0s autopkgtest [17:07:11]: starting date and time: 2024-03-16 17:07:11+0000 0s autopkgtest [17:07:11]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:07:11]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.85wchay_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:hdf5,src:curl,src:libpsl,src:mpich,src:openmpi,src:openssl,src:orthanc-python,src:pmix --apt-upgrade simka --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=hdf5/1.10.10+repack-3.1ubuntu3 curl/8.5.0-2ubuntu7 libpsl/0.21.2-1.1 mpich/4.2.0-5build1 openmpi/4.1.6-6ubuntu1 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-arm64-14.secgroup --name adt-noble-arm64-simka-20240316-170711-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 137s autopkgtest [17:09:28]: testbed dpkg architecture: arm64 138s autopkgtest [17:09:29]: testbed apt version: 2.7.12 138s autopkgtest [17:09:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 141s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 141s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 141s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 141s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 141s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 141s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 141s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 141s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 142s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 142s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 142s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 154s Fetched 9063 kB in 6s (1607 kB/s) 154s Reading package lists... 160s Reading package lists... 161s Building dependency tree... 161s Reading state information... 162s Calculating upgrade... 164s The following packages will be REMOVED: 164s libssl3 164s The following NEW packages will be installed: 164s libssl3t64 164s The following packages have been kept back: 164s curl 164s The following packages will be upgraded: 164s openssl 164s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 164s Need to get 2753 kB of archives. 164s After this operation, 72.7 kB of additional disk space will be used. 164s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 164s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 166s Fetched 2753 kB in 1s (3472 kB/s) 166s (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 ... 75850 files and directories currently installed.) 166s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 166s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 167s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 167s wget depends on libssl3 (>= 3.0.0). 167s u-boot-tools depends on libssl3 (>= 3.0.0). 167s tnftp depends on libssl3 (>= 3.0.0). 167s tcpdump depends on libssl3 (>= 3.0.0). 167s systemd-resolved depends on libssl3 (>= 3.0.0). 167s systemd depends on libssl3 (>= 3.0.0). 167s sudo depends on libssl3 (>= 3.0.0). 167s sbsigntool depends on libssl3 (>= 3.0.0). 167s rsync depends on libssl3 (>= 3.0.0). 167s python3-cryptography depends on libssl3 (>= 3.0.0). 167s openssh-server depends on libssl3 (>= 3.0.10). 167s openssh-client depends on libssl3 (>= 3.0.10). 167s mtd-utils depends on libssl3 (>= 3.0.0). 167s mokutil depends on libssl3 (>= 3.0.0). 167s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 167s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 167s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 167s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 167s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 167s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 167s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 167s libnvme1 depends on libssl3 (>= 3.0.0). 167s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 167s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 167s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 167s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 167s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 167s kmod depends on libssl3 (>= 3.0.0). 167s dhcpcd-base depends on libssl3 (>= 3.0.0). 167s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 167s 167s (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 ... 75850 files and directories currently installed.) 167s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 167s Selecting previously unselected package libssl3t64:arm64. 167s (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 ... 75839 files and directories currently installed.) 167s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 167s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 168s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 168s Setting up openssl (3.0.13-0ubuntu1) ... 168s Processing triggers for man-db (2.12.0-3) ... 169s Processing triggers for libc-bin (2.39-0ubuntu2) ... 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 174s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 176s sh: Attempting to set up Debian/Ubuntu apt sources automatically 176s sh: Distribution appears to be Ubuntu 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 181s eatmydata is already the newest version (131-1). 181s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 181s Reading package lists... 182s Building dependency tree... 182s Reading state information... 184s dbus is already the newest version (1.14.10-4ubuntu1). 184s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 184s Reading package lists... 185s Building dependency tree... 185s Reading state information... 187s rng-tools-debian is already the newest version (2.4). 187s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s The following packages will be REMOVED: 188s cloud-init* python3-configobj* python3-debconf* 190s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 190s After this operation, 3252 kB disk space will be freed. 190s (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 ... 75852 files and directories currently installed.) 190s Removing cloud-init (24.1.1-0ubuntu1) ... 192s Removing python3-configobj (5.0.8-3) ... 192s Removing python3-debconf (1.5.86) ... 192s Processing triggers for man-db (2.12.0-3) ... 193s (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 ... 75463 files and directories currently installed.) 193s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 196s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 196s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 196s invoke-rc.d: policy-rc.d denied execution of try-restart. 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 199s linux-generic is already the newest version (6.8.0-11.11+1). 199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 200s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 200s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 200s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 210s Reading package lists... 210s Reading package lists... 211s Building dependency tree... 211s Reading state information... 212s Calculating upgrade... 213s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 213s Reading package lists... 214s Building dependency tree... 214s Reading state information... 216s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 216s autopkgtest [17:10:47]: rebooting testbed after setup commands that affected boot 377s autopkgtest [17:13:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 381s autopkgtest [17:13:32]: @@@@@@@@@@@@@@@@@@@@ apt-source simka 385s Get:1 http://ftpmaster.internal/ubuntu noble/universe simka 1.5.3-8 (dsc) [2227 B] 385s Get:2 http://ftpmaster.internal/ubuntu noble/universe simka 1.5.3-8 (tar) [168 kB] 385s Get:3 http://ftpmaster.internal/ubuntu noble/universe simka 1.5.3-8 (diff) [22.0 kB] 386s gpgv: Signature made Wed Jan 10 19:31:21 2024 UTC 386s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 386s gpgv: issuer "tille@debian.org" 386s gpgv: Can't check signature: No public key 386s dpkg-source: warning: cannot verify inline signature for ./simka_1.5.3-8.dsc: no acceptable signature found 386s autopkgtest [17:13:37]: testing package simka version 1.5.3-8 387s autopkgtest [17:13:38]: build not needed 388s autopkgtest [17:13:39]: test run-unit-test: preparing testbed 389s Reading package lists... 390s Building dependency tree... 390s Reading state information... 391s Starting pkgProblemResolver with broken count: 0 391s Starting 2 pkgProblemResolver with broken count: 0 392s Done 393s The following additional packages will be installed: 393s libaec0 libgatbcore3 libhdf5-103-1 libsz2 simka simkamin 393s The following NEW packages will be installed: 393s autopkgtest-satdep libaec0 libgatbcore3 libhdf5-103-1 libsz2 simka simkamin 393s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 393s Need to get 3152 kB/3153 kB of archives. 393s After this operation, 14.2 MB of additional disk space will be used. 393s Get:1 /tmp/autopkgtest.gyvhX8/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 394s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 394s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libgatbcore3 arm64 1.4.2+dfsg-13 [1446 kB] 394s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 394s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 395s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 simka arm64 1.5.3-8 [456 kB] 395s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 simkamin all 1.5.3-8 [34.3 kB] 396s Fetched 3152 kB in 1s (2525 kB/s) 396s Selecting previously unselected package libaec0:arm64. 396s (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 ... 75408 files and directories currently installed.) 396s Preparing to unpack .../0-libaec0_1.1.2-1_arm64.deb ... 396s Unpacking libaec0:arm64 (1.1.2-1) ... 396s Selecting previously unselected package libgatbcore3:arm64. 396s Preparing to unpack .../1-libgatbcore3_1.4.2+dfsg-13_arm64.deb ... 396s Unpacking libgatbcore3:arm64 (1.4.2+dfsg-13) ... 396s Selecting previously unselected package libsz2:arm64. 396s Preparing to unpack .../2-libsz2_1.1.2-1_arm64.deb ... 396s Unpacking libsz2:arm64 (1.1.2-1) ... 396s Selecting previously unselected package libhdf5-103-1:arm64. 396s Preparing to unpack .../3-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 396s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 397s Selecting previously unselected package simka. 397s Preparing to unpack .../4-simka_1.5.3-8_arm64.deb ... 397s Unpacking simka (1.5.3-8) ... 397s Selecting previously unselected package simkamin. 397s Preparing to unpack .../5-simkamin_1.5.3-8_all.deb ... 397s Unpacking simkamin (1.5.3-8) ... 397s Selecting previously unselected package autopkgtest-satdep. 397s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 397s Unpacking autopkgtest-satdep (0) ... 397s Setting up simkamin (1.5.3-8) ... 398s Setting up libaec0:arm64 (1.1.2-1) ... 398s Setting up libgatbcore3:arm64 (1.4.2+dfsg-13) ... 398s Setting up libsz2:arm64 (1.1.2-1) ... 398s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 398s Setting up simka (1.5.3-8) ... 398s Setting up autopkgtest-satdep (0) ... 398s Processing triggers for man-db (2.12.0-3) ... 399s Processing triggers for libc-bin (2.39-0ubuntu2) ... 407s (Reading database ... 75777 files and directories currently installed.) 407s Removing autopkgtest-satdep (0) ... 408s autopkgtest [17:13:59]: test run-unit-test: [----------------------- 408s A.fasta 408s B.fasta 408s C.fasta 408s D_paired_1.fasta 408s D_paired_2.fasta 408s dataset_metadata.csv 408s potara_job 408s simkaMin 408s simka_input.txt 408s simple_test.py 408s simple_test.sh 408s truth 408s test_simkaMin.py 408s truth_simkaMin 408s truth_simkaMin_symetrical 408s Testing simka 409s 409s Creating input 409s Nb input datasets: 5 409s 409s Reads per sample used: all 409s 409s 409s Maximum ressources used by Simka: 409s - 1 simultaneous processes for counting the kmers (per job: 1 cores, 5000 MB memory) 409s - 1 simultaneous processes for merging the kmer counts (per job: 1 cores, memory undefined) 409s 409s Warning: default memory usage (5000 MB) is close or above system max, setting memory to: 968 MB 409s Warning: default memory usage (5000 MB) is close or above system max, setting memory to: 968 MB 409s Nb partitions: 1 partitions 409s 409s 409s 409s Counting k-mers... (log files are /tmp/autopkgtest.gyvhX8/autopkgtest_tmp/example/simka_temp_output/simka_output_temp//log/count_*) 410s [Counting datasets ] 0 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: 0.0 % mem: [ 16, 16, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 1 sec cpu: 45.0 % mem: [ 16, 16, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 1 sec cpu: 45.0 % mem: [ 16, 16, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 1 sec cpu: 42.9 % mem: [ 16, 16, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 1 sec cpu: 42.9 % mem: [ 16, 16, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 1 sec cpu: 42.9 % mem: [ 16, 16, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 1 sec cpu: 42.9 % mem: [ 16, 16, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec remaining: 0 min 1 sec cpu: 42.9 % mem: [ 16, 16, 17] MB [Counting datasets ] 20 % elapsed: 0 min 0 sec 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] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 1.0 % mem: [ 16, 16, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 1.0 % mem: [ 16, 16, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 1.0 % mem: [ 16, 16, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 1.0 % mem: [ 16, 16, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 1.0 % mem: [ 16, 16, 17] MB [Merging datasets ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 1.0 % mem: [ 16, 16, 17] MB 411s Computing stats... 411s 411s Stats 411s Reads 411s Total: 847 0M 0G 411s Min: 98 0M 0G 411s Max: 402 0M 0G 411s Average: 169 0M 0G 411s Kmers 411s Distinct Kmers (before merging): 14670 0M 0G 411s Distinct Kmers (after merging): 8100 0M 0G 411s Shared distinct Kmers: 4320 0M 0G 411s Kmers: 50130 0M 0G 411s Mean k-mer coverage: 2.66341 411s 411s 411s Output dir: ./simka_results/ 411s 411s 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411s 411s Command for visualizing results: 411s python ../scripts/visualization/run-visualization.py -in ./simka_results/ -out ./simka_results/ -pca -heatmap -tree 411s 411s Command for visualizing results with metadata annotations: 411s 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 411s TESTING k=31 t=0 411s 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 413s OK 413s TESTING k=21 t=0 413s 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 415s OK 415s TESTING k=31 t=2 415s 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 417s OK 417s TESTING k=21 t=2 417s 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 419s OK 419s TESTING parallelization 10408s autopkgtest [20:00:39]: ERROR: timed out on command "su -s /bin/bash ubuntu -c set -e; exec /tmp/autopkgtest.gyvhX8/wrapper.sh --artifacts=/tmp/autopkgtest.gyvhX8/run-unit-test-artifacts --chdir=/tmp/autopkgtest.gyvhX8/build.Jvw/src --env=AUTOPKGTEST_TESTBED_ARCH=arm64 --env=AUTOPKGTEST_TEST_ARCH=arm64 --env=DEB_BUILD_OPTIONS=parallel=1 --env=DEBIAN_FRONTEND=noninteractive --env=LANG=C.UTF-8 --unset-env=LANGUAGE --unset-env=LC_ADDRESS --unset-env=LC_ALL --unset-env=LC_COLLATE --unset-env=LC_CTYPE --unset-env=LC_IDENTIFICATION --unset-env=LC_MEASUREMENT --unset-env=LC_MESSAGES --unset-env=LC_MONETARY --unset-env=LC_NAME --unset-env=LC_NUMERIC --unset-env=LC_PAPER --unset-env=LC_TELEPHONE --unset-env=LC_TIME --script-pid-file=/tmp/autopkgtest_script_pid --source-profile --stderr=/tmp/autopkgtest.gyvhX8/run-unit-test-stderr --stdout=/tmp/autopkgtest.gyvhX8/run-unit-test-stdout --tmp=/tmp/autopkgtest.gyvhX8/autopkgtest_tmp '--env=ADT_TEST_TRIGGERS=hdf5/1.10.10+repack-3.1ubuntu3 curl/8.5.0-2ubuntu7 libpsl/0.21.2-1.1 mpich/4.2.0-5build1 openmpi/4.1.6-6ubuntu1 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 pmix/5.0.1-4.1' --make-executable=/tmp/autopkgtest.gyvhX8/build.Jvw/src/debian/tests/run-unit-test -- /tmp/autopkgtest.gyvhX8/build.Jvw/src/debian/tests/run-unit-test" (kind: test) 10408s autopkgtest [20:00:39]: test run-unit-test: -----------------------] 10409s run-unit-test FAIL timed out 10409s autopkgtest [20:00:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 10410s autopkgtest [20:00:41]: @@@@@@@@@@@@@@@@@@@@ summary 10410s run-unit-test FAIL timed out 10421s Creating nova instance adt-noble-arm64-simka-20240316-170711-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...