0s autopkgtest [01:10:18]: starting date and time: 2024-06-08 01:10:18+0000 0s autopkgtest [01:10:18]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [01:10:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.iakfxyup/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade gemmi --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 astropy/6.0.1-4' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-s390x-15.secgroup --name adt-oracular-s390x-gemmi-20240608-011018-juju-7f2275-prod-proposed-migration-environment-2-9264b03b-5021-4f9a-9d69-7985959e3f49 --image adt/ubuntu-oracular-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -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://us.ports.ubuntu.com/ubuntu-ports/ 163s autopkgtest [01:13:01]: testbed dpkg architecture: s390x 163s autopkgtest [01:13:01]: testbed apt version: 2.9.3 163s autopkgtest [01:13:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 164s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 164s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 165s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 165s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2864 B] 165s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 165s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x Packages [47.8 kB] 165s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x Packages [1860 B] 165s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x Packages [264 kB] 165s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x Packages [1768 B] 165s Fetched 820 kB in 1s (798 kB/s) 165s Reading package lists... 167s Reading package lists... 168s Building dependency tree... 168s Reading state information... 168s Calculating upgrade... 168s The following packages will be upgraded: 168s debianutils libheif-plugin-aomdec libheif-plugin-aomenc 168s libheif-plugin-libde265 libheif1 libnetplan1 liburcu8t64 netplan-generator 168s netplan.io python3-netplan 169s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 169s Need to get 758 kB of archives. 169s After this operation, 48.1 kB disk space will be freed. 169s Get:1 http://ftpmaster.internal/ubuntu oracular/main s390x debianutils s390x 5.18 [90.2 kB] 169s Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x netplan-generator s390x 1.0-3ubuntu1 [59.2 kB] 169s Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x python3-netplan s390x 1.0-3ubuntu1 [22.9 kB] 169s Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x netplan.io s390x 1.0-3ubuntu1 [65.8 kB] 169s Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x libnetplan1 s390x 1.0-3ubuntu1 [125 kB] 169s Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-aomdec s390x 1.17.6-3 [10.1 kB] 169s Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-aomenc s390x 1.17.6-3 [15.1 kB] 169s Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x libheif1 s390x 1.17.6-3 [295 kB] 169s Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-libde265 s390x 1.17.6-3 [8172 B] 169s Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x liburcu8t64 s390x 0.14.0-4 [66.5 kB] 169s Fetched 758 kB in 1s (1453 kB/s) 169s (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 ... 54607 files and directories currently installed.) 169s Preparing to unpack .../debianutils_5.18_s390x.deb ... 169s Unpacking debianutils (5.18) over (5.17build1) ... 170s Setting up debianutils (5.18) ... 170s (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 ... 54607 files and directories currently installed.) 170s Preparing to unpack .../0-netplan-generator_1.0-3ubuntu1_s390x.deb ... 170s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 170s Unpacking netplan-generator (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 170s Preparing to unpack .../1-python3-netplan_1.0-3ubuntu1_s390x.deb ... 170s Unpacking python3-netplan (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 170s Preparing to unpack .../2-netplan.io_1.0-3ubuntu1_s390x.deb ... 170s Unpacking netplan.io (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 170s Preparing to unpack .../3-libnetplan1_1.0-3ubuntu1_s390x.deb ... 170s Unpacking libnetplan1:s390x (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 170s Preparing to unpack .../4-libheif-plugin-aomdec_1.17.6-3_s390x.deb ... 170s Unpacking libheif-plugin-aomdec:s390x (1.17.6-3) over (1.17.6-1ubuntu4) ... 170s Preparing to unpack .../5-libheif-plugin-aomenc_1.17.6-3_s390x.deb ... 170s Unpacking libheif-plugin-aomenc:s390x (1.17.6-3) over (1.17.6-1ubuntu4) ... 170s Preparing to unpack .../6-libheif1_1.17.6-3_s390x.deb ... 170s Unpacking libheif1:s390x (1.17.6-3) over (1.17.6-1ubuntu4) ... 170s Preparing to unpack .../7-libheif-plugin-libde265_1.17.6-3_s390x.deb ... 170s Unpacking libheif-plugin-libde265:s390x (1.17.6-3) over (1.17.6-1ubuntu4) ... 170s Preparing to unpack .../8-liburcu8t64_0.14.0-4_s390x.deb ... 170s Unpacking liburcu8t64:s390x (0.14.0-4) over (0.14.0-3.1build1) ... 170s Setting up liburcu8t64:s390x (0.14.0-4) ... 170s Setting up libnetplan1:s390x (1.0-3ubuntu1) ... 170s Setting up python3-netplan (1.0-3ubuntu1) ... 170s Setting up netplan-generator (1.0-3ubuntu1) ... 170s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 170s Setting up netplan.io (1.0-3ubuntu1) ... 170s Setting up libheif-plugin-aomdec:s390x (1.17.6-3) ... 170s Setting up libheif-plugin-libde265:s390x (1.17.6-3) ... 170s Setting up libheif1:s390x (1.17.6-3) ... 170s Setting up libheif-plugin-aomenc:s390x (1.17.6-3) ... 170s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 170s Processing triggers for man-db (2.12.1-1) ... 171s Processing triggers for dbus (1.14.10-4ubuntu4) ... 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 172s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 172s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 172s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 172s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 174s Reading package lists... 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Calculating upgrade... 176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s autopkgtest [01:13:17]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:14:26 UTC 2024 179s autopkgtest [01:13:17]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 183s Get:1 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (dsc) [2280 B] 183s Get:2 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (tar) [1290 kB] 183s Get:3 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (diff) [7104 B] 183s gpgv: Signature made Tue May 21 10:42:01 2024 UTC 183s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 183s gpgv: issuer "merkys@debian.org" 183s gpgv: Can't check signature: No public key 183s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-1.dsc: no acceptable signature found 183s autopkgtest [01:13:21]: testing package gemmi version 0.6.5+ds-1 184s autopkgtest [01:13:22]: build not needed 185s autopkgtest [01:13:23]: test command1: preparing testbed 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 187s Starting pkgProblemResolver with broken count: 0 187s Starting 2 pkgProblemResolver with broken count: 0 187s Done 187s The following additional packages will be installed: 187s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 187s python3-iniconfig python3-numpy python3-packaging python3-pluggy 187s python3-pytest 187s Suggested packages: 187s gcc gfortran python-numpy-doc python3-dev 187s The following NEW packages will be installed: 187s autopkgtest-satdep gemmi gemmi-dev libblas3 libgfortran5 liblapack3 187s python3-gemmi python3-iniconfig python3-numpy python3-packaging 187s python3-pluggy python3-pytest 187s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 187s Need to get 13.0 MB/13.0 MB of archives. 187s After this operation, 50.5 MB of additional disk space will be used. 187s Get:1 /tmp/autopkgtest.wOiJLe/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [728 B] 187s Get:2 http://ftpmaster.internal/ubuntu oracular/universe s390x gemmi s390x 0.6.5+ds-1 [1156 kB] 188s Get:3 http://ftpmaster.internal/ubuntu oracular/universe s390x gemmi-dev s390x 0.6.5+ds-1 [1280 kB] 188s Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x libblas3 s390x 3.12.0-3build1 [245 kB] 189s Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x libgfortran5 s390x 14.1.0-1ubuntu1 [600 kB] 189s Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x liblapack3 s390x 3.12.0-3build1 [2976 kB] 189s Get:7 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-gemmi s390x 0.6.5+ds-1 [2343 kB] 190s Get:8 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 190s Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x python3-numpy s390x 1:1.26.4+ds-10 [4090 kB] 190s Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x python3-packaging all 24.0-1 [41.1 kB] 190s Get:11 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 190s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x python3-pytest all 8.2.2-1ubuntu1 [250 kB] 191s Fetched 13.0 MB in 3s (3970 kB/s) 191s Selecting previously unselected package gemmi. 191s (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 ... 54607 files and directories currently installed.) 191s Preparing to unpack .../00-gemmi_0.6.5+ds-1_s390x.deb ... 191s Unpacking gemmi (0.6.5+ds-1) ... 191s Selecting previously unselected package gemmi-dev. 191s Preparing to unpack .../01-gemmi-dev_0.6.5+ds-1_s390x.deb ... 191s Unpacking gemmi-dev (0.6.5+ds-1) ... 191s Selecting previously unselected package libblas3:s390x. 191s Preparing to unpack .../02-libblas3_3.12.0-3build1_s390x.deb ... 191s Unpacking libblas3:s390x (3.12.0-3build1) ... 191s Selecting previously unselected package libgfortran5:s390x. 191s Preparing to unpack .../03-libgfortran5_14.1.0-1ubuntu1_s390x.deb ... 191s Unpacking libgfortran5:s390x (14.1.0-1ubuntu1) ... 191s Selecting previously unselected package liblapack3:s390x. 191s Preparing to unpack .../04-liblapack3_3.12.0-3build1_s390x.deb ... 191s Unpacking liblapack3:s390x (3.12.0-3build1) ... 191s Selecting previously unselected package python3-gemmi. 191s Preparing to unpack .../05-python3-gemmi_0.6.5+ds-1_s390x.deb ... 191s Unpacking python3-gemmi (0.6.5+ds-1) ... 191s Selecting previously unselected package python3-iniconfig. 191s Preparing to unpack .../06-python3-iniconfig_1.1.1-2_all.deb ... 191s Unpacking python3-iniconfig (1.1.1-2) ... 191s Selecting previously unselected package python3-numpy. 191s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-10_s390x.deb ... 191s Unpacking python3-numpy (1:1.26.4+ds-10) ... 191s Selecting previously unselected package python3-packaging. 191s Preparing to unpack .../08-python3-packaging_24.0-1_all.deb ... 191s Unpacking python3-packaging (24.0-1) ... 191s Selecting previously unselected package python3-pluggy. 191s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 191s Unpacking python3-pluggy (1.5.0-1) ... 191s Selecting previously unselected package python3-pytest. 191s Preparing to unpack .../10-python3-pytest_8.2.2-1ubuntu1_all.deb ... 191s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 191s Selecting previously unselected package autopkgtest-satdep. 191s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 191s Unpacking autopkgtest-satdep (0) ... 191s Setting up python3-iniconfig (1.1.1-2) ... 192s Setting up python3-gemmi (0.6.5+ds-1) ... 192s Setting up gemmi-dev (0.6.5+ds-1) ... 192s Setting up libblas3:s390x (3.12.0-3build1) ... 192s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 192s Setting up python3-packaging (24.0-1) ... 192s Setting up libgfortran5:s390x (14.1.0-1ubuntu1) ... 192s Setting up python3-pluggy (1.5.0-1) ... 192s Setting up gemmi (0.6.5+ds-1) ... 192s Setting up liblapack3:s390x (3.12.0-3build1) ... 192s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 192s Setting up python3-pytest (8.2.2-1ubuntu1) ... 193s Setting up python3-numpy (1:1.26.4+ds-10) ... 196s Setting up autopkgtest-satdep (0) ... 196s Processing triggers for man-db (2.12.1-1) ... 196s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 199s (Reading database ... 55822 files and directories currently installed.) 199s Removing autopkgtest-satdep (0) ... 200s autopkgtest [01:13:38]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 200s autopkgtest [01:13:38]: test command1: [----------------------- 201s ........................................................................ [ 38%] 201s .............................s.................s..............ssssss.... [ 76%] 202s ............................................ [100%] 202s =========================== short test summary info ============================ 202s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 202s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 202s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 202s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 202s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 202s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 202s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 202s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 202s 180 passed, 8 skipped, 3 deselected in 1.28s 202s autopkgtest [01:13:40]: test command1: -----------------------] 203s autopkgtest [01:13:41]: test command1: - - - - - - - - - - results - - - - - - - - - - 203s command1 PASS 203s autopkgtest [01:13:41]: @@@@@@@@@@@@@@@@@@@@ summary 203s command1 PASS 219s nova [W] Using flock in scalingstack-bos01-s390x 219s Creating nova instance adt-oracular-s390x-gemmi-20240608-011018-juju-7f2275-prod-proposed-migration-environment-2-9264b03b-5021-4f9a-9d69-7985959e3f49 from image adt/ubuntu-oracular-s390x-server-20240607.img (UUID 7eeb2415-a1eb-49f2-b205-8690074843ed)...