0s autopkgtest [19:31:09]: starting date and time: 2025-03-15 19:31:09+0000 0s autopkgtest [19:31:09]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:31:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ybwdj8mq/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade tm-align --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-9.secgroup --name adt-plucky-s390x-tm-align-20250315-193108-juju-7f2275-prod-proposed-migration-environment-2-3503a349-808f-441b-a957-fc47c4f91569 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 133s autopkgtest [19:33:22]: testbed dpkg architecture: s390x 134s autopkgtest [19:33:23]: testbed apt version: 2.9.33 134s autopkgtest [19:33:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 134s autopkgtest [19:33:23]: testbed release detected to be: None 135s autopkgtest [19:33:24]: updating testbed package index (apt update) 135s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 136s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 136s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 136s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 136s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 136s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 136s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [45.1 kB] 136s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [77.3 kB] 136s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 136s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 136s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [314 kB] 136s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.3 kB] 136s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B] 136s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 136s Fetched 965 kB in 1s (1019 kB/s) 137s Reading package lists... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Calculating upgrade... 138s Calculating upgrade... 138s The following packages were automatically installed and are no longer required: 138s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 138s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 138s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 138s linux-tools-6.11.0-8-generic 138s Use 'sudo apt autoremove' to remove them. 138s The following packages will be upgraded: 138s pinentry-curses python3-jinja2 strace 138s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Need to get 652 kB of archives. 138s After this operation, 27.6 kB of additional disk space will be used. 138s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 139s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 139s Fetched 652 kB in 1s (1014 kB/s) 139s (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 ... 81428 files and directories currently installed.) 139s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 139s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 139s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 139s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 139s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 139s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 139s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 139s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 139s Setting up strace (6.13+ds-1ubuntu1) ... 139s Processing triggers for man-db (2.13.0-1) ... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Solving dependencies... 140s The following packages will be REMOVED: 140s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 140s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 140s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 140s linux-tools-6.11.0-8-generic* 140s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 140s After this operation, 167 MB disk space will be freed. 140s (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 ... 81428 files and directories currently installed.) 140s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 140s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 140s Removing libpython3.12t64:s390x (3.12.9-1) ... 140s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 140s Removing libnsl2:s390x (1.3.0-3build3) ... 140s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 141s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 141s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 141s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 141s Processing triggers for libc-bin (2.41-1ubuntu1) ... 141s (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 ... 56328 files and directories currently installed.) 141s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 142s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 142s autopkgtest [19:33:31]: upgrading testbed (apt dist-upgrade and autopurge) 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 142s Starting 2 pkgProblemResolver with broken count: 0 142s Done 142s Entering ResolveByKeep 143s 143s Calculating upgrade... 143s The following packages will be upgraded: 143s libc-bin libc-dev-bin libc6 libc6-dev locales 143s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 9512 kB of archives. 143s After this operation, 8192 B of additional disk space will be used. 143s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 144s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 144s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 145s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 145s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 146s Preconfiguring packages ... 146s Fetched 9512 kB in 4s (2698 kB/s) 147s (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 ... 56326 files and directories currently installed.) 147s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 147s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 147s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 147s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 147s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 147s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 147s Setting up libc6:s390x (2.41-1ubuntu2) ... 147s (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 ... 56326 files and directories currently installed.) 147s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 147s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 147s Setting up libc-bin (2.41-1ubuntu2) ... 147s (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 ... 56326 files and directories currently installed.) 147s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 147s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 147s Setting up locales (2.41-1ubuntu2) ... 147s Generating locales (this might take a while)... 148s en_US.UTF-8... done 148s Generation complete. 148s Setting up libc-dev-bin (2.41-1ubuntu2) ... 148s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 148s Processing triggers for man-db (2.13.0-1) ... 149s Processing triggers for systemd (257.3-1ubuntu3) ... 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s Starting pkgProblemResolver with broken count: 0 150s Starting 2 pkgProblemResolver with broken count: 0 150s Done 150s Solving dependencies... 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s autopkgtest [19:33:40]: rebooting testbed after setup commands that affected boot 172s autopkgtest [19:34:01]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 175s autopkgtest [19:34:04]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 177s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tm-align 20190822+dfsg-2build1 (dsc) [2131 B] 177s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tm-align 20190822+dfsg-2build1 (tar) [52.8 kB] 177s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tm-align 20190822+dfsg-2build1 (diff) [818 kB] 177s gpgv: Signature made Sun Mar 22 16:27:16 2020 UTC 177s gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 177s gpgv: issuer "doko@ubuntu.com" 177s gpgv: Can't check signature: No public key 177s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-2build1.dsc: no acceptable signature found 177s autopkgtest [19:34:06]: testing package tm-align version 20190822+dfsg-2build1 178s autopkgtest [19:34:07]: build not needed 178s autopkgtest [19:34:07]: test run-unit-test: preparing testbed 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 179s Starting pkgProblemResolver with broken count: 0 179s Starting 2 pkgProblemResolver with broken count: 0 179s Done 179s The following NEW packages will be installed: 179s libgfortran5 tm-align 179s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 1481 kB of archives. 179s After this operation, 4036 kB of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 180s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x tm-align s390x 20190822+dfsg-2build1 [862 kB] 180s Fetched 1481 kB in 1s (1377 kB/s) 180s Selecting previously unselected package libgfortran5:s390x. 180s (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 ... 56326 files and directories currently installed.) 180s Preparing to unpack .../libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 180s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 180s Selecting previously unselected package tm-align. 180s Preparing to unpack .../tm-align_20190822+dfsg-2build1_s390x.deb ... 180s Unpacking tm-align (20190822+dfsg-2build1) ... 181s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 181s Setting up tm-align (20190822+dfsg-2build1) ... 181s Processing triggers for libc-bin (2.41-1ubuntu2) ... 181s Processing triggers for man-db (2.13.0-1) ... 182s autopkgtest [19:34:11]: test run-unit-test: [----------------------- 182s Run TMalign... 182s 182s ************************************************************************** 182s * TM-align (Version 20190822) * 182s * An algorithm for protein structure alignment and comparison * 182s * Based on statistics: * 182s * 0.0 < TM-score < 0.30, random structural similarity * 182s * 0.5 < TM-score < 1.00, in about the same fold * 182s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 182s * Please email your comments and suggestions to: zhng@umich.edu * 182s ************************************************************************** 182s 182s Name of Chain_1: 1ni7.pdb 182s Name of Chain_2: 5eep.pdb 182s Length of Chain_1: 149 residues 182s Length of Chain_2: 140 residues 182s 182s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 182s TM-score= 0.85044 (if normalized by length of Chain_1) 182s TM-score= 0.90009 (if normalized by length of Chain_2) 182s (You should use TM-score normalized by length of the reference protein) 182s 182s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 182s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 182s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 182s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 182s 182s Run TMscore... 182s 182s ***************************************************************************** 182s * TM-SCORE * 182s * A scoring function to assess the similarity of protein structures * 182s * Based on statistics: * 182s * 0.0 < TM-score < 0.17, random structural similarity * 182s * 0.5 < TM-score < 1.00, in about the same fold * 182s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 182s * For comments, please email to: zhng@umich.edu * 182s ***************************************************************************** 182s 182s Structure1: 1ni7.pdb Length= 149 182s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 182s Number of residues in common= 140 182s RMSD of the common residues= 1.616 182s 182s TM-score = 0.8987 (d0= 4.40) 182s MaxSub-score= 0.8459 (d0= 3.50) 182s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 182s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 182s 182s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 182s i t(i) u(i,1) u(i,2) u(i,3) 182s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 182s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 182s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 182s 182s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 182s (":" denotes the residue pairs of distance < 5.0 Angstrom) 182s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 182s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 182s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 182s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 182s 183s autopkgtest [19:34:12]: test run-unit-test: -----------------------] 183s run-unit-test PASS 183s autopkgtest [19:34:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 184s autopkgtest [19:34:13]: @@@@@@@@@@@@@@@@@@@@ summary 184s run-unit-test PASS 189s nova [W] Using flock in prodstack6-s390x 189s Creating nova instance adt-plucky-s390x-tm-align-20250315-193108-juju-7f2275-prod-proposed-migration-environment-2-3503a349-808f-441b-a957-fc47c4f91569 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 189s nova [W] Timed out waiting for bebb537d-a4d9-46da-b37f-8fb3a68324f9 to get deleted.