0s autopkgtest [16:45:44]: starting date and time: 2025-03-15 16:45:44+0000 0s autopkgtest [16:45:44]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:45:44]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b9115vn5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade simka --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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-15.secgroup --name adt-plucky-arm64-simka-20250315-164544-juju-7f2275-prod-proposed-migration-environment-20-3b0eba58-7a6e-4ead-a6d6-88310e6b04c2 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 154s autopkgtest [16:48:18]: testbed dpkg architecture: arm64 154s autopkgtest [16:48:18]: testbed apt version: 2.9.33 155s autopkgtest [16:48:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s autopkgtest [16:48:19]: testbed release detected to be: None 156s autopkgtest [16:48:20]: updating testbed package index (apt update) 156s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 156s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 156s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 156s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 156s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 157s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 157s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 157s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 157s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 157s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 157s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 157s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 157s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 157s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 158s Fetched 1078 kB in 2s (663 kB/s) 159s Reading package lists... 159s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Calculating upgrade... 160s Calculating upgrade... 161s The following packages will be upgraded: 161s pinentry-curses python3-jinja2 strace 161s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 647 kB of archives. 161s After this operation, 11.3 kB of additional disk space will be used. 161s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 162s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 162s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 162s Fetched 647 kB in 1s (485 kB/s) 163s (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 ... 117701 files and directories currently installed.) 163s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 163s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 163s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 163s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 163s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 163s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 163s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 163s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 163s Setting up strace (6.13+ds-1ubuntu1) ... 163s Processing triggers for man-db (2.13.0-1) ... 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s Solving dependencies... 165s The following packages will be REMOVED: 165s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 165s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 165s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 165s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 165s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 165s After this operation, 267 MB disk space will be freed. 165s (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 ... 117701 files and directories currently installed.) 165s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 165s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 165s Removing libpython3.12t64:arm64 (3.12.9-1) ... 165s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 166s Removing libnsl2:arm64 (1.3.0-3build3) ... 166s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 166s Removing libunwind8:arm64 (1.6.2-3.1) ... 166s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 166s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 167s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 168s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 168s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 168s /etc/kernel/postrm.d/initramfs-tools: 168s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 168s /etc/kernel/postrm.d/zz-flash-kernel: 168s flash-kernel: Kernel 6.11.0-8-generic has been removed. 168s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 168s /etc/kernel/postrm.d/zz-update-grub: 168s Sourcing file `/etc/default/grub' 168s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 168s Generating grub configuration file ... 168s Found linux image: /boot/vmlinuz-6.14.0-10-generic 168s Found initrd image: /boot/initrd.img-6.14.0-10-generic 169s Warning: os-prober will not be executed to detect other bootable partitions. 169s Systems on them will not be added to the GRUB boot configuration. 169s Check GRUB_DISABLE_OS_PROBER documentation entry. 169s Adding boot menu entry for UEFI Firmware Settings ... 169s done 169s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 169s Processing triggers for libc-bin (2.41-1ubuntu1) ... 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 ... 81650 files and directories currently installed.) 169s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 169s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 169s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 169s autopkgtest [16:48:33]: upgrading testbed (apt dist-upgrade and autopurge) 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 170s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 170s Starting 2 pkgProblemResolver with broken count: 0 171s Done 171s Entering ResolveByKeep 172s 172s Calculating upgrade... 172s The following packages will be upgraded: 172s libc-bin libc-dev-bin libc6 libc6-dev locales 172s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 9530 kB of archives. 172s After this operation, 0 B of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 174s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 177s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 177s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 182s Preconfiguring packages ... 182s Fetched 9530 kB in 9s (1006 kB/s) 182s (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 ... 81647 files and directories currently installed.) 182s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 182s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 183s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 183s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 183s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 183s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 183s Setting up libc6:arm64 (2.41-1ubuntu2) ... 183s (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 ... 81647 files and directories currently installed.) 183s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 183s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 183s Setting up libc-bin (2.41-1ubuntu2) ... 184s (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 ... 81647 files and directories currently installed.) 184s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 184s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 184s Setting up locales (2.41-1ubuntu2) ... 185s Generating locales (this might take a while)... 187s en_US.UTF-8... done 187s Generation complete. 187s Setting up libc-dev-bin (2.41-1ubuntu2) ... 187s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 187s Processing triggers for man-db (2.13.0-1) ... 187s Processing triggers for systemd (257.3-1ubuntu3) ... 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 190s Solving dependencies... 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s autopkgtest [16:48:54]: rebooting testbed after setup commands that affected boot 214s autopkgtest [16:49:18]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 217s autopkgtest [16:49:21]: @@@@@@@@@@@@@@@@@@@@ apt-source simka 220s Get:1 http://ftpmaster.internal/ubuntu plucky/universe simka 1.5.3-8build3 (dsc) [2305 B] 220s Get:2 http://ftpmaster.internal/ubuntu plucky/universe simka 1.5.3-8build3 (tar) [168 kB] 220s Get:3 http://ftpmaster.internal/ubuntu plucky/universe simka 1.5.3-8build3 (diff) [22.2 kB] 220s gpgv: Signature made Mon Jan 27 18:06:39 2025 UTC 220s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 220s gpgv: Can't check signature: No public key 220s dpkg-source: warning: cannot verify inline signature for ./simka_1.5.3-8build3.dsc: no acceptable signature found 221s autopkgtest [16:49:25]: testing package simka version 1.5.3-8build3 222s autopkgtest [16:49:26]: build not needed 223s autopkgtest [16:49:27]: test run-unit-test: preparing testbed 223s Reading package lists... 224s Building dependency tree... 224s Reading state information... 224s Starting pkgProblemResolver with broken count: 0 224s Starting 2 pkgProblemResolver with broken count: 0 224s Done 225s The following NEW packages will be installed: 225s libaec0 libgatbcore3 libhdf5-310 libsz2 simka simkamin 225s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 225s Need to get 3335 kB of archives. 225s After this operation, 14.7 MB of additional disk space will be used. 225s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 225s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgatbcore3 arm64 1.4.2+dfsg-13ubuntu1 [1477 kB] 227s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 227s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 229s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 simka arm64 1.5.3-8build3 [466 kB] 229s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 simkamin all 1.5.3-8build3 [34.2 kB] 230s Fetched 3335 kB in 4s (766 kB/s) 230s Selecting previously unselected package libaec0:arm64. 230s (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 ... 81647 files and directories currently installed.) 230s Preparing to unpack .../0-libaec0_1.1.3-1_arm64.deb ... 230s Unpacking libaec0:arm64 (1.1.3-1) ... 230s Selecting previously unselected package libgatbcore3:arm64. 230s Preparing to unpack .../1-libgatbcore3_1.4.2+dfsg-13ubuntu1_arm64.deb ... 230s Unpacking libgatbcore3:arm64 (1.4.2+dfsg-13ubuntu1) ... 230s Selecting previously unselected package libsz2:arm64. 230s Preparing to unpack .../2-libsz2_1.1.3-1_arm64.deb ... 230s Unpacking libsz2:arm64 (1.1.3-1) ... 230s Selecting previously unselected package libhdf5-310:arm64. 230s Preparing to unpack .../3-libhdf5-310_1.14.5+repack-3_arm64.deb ... 230s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 230s Selecting previously unselected package simka. 230s Preparing to unpack .../4-simka_1.5.3-8build3_arm64.deb ... 230s Unpacking simka (1.5.3-8build3) ... 230s Selecting previously unselected package simkamin. 230s Preparing to unpack .../5-simkamin_1.5.3-8build3_all.deb ... 230s Unpacking simkamin (1.5.3-8build3) ... 230s Setting up simkamin (1.5.3-8build3) ... 230s Setting up libaec0:arm64 (1.1.3-1) ... 230s Setting up libgatbcore3:arm64 (1.4.2+dfsg-13ubuntu1) ... 230s Setting up libsz2:arm64 (1.1.3-1) ... 230s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 230s Setting up simka (1.5.3-8build3) ... 230s Processing triggers for man-db (2.13.0-1) ... 232s Processing triggers for libc-bin (2.41-1ubuntu2) ... 233s autopkgtest [16:49:37]: test run-unit-test: [----------------------- 233s A.fasta 233s B.fasta 233s C.fasta 233s D_paired_1.fasta 233s D_paired_2.fasta 233s dataset_metadata.csv 233s potara_job 233s simkaMin 233s simka_input.txt 233s simple_test.py 233s simple_test.sh 233s truth 233s test_simkaMin.py 233s truth_simkaMin 233s truth_simkaMin_symetrical 233s Testing simka 233s 233s Creating input 233s Nb input datasets: 5 233s 233s Reads per sample used: all 233s 233s 233s Maximum ressources used by Simka: 233s - 1 simultaneous processes for counting the kmers (per job: 2 cores, 5000 MB memory) 233s - 2 simultaneous processes for merging the kmer counts (per job: 1 cores, memory undefined) 233s 233s Warning: default memory usage (5000 MB) is close or above system max, setting memory to: 2598 MB 233s Warning: default memory usage (5000 MB) is close or above system max, setting memory to: 2598 MB 233s Nb partitions: 2 partitions 233s 233s 233s 233s Counting k-mers... (log files are /tmp/autopkgtest.xnxu9l/autopkgtest_tmp/example/simka_temp_output/simka_output_temp//log/count_*) 233s [Counting datasets ] 0 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 80.0 % mem: [ 17, 17, 17] MB 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(log files are /tmp/autopkgtest.xnxu9l/autopkgtest_tmp/example/simka_temp_output/simka_output_temp//log/merge_*) 234s [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 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remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB 234s Computing stats... 234s 234s Stats 234s Reads 234s Total: 847 0M 0G 234s Min: 98 0M 0G 234s Max: 402 0M 0G 234s Average: 169 0M 0G 234s Kmers 234s Distinct Kmers (before merging): 14670 0M 0G 234s Distinct Kmers (after merging): 8100 0M 0G 234s Shared distinct Kmers: 4320 0M 0G 234s Kmers: 50130 0M 0G 234s Mean k-mer coverage: 2.66341 234s 234s 234s Output dir: ./simka_results/ 234s 234s 234s 234s 234s *** Test: PASSED 234s 234s Command used: 234s /usr/bin/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output -nb-cores 2 234s 234s Command for visualizing results: 234s python ../scripts/visualization/run-visualization.py -in ./simka_results/ -out ./simka_results/ -pca -heatmap -tree 234s 234s Command for visualizing results with metadata annotations: 234s python ../scripts/visualization/run-visualization.py -in ./simka_results/ -out ./simka_results/ -pca -heatmap -tree -metadata-in ../example/dataset_metadata.csv -metadata-variable VARIABLE_1 234s TESTING k=31 t=0 234s simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0 -nb-cores 1 234s [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 50 % 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elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 0.0 % mem: [ 17, 17, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 0.0 % mem: [ 17, 17, 17] MB 235s OK 235s TESTING k=21 t=0 235s simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0 -nb-cores 1 237s OK 237s TESTING k=31 t=2 237s simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0 -nb-cores 1 238s OK 238s TESTING k=21 t=2 238s simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0 -nb-cores 1 239s OK 239s TESTING parallelization 243s OK 243s FIXME: Testing simkaMin does not work - needs more investigation 243s FIXME: The test suite slows dramatically down when exceeding 8 cores. 243s autopkgtest [16:49:47]: test run-unit-test: -----------------------] 244s run-unit-test PASS 244s autopkgtest [16:49:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 244s autopkgtest [16:49:48]: @@@@@@@@@@@@@@@@@@@@ summary 244s run-unit-test PASS 263s nova [W] Using flock in prodstack6-arm64 263s Creating nova instance adt-plucky-arm64-simka-20250315-164544-juju-7f2275-prod-proposed-migration-environment-20-3b0eba58-7a6e-4ead-a6d6-88310e6b04c2 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 263s nova [W] Timed out waiting for 2ecc5239-a7a9-4704-a912-50bfa65d8435 to get deleted.