0s autopkgtest [02:55:34]: starting date and time: 2024-11-02 02:55:34+0000 0s autopkgtest [02:55:34]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [02:55:34]: host juju-7f2275-prod-proposed-migration-environment-14; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8hn5tns_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:tm-align --apt-upgrade tm-align --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=tm-align/20190822+dfsg-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-14@bos03-s390x-23.secgroup --name adt-plucky-s390x-tm-align-20241102-025534-juju-7f2275-prod-proposed-migration-environment-14-bac79d32-c487-406d-87c5-a2569fc6dec0 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-14 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 133s autopkgtest [02:57:47]: testbed dpkg architecture: s390x 133s autopkgtest [02:57:47]: testbed apt version: 2.9.8 133s autopkgtest [02:57:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 134s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 134s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [178 kB] 135s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [41.0 kB] 135s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2614 kB] 135s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 135s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [215 kB] 135s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [1851 kB] 135s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [33.3 kB] 135s Fetched 5013 kB in 1s (4015 kB/s) 135s Reading package lists... 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Calculating upgrade... 140s The following packages will be upgraded: 140s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 140s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 140s libblockdev3 libevdev2 libftdi1-2 libinih1 libpipeline1 nano 140s python3-lazr.uri 140s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 611 kB of archives. 140s After this operation, 52.2 kB of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libevdev2 s390x 1.13.3+dfsg-1 [35.9 kB] 140s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpipeline1 s390x 1.5.8-1 [32.5 kB] 140s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x nano s390x 8.2-1 [298 kB] 140s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-utils3 s390x 3.2.0-2 [19.3 kB] 140s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-crypto3 s390x 3.2.0-2 [23.7 kB] 140s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-fs3 s390x 3.2.0-2 [36.1 kB] 140s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-loop3 s390x 3.2.0-2 [7092 B] 140s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-mdraid3 s390x 3.2.0-2 [12.8 kB] 140s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-nvme3 s390x 3.2.0-2 [18.1 kB] 140s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-part3 s390x 3.2.0-2 [15.3 kB] 140s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-swap3 s390x 3.2.0-2 [7704 B] 140s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev3 s390x 3.2.0-2 [53.8 kB] 141s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libftdi1-2 s390x 1.5-7 [29.2 kB] 141s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libinih1 s390x 58-1ubuntu1 [7602 B] 141s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lazr.uri all 1.0.6-4 [13.6 kB] 141s Fetched 611 kB in 1s (640 kB/s) 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 ... 55483 files and directories currently installed.) 141s Preparing to unpack .../00-libevdev2_1.13.3+dfsg-1_s390x.deb ... 141s Unpacking libevdev2:s390x (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 141s Preparing to unpack .../01-libpipeline1_1.5.8-1_s390x.deb ... 141s Unpacking libpipeline1:s390x (1.5.8-1) over (1.5.7-2) ... 141s Preparing to unpack .../02-nano_8.2-1_s390x.deb ... 141s Unpacking nano (8.2-1) over (8.1-1) ... 141s Preparing to unpack .../03-libblockdev-utils3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev-utils3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../04-libblockdev-crypto3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev-crypto3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../05-libblockdev-fs3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev-fs3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../06-libblockdev-loop3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev-loop3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../07-libblockdev-mdraid3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev-mdraid3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../08-libblockdev-nvme3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev-nvme3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../09-libblockdev-part3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev-part3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../10-libblockdev-swap3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev-swap3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../11-libblockdev3_3.2.0-2_s390x.deb ... 141s Unpacking libblockdev3:s390x (3.2.0-2) over (3.1.1-2) ... 141s Preparing to unpack .../12-libftdi1-2_1.5-7_s390x.deb ... 141s Unpacking libftdi1-2:s390x (1.5-7) over (1.5-6build5) ... 141s Preparing to unpack .../13-libinih1_58-1ubuntu1_s390x.deb ... 141s Unpacking libinih1:s390x (58-1ubuntu1) over (55-1ubuntu2) ... 141s Preparing to unpack .../14-python3-lazr.uri_1.0.6-4_all.deb ... 141s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 141s Setting up libpipeline1:s390x (1.5.8-1) ... 141s Setting up libinih1:s390x (58-1ubuntu1) ... 141s Setting up python3-lazr.uri (1.0.6-4) ... 141s Setting up libftdi1-2:s390x (1.5-7) ... 141s Setting up libblockdev-utils3:s390x (3.2.0-2) ... 141s Setting up libblockdev-nvme3:s390x (3.2.0-2) ... 141s Setting up nano (8.2-1) ... 141s Setting up libblockdev-fs3:s390x (3.2.0-2) ... 141s Setting up libevdev2:s390x (1.13.3+dfsg-1) ... 141s Setting up libblockdev-mdraid3:s390x (3.2.0-2) ... 141s Setting up libblockdev-crypto3:s390x (3.2.0-2) ... 141s Setting up libblockdev-swap3:s390x (3.2.0-2) ... 141s Setting up libblockdev-loop3:s390x (3.2.0-2) ... 141s Setting up libblockdev3:s390x (3.2.0-2) ... 141s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 141s Setting up libblockdev-part3:s390x (3.2.0-2) ... 141s Processing triggers for libc-bin (2.40-1ubuntu3) ... 141s Processing triggers for man-db (2.12.1-3) ... 142s Processing triggers for install-info (7.1.1-1) ... 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 143s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 143s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 143s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 144s Reading package lists... 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [02:58:02]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 148s autopkgtest [02:58:02]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 150s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 150s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 150s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 150s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 150s gpgv: issuer "tille@debian.org" 150s gpgv: Can't check signature: No public key 150s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 150s autopkgtest [02:58:04]: testing package tm-align version 20190822+dfsg-3 151s autopkgtest [02:58:05]: build not needed 151s autopkgtest [02:58:05]: test run-unit-test: preparing testbed 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Starting pkgProblemResolver with broken count: 0 154s Starting 2 pkgProblemResolver with broken count: 0 154s Done 154s The following additional packages will be installed: 154s libgfortran5 tm-align 154s Suggested packages: 154s pymol rasmol 154s The following NEW packages will be installed: 154s autopkgtest-satdep libgfortran5 tm-align 154s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 154s Need to get 1463 kB/1464 kB of archives. 154s After this operation, 3357 kB of additional disk space will be used. 154s Get:1 /tmp/autopkgtest.OJgbW1/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 155s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-7ubuntu1 [587 kB] 155s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x tm-align s390x 20190822+dfsg-3 [876 kB] 155s Fetched 1463 kB in 1s (2445 kB/s) 155s Selecting previously unselected package libgfortran5:s390x. 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 ... 55483 files and directories currently installed.) 155s Preparing to unpack .../libgfortran5_14.2.0-7ubuntu1_s390x.deb ... 155s Unpacking libgfortran5:s390x (14.2.0-7ubuntu1) ... 155s Selecting previously unselected package tm-align. 155s Preparing to unpack .../tm-align_20190822+dfsg-3_s390x.deb ... 155s Unpacking tm-align (20190822+dfsg-3) ... 155s Selecting previously unselected package autopkgtest-satdep. 155s Preparing to unpack .../1-autopkgtest-satdep.deb ... 155s Unpacking autopkgtest-satdep (0) ... 155s Setting up libgfortran5:s390x (14.2.0-7ubuntu1) ... 155s Setting up tm-align (20190822+dfsg-3) ... 155s Setting up autopkgtest-satdep (0) ... 155s Processing triggers for man-db (2.12.1-3) ... 156s Processing triggers for libc-bin (2.40-1ubuntu3) ... 158s (Reading database ... 55499 files and directories currently installed.) 158s Removing autopkgtest-satdep (0) ... 159s autopkgtest [02:58:13]: test run-unit-test: [----------------------- 159s Run TMalign... 159s 159s ************************************************************************** 159s * TM-align (Version 20190822) * 159s * An algorithm for protein structure alignment and comparison * 159s * Based on statistics: * 159s * 0.0 < TM-score < 0.30, random structural similarity * 159s * 0.5 < TM-score < 1.00, in about the same fold * 159s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 159s * Please email your comments and suggestions to: zhng@umich.edu * 159s ************************************************************************** 159s 159s Name of Chain_1: 1ni7.pdb 159s Name of Chain_2: 5eep.pdb 159s Length of Chain_1: 149 residues 159s Length of Chain_2: 140 residues 159s 159s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 159s TM-score= 0.85044 (if normalized by length of Chain_1) 159s TM-score= 0.90009 (if normalized by length of Chain_2) 159s (You should use TM-score normalized by length of the reference protein) 159s 159s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 159s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 159s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 159s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 159s 159s Run TMscore... 159s 159s ***************************************************************************** 159s * TM-SCORE * 159s * A scoring function to assess the similarity of protein structures * 159s * Based on statistics: * 159s * 0.0 < TM-score < 0.17, random structural similarity * 159s * 0.5 < TM-score < 1.00, in about the same fold * 159s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 159s * For comments, please email to: zhng@umich.edu * 159s ***************************************************************************** 159s 159s Structure1: 1ni7.pdb Length= 149 159s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 159s Number of residues in common= 140 159s RMSD of the common residues= 1.616 159s 159s TM-score = 0.8987 (d0= 4.40) 159s MaxSub-score= 0.8459 (d0= 3.50) 159s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 159s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 159s 159s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 159s i t(i) u(i,1) u(i,2) u(i,3) 159s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 159s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 159s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 159s 159s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 159s (":" denotes the residue pairs of distance < 5.0 Angstrom) 159s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 159s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 159s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 159s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 159s 159s autopkgtest [02:58:13]: test run-unit-test: -----------------------] 160s autopkgtest [02:58:14]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 160s run-unit-test PASS 160s autopkgtest [02:58:14]: @@@@@@@@@@@@@@@@@@@@ summary 160s run-unit-test PASS 174s nova [W] Using flock in prodstack6-s390x 174s Creating nova instance adt-plucky-s390x-tm-align-20241102-025534-juju-7f2275-prod-proposed-migration-environment-14-bac79d32-c487-406d-87c5-a2569fc6dec0 from image adt/ubuntu-plucky-s390x-server-20241101.img (UUID efc880a6-ff20-4207-a161-b1113fd9bea7)...