0s autopkgtest [12:23:13]: starting date and time: 2024-03-18 12:23:13+0000 0s autopkgtest [12:23:13]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [12:23:13]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zlotomgt/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-3@bos01-arm64-10.secgroup --name adt-noble-arm64-relion-20240318-122313-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://us.ports.ubuntu.com/ubuntu-ports/ 154s autopkgtest [12:25:47]: testbed dpkg architecture: arm64 155s autopkgtest [12:25:48]: testbed apt version: 2.7.12 155s autopkgtest [12:25:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 156s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 156s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 156s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3727 kB] 156s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 156s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 156s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 156s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 156s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 156s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4102 kB] 156s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 156s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 156s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 159s Fetched 9245 kB in 2s (5536 kB/s) 159s Reading package lists... 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 162s Calculating upgrade... 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 163s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s sh: Attempting to set up Debian/Ubuntu apt sources automatically 163s sh: Distribution appears to be Ubuntu 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s eatmydata is already the newest version (131-1). 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s dbus is already the newest version (1.14.10-4ubuntu1). 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s rng-tools-debian is already the newest version (2.4). 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 167s The following packages will be REMOVED: 167s cloud-init* python3-configobj* python3-debconf* 167s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 167s After this operation, 3252 kB disk space will be freed. 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 cloud-init (24.1.1-0ubuntu1) ... 168s Removing python3-configobj (5.0.8-3) ... 168s Removing python3-debconf (1.5.86) ... 168s Processing triggers for man-db (2.12.0-3) ... 168s (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 ... 75461 files and directories currently installed.) 168s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 169s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 169s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 169s invoke-rc.d: policy-rc.d denied execution of try-restart. 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s linux-generic is already the newest version (6.8.0-11.11+1). 170s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 170s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 170s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 170s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 172s Reading package lists... 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s Calculating upgrade... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s autopkgtest [12:26:07]: rebooting testbed after setup commands that affected boot 214s autopkgtest [12:26:47]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 217s autopkgtest [12:26:50]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 219s Get:1 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (dsc) [2135 B] 219s Get:2 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (tar) [2345 kB] 219s Get:3 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (diff) [12.0 kB] 219s gpgv: Signature made Sat Feb 4 12:33:57 2023 UTC 219s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 219s gpgv: Can't check signature: No public key 219s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3build1.dsc: no acceptable signature found 219s autopkgtest [12:26:52]: testing package relion version 3.1.3-3build1 219s autopkgtest [12:26:52]: build not needed 220s autopkgtest [12:26:53]: test command1: preparing testbed 244s Reading package lists... 244s Building dependency tree... 244s Reading state information... 244s Starting pkgProblemResolver with broken count: 0 244s Starting 2 pkgProblemResolver with broken count: 0 244s Done 245s The following additional packages will be installed: 245s libamd-comgr2 libamdhip64-5 libatomic1 libdeflate0 libdrm-amdgpu1 245s libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 libfftw3-single3 245s libgomp1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libjbig0 245s libjpeg-turbo8 libjpeg8 liblerc4 libllvm17 libmunge2 libopenmpi3 245s libpciaccess0 libpmix2 librdmacm1t64 libsharpyuv0 libtiff6 libucx0 libwebp7 245s libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common relion 245s Suggested packages: 245s libfftw3-bin libfftw3-dev opencl-icd gfortran | fortran-compiler 245s The following NEW packages will be installed: 245s autopkgtest-satdep libamd-comgr2 libamdhip64-5 libatomic1 libdeflate0 245s libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 245s libfftw3-single3 libgomp1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins 245s libhwloc15 libjbig0 libjpeg-turbo8 libjpeg8 liblerc4 libllvm17 libmunge2 245s libopenmpi3 libpciaccess0 libpmix2 librdmacm1t64 libsharpyuv0 libtiff6 245s libucx0 libwebp7 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common 245s relion 245s 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. 245s Need to get 65.0 MB/65.0 MB of archives. 245s After this operation, 300 MB of additional disk space will be used. 245s Get:1 /tmp/autopkgtest.H4s201/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 245s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 246s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 247s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 247s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 247s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 247s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 247s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 247s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 247s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 247s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 247s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 247s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 247s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu1 [380 kB] 247s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-single3 arm64 3.3.10-1ubuntu1 [579 kB] 247s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 247s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 247s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 247s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 247s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 247s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 247s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 247s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 247s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 247s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2 arm64 5.0.1-4 [659 kB] 247s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 247s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 247s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 247s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 247s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 247s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 247s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] 247s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-bin arm64 4.1.6-5ubuntu1 [123 kB] 247s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 relion arm64 3.1.3-3build1 [12.5 MB] 248s Fetched 65.0 MB in 3s (25.6 MB/s) 248s Selecting previously unselected package libllvm17:arm64. 248s (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 ... 75406 files and directories currently installed.) 248s Preparing to unpack .../00-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 248s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 249s Selecting previously unselected package libamd-comgr2:arm64. 249s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 249s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 249s Selecting previously unselected package libdrm-amdgpu1:arm64. 249s Preparing to unpack .../02-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 249s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 249s Selecting previously unselected package libhsakmt1:arm64. 249s Preparing to unpack .../03-libhsakmt1_5.7.0-1_arm64.deb ... 249s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 249s Selecting previously unselected package libhsa-runtime64-1. 249s Preparing to unpack .../04-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 249s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 249s Selecting previously unselected package libamdhip64-5. 249s Preparing to unpack .../05-libamdhip64-5_5.2.3-12_arm64.deb ... 249s Unpacking libamdhip64-5 (5.2.3-12) ... 249s Selecting previously unselected package libatomic1:arm64. 249s Preparing to unpack .../06-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 249s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 249s Selecting previously unselected package libdeflate0:arm64. 249s Preparing to unpack .../07-libdeflate0_1.19-1_arm64.deb ... 249s Unpacking libdeflate0:arm64 (1.19-1) ... 249s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 249s Preparing to unpack .../08-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 249s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 249s Selecting previously unselected package librdmacm1t64:arm64. 249s Preparing to unpack .../09-librdmacm1t64_50.0-2_arm64.deb ... 249s Unpacking librdmacm1t64:arm64 (50.0-2) ... 249s Selecting previously unselected package libfabric1:arm64. 249s Preparing to unpack .../10-libfabric1_1.17.0-3_arm64.deb ... 249s Unpacking libfabric1:arm64 (1.17.0-3) ... 249s Selecting previously unselected package libgomp1:arm64. 249s Preparing to unpack .../11-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 249s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 249s Selecting previously unselected package libfftw3-double3:arm64. 249s Preparing to unpack .../12-libfftw3-double3_3.3.10-1ubuntu1_arm64.deb ... 249s Unpacking libfftw3-double3:arm64 (3.3.10-1ubuntu1) ... 249s Selecting previously unselected package libfftw3-single3:arm64. 249s Preparing to unpack .../13-libfftw3-single3_3.3.10-1ubuntu1_arm64.deb ... 249s Unpacking libfftw3-single3:arm64 (3.3.10-1ubuntu1) ... 249s Selecting previously unselected package libhwloc15:arm64. 249s Preparing to unpack .../14-libhwloc15_2.10.0-1_arm64.deb ... 249s Unpacking libhwloc15:arm64 (2.10.0-1) ... 249s Selecting previously unselected package libjpeg-turbo8:arm64. 249s Preparing to unpack .../15-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 249s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 249s Selecting previously unselected package libjpeg8:arm64. 249s Preparing to unpack .../16-libjpeg8_8c-2ubuntu11_arm64.deb ... 249s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 249s Selecting previously unselected package liblerc4:arm64. 249s Preparing to unpack .../17-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 249s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 249s Selecting previously unselected package libmunge2:arm64. 249s Preparing to unpack .../18-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 249s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 249s Selecting previously unselected package libpciaccess0:arm64. 249s Preparing to unpack .../19-libpciaccess0_0.17-3_arm64.deb ... 249s Unpacking libpciaccess0:arm64 (0.17-3) ... 249s Selecting previously unselected package libxnvctrl0:arm64. 249s Preparing to unpack .../20-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 249s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 249s Selecting previously unselected package ocl-icd-libopencl1:arm64. 249s Preparing to unpack .../21-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 249s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 249s Selecting previously unselected package libhwloc-plugins:arm64. 249s Preparing to unpack .../22-libhwloc-plugins_2.10.0-1_arm64.deb ... 249s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 249s Selecting previously unselected package libpmix2:arm64. 249s Preparing to unpack .../23-libpmix2_5.0.1-4_arm64.deb ... 249s Unpacking libpmix2:arm64 (5.0.1-4) ... 250s Selecting previously unselected package libucx0:arm64. 250s Preparing to unpack .../24-libucx0_1.16.0+ds-4_arm64.deb ... 250s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 250s Selecting previously unselected package libopenmpi3:arm64. 250s Preparing to unpack .../25-libopenmpi3_4.1.6-5ubuntu1_arm64.deb ... 250s Unpacking libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 250s Selecting previously unselected package libsharpyuv0:arm64. 250s Preparing to unpack .../26-libsharpyuv0_1.3.2-0.4_arm64.deb ... 250s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 250s Selecting previously unselected package libjbig0:arm64. 250s Preparing to unpack .../27-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 250s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 250s Selecting previously unselected package libwebp7:arm64. 250s Preparing to unpack .../28-libwebp7_1.3.2-0.4_arm64.deb ... 250s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 250s Selecting previously unselected package libtiff6:arm64. 250s Preparing to unpack .../29-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 250s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 250s Selecting previously unselected package openmpi-common. 250s Preparing to unpack .../30-openmpi-common_4.1.6-5ubuntu1_all.deb ... 250s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 250s Selecting previously unselected package openmpi-bin. 250s Preparing to unpack .../31-openmpi-bin_4.1.6-5ubuntu1_arm64.deb ... 250s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 250s Selecting previously unselected package relion. 250s Preparing to unpack .../32-relion_3.1.3-3build1_arm64.deb ... 250s Unpacking relion (3.1.3-3build1) ... 250s Selecting previously unselected package autopkgtest-satdep. 250s Preparing to unpack .../33-1-autopkgtest-satdep.deb ... 250s Unpacking autopkgtest-satdep (0) ... 250s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 250s Setting up libpciaccess0:arm64 (0.17-3) ... 250s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 250s Setting up libdeflate0:arm64 (1.19-1) ... 250s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 250s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 250s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 250s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 250s Setting up libhwloc15:arm64 (2.10.0-1) ... 250s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 250s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 250s Setting up libfftw3-double3:arm64 (3.3.10-1ubuntu1) ... 250s Setting up libwebp7:arm64 (1.3.2-0.4) ... 250s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 250s Setting up openmpi-common (4.1.6-5ubuntu1) ... 250s Setting up librdmacm1t64:arm64 (50.0-2) ... 250s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 250s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 250s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 250s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 250s Setting up libfabric1:arm64 (1.17.0-3) ... 250s Setting up libfftw3-single3:arm64 (3.3.10-1ubuntu1) ... 250s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 250s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 250s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 250s Setting up libhsakmt1:arm64 (5.7.0-1) ... 250s Setting up libpmix2:arm64 (5.0.1-4) ... 250s Setting up libhsa-runtime64-1 (5.7.1-1) ... 250s Setting up libamdhip64-5 (5.2.3-12) ... 250s Setting up libucx0:arm64 (1.16.0+ds-4) ... 250s Setting up libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 250s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 250s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 250s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 250s Setting up relion (3.1.3-3build1) ... 250s Setting up autopkgtest-satdep (0) ... 250s Processing triggers for man-db (2.12.0-3) ... 251s Processing triggers for libc-bin (2.39-0ubuntu2) ... 254s (Reading database ... 76074 files and directories currently installed.) 254s Removing autopkgtest-satdep (0) ... 254s autopkgtest [12:27:27]: test command1: /usr/bin/relion_refine 254s autopkgtest [12:27:27]: test command1: [----------------------- 254s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 254s ====== General options ===== 254s --i () : Input images (in a star-file) 254s --o () : Output rootname 254s --iter (50) : Maximum number of iterations to perform 254s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 254s --K (1) : Number of references to be refined 254s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 254s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 254s --flatten_solvent (false) : Perform masking on the references as well? 254s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 254s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 254s --lowpass_mask (None) : User-provided mask for low-pass filtering 254s --lowpass (0) : User-provided cutoff for region specified above 254s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 254s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 254s --split_random_halves (false) : Refine two random halves of the data completely separately 254s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 254s ====== Initialisation ===== 254s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 254s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 254s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 254s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 254s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 254s ====== Orientations ===== 254s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 254s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 254s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 254s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 254s --sym (c1) : Symmetry group 254s --relax_sym () : Symmetry to be relaxed 254s --offset_range (6) : Search range for origin offsets (in pixels) 254s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 254s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 254s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 254s --auto_refine (false) : Perform 3D auto-refine procedure? 254s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 254s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 254s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 254s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 254s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 254s --skip_align (false) : Skip orientational assignment (only classify)? 254s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 254s --bimodal_psi (false) : Do bimodal searches of psi angle? 254s ====== Helical reconstruction (in development...) ===== 254s --helix (false) : Perform 3D classification or refinement for helices? 254s --ignore_helical_symmetry (false) : Ignore helical symmetry? 254s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 254s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 254s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 254s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 254s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 254s --helical_rise_initial (0.) : Helical rise (in Angstroms) 254s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 254s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 254s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 254s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 254s --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 254s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 254s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 254s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 254s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 254s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 254s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 254s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 254s ====== Corrections ===== 254s --ctf (false) : Perform CTF correction? 254s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 254s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 254s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 254s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 254s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 254s --norm (false) : Perform normalisation-error correction? 254s --scale (false) : Perform intensity-scale corrections on image groups? 254s --no_norm (false) : Switch off normalisation-error correction? 254s --no_scale (false) : Switch off intensity-scale corrections on image groups? 254s ====== Stochastic Gradient Descent ===== 254s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 254s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 254s --sgd_ini_iter (50) : Number of initial SGD iterations 254s --sgd_fin_iter (50) : Number of final SGD iterations 254s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 254s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 254s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 254s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 254s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 254s --mu (0.9) : Momentum parameter for SGD updates 254s --sgd_stepsize (0.5) : Step size parameter for SGD updates 254s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 254s --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) 254s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 254s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 254s ====== Computation ===== 254s --pool (1) : Number of images to pool for each thread task 254s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 254s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 254s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 254s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 254s --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! 254s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 254s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 254s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 254s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 254s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 254s --gpu (false) : Use available gpu resources for some calculations 254s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 254s ====== Expert options ===== 254s --pad (2) : Oversampling factor for the Fourier transforms of the references 254s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 254s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 254s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 254s --verb (1) : Verbosity (1=normal, 0=silent) 254s --random_seed (-1) : Number for the random seed generator 254s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 254s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 254s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 254s --fix_sigma_noise (false) : Fix the experimental noise spectra? 254s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 254s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 254s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 254s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 254s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 254s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 254s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 254s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 254s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 254s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 254s --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). 254s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 254s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 254s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 254s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 254s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 254s --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 254s --maxsig (-1) : Maximum number of poses & translations to consider 254s --skip_gridding (false) : Skip gridding in the M step 254s --version : Print RELION version and exit 255s autopkgtest [12:27:28]: test command1: -----------------------] 255s command1 PASS (superficial) 255s autopkgtest [12:27:28]: test command1: - - - - - - - - - - results - - - - - - - - - - 256s autopkgtest [12:27:29]: @@@@@@@@@@@@@@@@@@@@ summary 256s command1 PASS (superficial) 291s Creating nova instance adt-noble-arm64-relion-20240318-122313-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240317.img (UUID 7a23b7f2-4731-4803-bcc6-08355044298e)...