0s autopkgtest [14:31:18]: starting date and time: 2024-03-21 14:31:18+0000 0s autopkgtest [14:31:18]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [14:31:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cpcyufw8/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:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade relion --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 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-2@bos02-s390x-7.secgroup --name adt-noble-s390x-relion-20240321-143118-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 100s autopkgtest [14:32:58]: testbed dpkg architecture: s390x 100s autopkgtest [14:32:58]: testbed apt version: 2.7.12 100s autopkgtest [14:32:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 102s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 102s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 102s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 103s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3804 kB] 105s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 105s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [663 kB] 106s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 106s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 106s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 106s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3989 kB] 108s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 108s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [45.1 kB] 108s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 110s Fetched 9186 kB in 7s (1256 kB/s) 110s Reading package lists... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 115s The following packages will be upgraded: 115s debianutils 115s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 90.1 kB of archives. 115s After this operation, 1024 B of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 116s Fetched 90.1 kB in 0s (214 kB/s) 116s (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 ... 52171 files and directories currently installed.) 116s Preparing to unpack .../debianutils_5.17_s390x.deb ... 116s Unpacking debianutils (5.17) over (5.16) ... 116s Setting up debianutils (5.17) ... 116s Processing triggers for man-db (2.12.0-3) ... 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Unknown architecture, assuming PC-style ttyS0 117s sh: Attempting to set up Debian/Ubuntu apt sources automatically 117s sh: Distribution appears to be Ubuntu 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s eatmydata is already the newest version (131-1). 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s dbus is already the newest version (1.14.10-4ubuntu1). 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s rng-tools-debian is already the newest version (2.4). 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s The following packages will be REMOVED: 120s cloud-init* python3-configobj* python3-debconf* 120s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 120s After this operation, 3252 kB disk space will be freed. 120s (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 ... 52171 files and directories currently installed.) 120s Removing cloud-init (24.1.1-0ubuntu1) ... 120s Removing python3-configobj (5.0.8-3) ... 120s Removing python3-debconf (1.5.86) ... 120s Processing triggers for man-db (2.12.0-3) ... 121s (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 ... 51782 files and directories currently installed.) 121s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 121s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 121s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 121s invoke-rc.d: policy-rc.d denied execution of try-restart. 121s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s linux-generic is already the newest version (6.8.0-11.11+1). 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 122s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 122s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 124s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s autopkgtest [14:33:23]: rebooting testbed after setup commands that affected boot 142s autopkgtest [14:33:40]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 144s autopkgtest [14:33:42]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 148s Get:1 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (dsc) [2135 B] 148s Get:2 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (tar) [2345 kB] 148s Get:3 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (diff) [12.0 kB] 149s gpgv: Signature made Sat Feb 4 12:33:57 2023 UTC 149s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 149s gpgv: Can't check signature: No public key 149s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3build1.dsc: no acceptable signature found 149s autopkgtest [14:33:47]: testing package relion version 3.1.3-3build1 149s autopkgtest [14:33:47]: build not needed 151s autopkgtest [14:33:49]: test command1: preparing testbed 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 157s The following additional packages will be installed: 157s libatomic1 libdeflate0 libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 157s libfftw3-single3 libgomp1 libhwloc-plugins libhwloc15 libjbig0 157s libjpeg-turbo8 libjpeg8 libmunge2 libopenmpi3 libpciaccess0 libpmix2 157s librdmacm1t64 libsharpyuv0 libtiff6 libwebp7 libxnvctrl0 ocl-icd-libopencl1 157s openmpi-bin openmpi-common relion 157s Suggested packages: 157s libfftw3-bin libfftw3-dev opencl-icd gfortran | fortran-compiler 157s The following NEW packages will be installed: 157s autopkgtest-satdep libatomic1 libdeflate0 libevent-pthreads-2.1-7 libfabric1 157s libfftw3-double3 libfftw3-single3 libgomp1 libhwloc-plugins libhwloc15 157s libjbig0 libjpeg-turbo8 libjpeg8 libmunge2 libopenmpi3 libpciaccess0 157s libpmix2 librdmacm1t64 libsharpyuv0 libtiff6 libwebp7 libxnvctrl0 157s ocl-icd-libopencl1 openmpi-bin openmpi-common relion 157s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 19.3 MB/19.3 MB of archives. 157s After this operation, 101 MB of additional disk space will be used. 157s Get:1 /tmp/autopkgtest.ZbW7nV/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 157s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240303-1ubuntu1 [9392 B] 157s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 157s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libevent-pthreads-2.1-7 s390x 2.1.12-stable-9 [7692 B] 157s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x librdmacm1t64 s390x 50.0-2 [74.1 kB] 157s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libfabric1 s390x 1.17.0-3build1 [566 kB] 158s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 158s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libfftw3-double3 s390x 3.3.10-1ubuntu1 [465 kB] 159s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libfftw3-single3 s390x 3.3.10-1ubuntu1 [449 kB] 160s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x libhwloc15 s390x 2.10.0-1 [174 kB] 160s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 160s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 160s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x libmunge2 s390x 0.5.15-3ubuntu1 [17.3 kB] 161s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libpciaccess0 s390x 0.17-3 [18.5 kB] 161s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu1 [11.7 kB] 161s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1 [39.1 kB] 161s Get:17 http://ftpmaster.internal/ubuntu noble/universe s390x libhwloc-plugins s390x 2.10.0-1 [16.1 kB] 161s Get:18 http://ftpmaster.internal/ubuntu noble/universe s390x libpmix2 s390x 5.0.1-4 [722 kB] 162s Get:19 http://ftpmaster.internal/ubuntu noble/universe s390x libopenmpi3 s390x 4.1.6-5ubuntu1 [3024 kB] 166s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 167s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 167s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 167s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 167s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x openmpi-common all 4.1.6-5ubuntu1 [178 kB] 167s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x openmpi-bin s390x 4.1.6-5ubuntu1 [92.5 kB] 168s Get:26 http://ftpmaster.internal/ubuntu noble/universe s390x relion s390x 3.1.3-3build1 [12.6 MB] 176s Fetched 19.3 MB in 19s (1038 kB/s) 176s Selecting previously unselected package libatomic1:s390x. 176s (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 ... 51727 files and directories currently installed.) 176s Preparing to unpack .../00-libatomic1_14-20240303-1ubuntu1_s390x.deb ... 176s Unpacking libatomic1:s390x (14-20240303-1ubuntu1) ... 176s Selecting previously unselected package libdeflate0:s390x. 176s Preparing to unpack .../01-libdeflate0_1.19-1_s390x.deb ... 176s Unpacking libdeflate0:s390x (1.19-1) ... 176s Selecting previously unselected package libevent-pthreads-2.1-7:s390x. 176s Preparing to unpack .../02-libevent-pthreads-2.1-7_2.1.12-stable-9_s390x.deb ... 176s Unpacking libevent-pthreads-2.1-7:s390x (2.1.12-stable-9) ... 176s Selecting previously unselected package librdmacm1t64:s390x. 176s Preparing to unpack .../03-librdmacm1t64_50.0-2_s390x.deb ... 176s Unpacking librdmacm1t64:s390x (50.0-2) ... 176s Selecting previously unselected package libfabric1:s390x. 176s Preparing to unpack .../04-libfabric1_1.17.0-3build1_s390x.deb ... 176s Unpacking libfabric1:s390x (1.17.0-3build1) ... 176s Selecting previously unselected package libgomp1:s390x. 176s Preparing to unpack .../05-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 176s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 176s Selecting previously unselected package libfftw3-double3:s390x. 176s Preparing to unpack .../06-libfftw3-double3_3.3.10-1ubuntu1_s390x.deb ... 176s Unpacking libfftw3-double3:s390x (3.3.10-1ubuntu1) ... 176s Selecting previously unselected package libfftw3-single3:s390x. 176s Preparing to unpack .../07-libfftw3-single3_3.3.10-1ubuntu1_s390x.deb ... 176s Unpacking libfftw3-single3:s390x (3.3.10-1ubuntu1) ... 176s Selecting previously unselected package libhwloc15:s390x. 176s Preparing to unpack .../08-libhwloc15_2.10.0-1_s390x.deb ... 176s Unpacking libhwloc15:s390x (2.10.0-1) ... 176s Selecting previously unselected package libjpeg-turbo8:s390x. 176s Preparing to unpack .../09-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 176s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 176s Selecting previously unselected package libjpeg8:s390x. 176s Preparing to unpack .../10-libjpeg8_8c-2ubuntu11_s390x.deb ... 176s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 176s Selecting previously unselected package libmunge2:s390x. 176s Preparing to unpack .../11-libmunge2_0.5.15-3ubuntu1_s390x.deb ... 176s Unpacking libmunge2:s390x (0.5.15-3ubuntu1) ... 176s Selecting previously unselected package libpciaccess0:s390x. 176s Preparing to unpack .../12-libpciaccess0_0.17-3_s390x.deb ... 176s Unpacking libpciaccess0:s390x (0.17-3) ... 176s Selecting previously unselected package libxnvctrl0:s390x. 176s Preparing to unpack .../13-libxnvctrl0_510.47.03-0ubuntu1_s390x.deb ... 176s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu1) ... 176s Selecting previously unselected package ocl-icd-libopencl1:s390x. 176s Preparing to unpack .../14-ocl-icd-libopencl1_2.3.2-1_s390x.deb ... 176s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1) ... 176s Selecting previously unselected package libhwloc-plugins:s390x. 176s Preparing to unpack .../15-libhwloc-plugins_2.10.0-1_s390x.deb ... 176s Unpacking libhwloc-plugins:s390x (2.10.0-1) ... 176s Selecting previously unselected package libpmix2:s390x. 176s Preparing to unpack .../16-libpmix2_5.0.1-4_s390x.deb ... 176s Unpacking libpmix2:s390x (5.0.1-4) ... 176s Selecting previously unselected package libopenmpi3:s390x. 176s Preparing to unpack .../17-libopenmpi3_4.1.6-5ubuntu1_s390x.deb ... 176s Unpacking libopenmpi3:s390x (4.1.6-5ubuntu1) ... 176s Selecting previously unselected package libsharpyuv0:s390x. 176s Preparing to unpack .../18-libsharpyuv0_1.3.2-0.4_s390x.deb ... 176s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 176s Selecting previously unselected package libjbig0:s390x. 176s Preparing to unpack .../19-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 176s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 176s Selecting previously unselected package libwebp7:s390x. 176s Preparing to unpack .../20-libwebp7_1.3.2-0.4_s390x.deb ... 176s Unpacking libwebp7:s390x (1.3.2-0.4) ... 176s Selecting previously unselected package libtiff6:s390x. 176s Preparing to unpack .../21-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 176s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 176s Selecting previously unselected package openmpi-common. 176s Preparing to unpack .../22-openmpi-common_4.1.6-5ubuntu1_all.deb ... 176s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 176s Selecting previously unselected package openmpi-bin. 176s Preparing to unpack .../23-openmpi-bin_4.1.6-5ubuntu1_s390x.deb ... 176s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 176s Selecting previously unselected package relion. 176s Preparing to unpack .../24-relion_3.1.3-3build1_s390x.deb ... 176s Unpacking relion (3.1.3-3build1) ... 177s Selecting previously unselected package autopkgtest-satdep. 177s Preparing to unpack .../25-1-autopkgtest-satdep.deb ... 177s Unpacking autopkgtest-satdep (0) ... 177s Setting up libsharpyuv0:s390x (1.3.2-0.4) ... 177s Setting up libpciaccess0:s390x (0.17-3) ... 177s Setting up libdeflate0:s390x (1.19-1) ... 177s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 177s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... 177s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu1) ... 177s Setting up libmunge2:s390x (0.5.15-3ubuntu1) ... 177s Setting up libhwloc15:s390x (2.10.0-1) ... 177s Setting up libatomic1:s390x (14-20240303-1ubuntu1) ... 177s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 177s Setting up libfftw3-double3:s390x (3.3.10-1ubuntu1) ... 177s Setting up libwebp7:s390x (1.3.2-0.4) ... 177s Setting up ocl-icd-libopencl1:s390x (2.3.2-1) ... 177s Setting up openmpi-common (4.1.6-5ubuntu1) ... 177s Setting up librdmacm1t64:s390x (50.0-2) ... 177s Setting up libevent-pthreads-2.1-7:s390x (2.1.12-stable-9) ... 177s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 177s Setting up libfabric1:s390x (1.17.0-3build1) ... 177s Setting up libfftw3-single3:s390x (3.3.10-1ubuntu1) ... 177s Setting up libhwloc-plugins:s390x (2.10.0-1) ... 177s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 177s Setting up libpmix2:s390x (5.0.1-4) ... 177s Setting up libopenmpi3:s390x (4.1.6-5ubuntu1) ... 177s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 177s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 177s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 177s Setting up relion (3.1.3-3build1) ... 177s Setting up autopkgtest-satdep (0) ... 177s Processing triggers for man-db (2.12.0-3) ... 177s Processing triggers for libc-bin (2.39-0ubuntu2) ... 180s (Reading database ... 52291 files and directories currently installed.) 180s Removing autopkgtest-satdep (0) ... 180s autopkgtest [14:34:18]: test command1: /usr/bin/relion_refine 180s autopkgtest [14:34:18]: test command1: [----------------------- 181s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 181s ====== General options ===== 181s --i () : Input images (in a star-file) 181s --o () : Output rootname 181s --iter (50) : Maximum number of iterations to perform 181s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 181s --K (1) : Number of references to be refined 181s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 181s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 181s --flatten_solvent (false) : Perform masking on the references as well? 181s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 181s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 181s --lowpass_mask (None) : User-provided mask for low-pass filtering 181s --lowpass (0) : User-provided cutoff for region specified above 181s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 181s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 181s --split_random_halves (false) : Refine two random halves of the data completely separately 181s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 181s ====== Initialisation ===== 181s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 181s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 181s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 181s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 181s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 181s ====== Orientations ===== 181s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 181s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 181s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 181s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 181s --sym (c1) : Symmetry group 181s --relax_sym () : Symmetry to be relaxed 181s --offset_range (6) : Search range for origin offsets (in pixels) 181s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 181s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 181s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 181s --auto_refine (false) : Perform 3D auto-refine procedure? 181s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 181s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 181s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 181s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 181s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 181s --skip_align (false) : Skip orientational assignment (only classify)? 181s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 181s --bimodal_psi (false) : Do bimodal searches of psi angle? 181s ====== Helical reconstruction (in development...) ===== 181s --helix (false) : Perform 3D classification or refinement for helices? 181s --ignore_helical_symmetry (false) : Ignore helical symmetry? 181s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 181s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 181s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 181s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 181s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 181s --helical_rise_initial (0.) : Helical rise (in Angstroms) 181s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 181s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 181s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 181s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 181s --helical_z_percentage (0.3) : This box length along the center of Z axis contains good information of the helix. Important in imposing and refining symmetry 181s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 181s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 181s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 181s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 181s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 181s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 181s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 181s ====== Corrections ===== 181s --ctf (false) : Perform CTF correction? 181s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 181s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 181s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 181s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 181s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 181s --norm (false) : Perform normalisation-error correction? 181s --scale (false) : Perform intensity-scale corrections on image groups? 181s --no_norm (false) : Switch off normalisation-error correction? 181s --no_scale (false) : Switch off intensity-scale corrections on image groups? 181s ====== Stochastic Gradient Descent ===== 181s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 181s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 181s --sgd_ini_iter (50) : Number of initial SGD iterations 181s --sgd_fin_iter (50) : Number of final SGD iterations 181s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 181s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 181s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 181s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 181s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 181s --mu (0.9) : Momentum parameter for SGD updates 181s --sgd_stepsize (0.5) : Step size parameter for SGD updates 181s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 181s --sgd_sigma2fudge_halflife (-1) : Initialise SGD with 8x higher noise-variance, and reduce with this half-life in # of particles (default is keep normal variance) 181s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 181s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 181s ====== Computation ===== 181s --pool (1) : Number of images to pool for each thread task 181s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 181s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 181s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 181s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 181s --preread_images (false) : Use this to let the leader process read all particles into memory. Be careful you have enough RAM for large data sets! 181s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 181s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 181s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 181s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 181s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 181s --gpu (false) : Use available gpu resources for some calculations 181s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 181s ====== Expert options ===== 181s --pad (2) : Oversampling factor for the Fourier transforms of the references 181s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 181s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 181s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 181s --verb (1) : Verbosity (1=normal, 0=silent) 181s --random_seed (-1) : Number for the random seed generator 181s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 181s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 181s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 181s --fix_sigma_noise (false) : Fix the experimental noise spectra? 181s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 181s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 181s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 181s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 181s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 181s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 181s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 181s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 181s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 181s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 181s --failsafe_threshold (40) : Maximum number of particles permitted to be handled by fail-safe mode, due to zero sum of weights, before exiting with an error (GPU only). 181s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 181s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 181s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 181s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 181s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 181s --trust_ref_size (false) : Trust the pixel and box size of the input reference; by default the program will die if these are different from the first optics group of the data 181s --maxsig (-1) : Maximum number of poses & translations to consider 181s --skip_gridding (false) : Skip gridding in the M step 181s --version : Print RELION version and exit 181s autopkgtest [14:34:19]: test command1: -----------------------] 181s command1 PASS (superficial) 181s autopkgtest [14:34:19]: test command1: - - - - - - - - - - results - - - - - - - - - - 182s autopkgtest [14:34:20]: @@@@@@@@@@@@@@@@@@@@ summary 182s command1 PASS (superficial) 198s Creating nova instance adt-noble-s390x-relion-20240321-143118-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID f7ee8f0f-480f-4014-94f0-3be2a19e259d)...