2+dfsg-12 [943 kB] 154s Get:28 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmm-dev arm64 8.1.2+dfsg-12 [330 kB] 154s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 154s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 154s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.9-3 [890 B] 154s Get:32 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-2 [6962 B] 154s Get:33 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-openmm arm64 8.1.2+dfsg-12 [7717 kB] 154s Get:34 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-2 [21.1 kB] 154s Get:35 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 9.0.2-2 [277 kB] 155s Fetched 72.5 MB in 2s (31.6 MB/s) 155s Selecting previously unselected package python3-numpy-dev:arm64. 155s (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 ... 89360 files and directories currently installed.) 155s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 155s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 155s Selecting previously unselected package libblas3:arm64. 155s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_arm64.deb ... 155s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 155s Selecting previously unselected package libgfortran5:arm64. 155s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 155s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 155s Selecting previously unselected package liblapack3:arm64. 155s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 155s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 155s Selecting previously unselected package python3-numpy. 155s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 155s Unpacking python3-numpy (1:2.3.5+ds-3) ... 155s Selecting previously unselected package libpython3.14-minimal:arm64. 155s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_arm64.deb ... 155s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 156s Selecting previously unselected package python3.14-minimal. 156s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_arm64.deb ... 156s Unpacking python3.14-minimal (3.14.2-1) ... 156s Selecting previously unselected package libisl23:arm64. 156s Preparing to unpack .../07-libisl23_0.27-1build1_arm64.deb ... 156s Unpacking libisl23:arm64 (0.27-1build1) ... 156s Selecting previously unselected package libmpc3:arm64. 156s Preparing to unpack .../08-libmpc3_1.3.1-2_arm64.deb ... 156s Unpacking libmpc3:arm64 (1.3.1-2) ... 156s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 156s Preparing to unpack .../09-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package cpp-15. 156s Preparing to unpack .../10-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package cpp-aarch64-linux-gnu. 156s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 156s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 156s Selecting previously unselected package cpp. 156s Preparing to unpack .../12-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 156s Unpacking cpp (4:15.2.0-4ubuntu1) ... 156s Selecting previously unselected package libcc1-0:arm64. 156s Preparing to unpack .../13-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package libgomp1:arm64. 156s Preparing to unpack .../14-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package libitm1:arm64. 156s Preparing to unpack .../15-libitm1_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package libasan8:arm64. 156s Preparing to unpack .../16-libasan8_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package liblsan0:arm64. 156s Preparing to unpack .../17-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package libtsan2:arm64. 156s Preparing to unpack .../18-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package libubsan1:arm64. 156s Preparing to unpack .../19-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 156s Selecting previously unselected package libhwasan0:arm64. 156s Preparing to unpack .../20-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 156s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 157s Selecting previously unselected package libgcc-15-dev:arm64. 157s Preparing to unpack .../21-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 157s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 157s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 157s Preparing to unpack .../22-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 157s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 157s Selecting previously unselected package gcc-15. 157s Preparing to unpack .../23-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 157s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 157s Selecting previously unselected package gcc-aarch64-linux-gnu. 157s Preparing to unpack .../24-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 157s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 157s Selecting previously unselected package gcc. 157s Preparing to unpack .../25-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 157s Unpacking gcc (4:15.2.0-4ubuntu1) ... 157s Selecting previously unselected package libopenmm8.1. 157s Preparing to unpack .../26-libopenmm8.1_8.1.2+dfsg-12_arm64.deb ... 157s Unpacking libopenmm8.1 (8.1.2+dfsg-12) ... 157s Selecting previously unselected package libopenmm-dev. 157s Preparing to unpack .../27-libopenmm-dev_8.1.2+dfsg-12_arm64.deb ... 157s Unpacking libopenmm-dev (8.1.2+dfsg-12) ... 157s Selecting previously unselected package libpython3.14-stdlib:arm64. 157s Preparing to unpack .../28-libpython3.14-stdlib_3.14.2-1_arm64.deb ... 157s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 157s Selecting previously unselected package python3.14. 157s Preparing to unpack .../29-python3.14_3.14.2-1_arm64.deb ... 157s Unpacking python3.14 (3.14.2-1) ... 158s Selecting previously unselected package python3-all. 158s Preparing to unpack .../30-python3-all_3.13.9-3_arm64.deb ... 158s Unpacking python3-all (3.13.9-3) ... 158s Selecting previously unselected package python3-iniconfig. 158s Preparing to unpack .../31-python3-iniconfig_2.1.0-2_all.deb ... 158s Unpacking python3-iniconfig (2.1.0-2) ... 158s Selecting previously unselected package python3-openmm. 158s Preparing to unpack .../32-python3-openmm_8.1.2+dfsg-12_arm64.deb ... 158s Unpacking python3-openmm (8.1.2+dfsg-12) ... 158s Selecting previously unselected package python3-pluggy. 158s Preparing to unpack .../33-python3-pluggy_1.6.0-2_all.deb ... 158s Unpacking python3-pluggy (1.6.0-2) ... 158s Selecting previously unselected package python3-pytest. 158s Preparing to unpack .../34-python3-pytest_9.0.2-2_all.deb ... 158s Unpacking python3-pytest (9.0.2-2) ... 158s Setting up python3-iniconfig (2.1.0-2) ... 158s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 158s Setting up libgomp1:arm64 (15.2.0-12ubuntu1) ... 158s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 158s 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 158s Setting up libmpc3:arm64 (1.3.1-2) ... 158s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 158s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 158s Setting up python3-pluggy (1.6.0-2) ... 159s Setting up libubsan1:arm64 (15.2.0-12ubuntu1) ... 159s Setting up libhwasan0:arm64 (15.2.0-12ubuntu1) ... 159s Setting up libasan8:arm64 (15.2.0-12ubuntu1) ... 159s Setting up libtsan2:arm64 (15.2.0-12ubuntu1) ... 159s Setting up libisl23:arm64 (0.27-1build1) ... 159s Setting up libopenmm8.1 (8.1.2+dfsg-12) ... 159s Setting up python3.14-minimal (3.14.2-1) ... 160s Setting up libcc1-0:arm64 (15.2.0-12ubuntu1) ... 160s Setting up liblsan0:arm64 (15.2.0-12ubuntu1) ... 160s Setting up libitm1:arm64 (15.2.0-12ubuntu1) ... 160s Setting up cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 160s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 160s 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 160s Setting up libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 160s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 160s Setting up python3-pytest (9.0.2-2) ... 160s Setting up libopenmm-dev (8.1.2+dfsg-12) ... 160s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 160s Setting up python3-numpy (1:2.3.5+ds-3) ... 164s Setting up python3-openmm (8.1.2+dfsg-12) ... 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 165s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 165s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 165s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 165s "(?:\s*#.*$)" "|" # comments (dumped) 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 165s "(\S+)" # unquoted words 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 165s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 165s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option. 165s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option. 165s "(?:\s*#.*$)" "|" # comments (dumped) 165s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 165s "(\S+)" # unquoted words 165s Setting up cpp-15 (15.2.0-12ubuntu1) ... 165s Setting up cpp (4:15.2.0-4ubuntu1) ... 165s Setting up python3.14 (3.14.2-1) ... 166s Setting up gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 166s Setting up python3-all (3.13.9-3) ... 166s Setting up gcc-15 (15.2.0-12ubuntu1) ... 166s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 166s Setting up gcc (4:15.2.0-4ubuntu1) ... 166s Processing triggers for systemd (259-1ubuntu3) ... 166s Processing triggers for man-db (2.13.1-1) ... 167s Processing triggers for libc-bin (2.42-2ubuntu5) ... 168s autopkgtest [04:49:11]: test test-python: [----------------------- 170s ============================= test session starts ============================== 170s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 170s rootdir: /tmp/autopkgtest.9T8O8o/build.VAG/src/wrappers/python/tests 170s configfile: pytest.ini 170s plugins: typeguard-4.4.4 170s collected 327 items 170s 170s TestAPIUnits.py .................................. [ 10%] 170s TestATMForce.py . [ 10%] 170s TestAmberInpcrdFile.py .....s [ 12%] 177s TestAmberPrmtopFile.py ....................... [ 19%] 177s TestBytes.py . [ 19%] 198s TestCharmmFiles.py ....s..........s......... [ 27%] 198s TestCheckpointReporter.py . [ 27%] 198s TestDcdFile.py ... [ 28%] 200s TestDesmondDMSFile.py ....... [ 30%] 200s TestElement.py .... [ 32%] 221s TestForceField.py s........................................ss..s.. [ 46%] 221s TestForceGroups.py ... [ 47%] 221s TestGenerators.py .. [ 48%] 221s TestGromacsGroFile.py . [ 48%] 222s TestGromacsTopFile.py sssssssssssss [ 52%] 667s TestIntegrators.py .s..... [ 54%] 669s TestMetadynamics.py . [ 55%] 706s TestModeller.py .............s............. [ 63%] 706s TestNumpyCompatibility.py ......... [ 66%] 706s TestPatches.py ..... [ 67%] 712s TestPdbFile.py ...... [ 69%] 717s TestPdbReporter.py ........ [ 71%] 719s TestPdbxFile.py ....... [ 74%] 720s TestPickle.py ... [ 74%] 723s TestSimulatedTempering.py .. [ 75%] 754s TestSimulation.py ....... [ 77%] 754s TestStateDataReporter.py . [ 77%] 754s TestSwigWrappers.py . [ 78%] 754s TestTopology.py ... [ 79%] 754s TestUnitCell.py .. [ 79%] 754s TestUnits.py ...................................................... [ 96%] 754s TestVec3.py ....... [ 98%] 755s TestXtcFile.py ..... [100%] 755s 755s =============================== warnings summary =============================== 755s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 755s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 755s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 755s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 755s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 755s warnings.warn( 755s 755s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 755s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 755s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 755s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 755s warnings.warn( 755s 755s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 755s =========== 305 passed, 22 skipped, 7 warnings in 585.60s (0:09:45) ============ 756s ============================= test session starts ============================== 756s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 756s rootdir: /tmp/autopkgtest.9T8O8o/build.VAG/src/wrappers/python/tests 756s configfile: pytest.ini 756s plugins: typeguard-4.4.4 756s collected 327 items 756s 756s TestAPIUnits.py .................................. [ 10%] 756s TestATMForce.py . [ 10%] 756s TestAmberInpcrdFile.py .....s [ 12%] 763s TestAmberPrmtopFile.py ....................... [ 19%] 763s TestBytes.py . [ 19%] 790s TestCharmmFiles.py ....s..........s......... [ 27%] 790s TestCheckpointReporter.py . [ 27%] 790s TestDcdFile.py ... [ 28%] 792s TestDesmondDMSFile.py ....... [ 30%] 792s TestElement.py .... [ 32%] 815s TestForceField.py s........................................ss..s.. [ 46%] 815s TestForceGroups.py ... [ 47%] 816s TestGenerators.py .. [ 48%] 816s TestGromacsGroFile.py . [ 48%] 816s TestGromacsTopFile.py sssssssssssss [ 52%] 1250s TestIntegrators.py .s..... [ 54%] 1251s TestMetadynamics.py . [ 55%] 1288s TestModeller.py .............s............. [ 63%] 1288s TestNumpyCompatibility.py ......... [ 66%] 1288s TestPatches.py ..... [ 67%] 1295s TestPdbFile.py ...... [ 69%] 1300s TestPdbReporter.py ........ [ 71%] 1302s TestPdbxFile.py ....... [ 74%] 1303s TestPickle.py ... [ 74%] 1306s TestSimulatedTempering.py .. [ 75%] 1337s TestSimulation.py ....... [ 77%] 1337s TestStateDataReporter.py . [ 77%] 1337s TestSwigWrappers.py . [ 78%] 1337s TestTopology.py ... [ 79%] 1337s TestUnitCell.py .. [ 79%] 1337s TestUnits.py ...................................................... [ 96%] 1337s TestVec3.py ....... [ 98%] 1338s TestXtcFile.py ..... [100%] 1338s 1338s =============================== warnings summary =============================== 1338s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 1338s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1338s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1338s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1338s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 1338s warnings.warn( 1338s 1338s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1338s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1338s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1338s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 1338s warnings.warn( 1338s 1338s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1338s =========== 305 passed, 22 skipped, 7 warnings in 581.96s (0:09:41) ============ 1338s autopkgtest [05:08:41]: test test-python: -----------------------] 1339s test-python PASS 1339s autopkgtest [05:08:42]: test test-python: - - - - - - - - - - results - - - - - - - - - - 1339s autopkgtest [05:08:42]: @@@@@@@@@@@@@@@@@@@@ summary 1339s test-python PASS