0s autopkgtest [09:45:33]: starting date and time: 2024-03-26 09:45:33+0000 0s autopkgtest [09:45:33]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [09:45:33]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.morms05_/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 --apt-upgrade relion --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=fftw3/3.3.10-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-11.secgroup --name adt-noble-s390x-relion-20240326-094533-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/ 89s autopkgtest [09:47:02]: testbed dpkg architecture: s390x 89s autopkgtest [09:47:02]: testbed apt version: 2.7.12 89s autopkgtest [09:47:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 90s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 90s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 91s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4022 kB] 92s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 92s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 92s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [690 kB] 93s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 93s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 93s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 93s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4143 kB] 93s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 93s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 93s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 95s Fetched 9589 kB in 4s (2422 kB/s) 95s Reading package lists... 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Calculating upgrade... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 242 not upgraded. 98s Unknown architecture, assuming PC-style ttyS0 98s sh: Attempting to set up Debian/Ubuntu apt sources automatically 98s sh: Distribution appears to be Ubuntu 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s eatmydata is already the newest version (131-1). 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s dbus is already the newest version (1.14.10-4ubuntu1). 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s rng-tools-debian is already the newest version (2.4). 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s The following packages will be REMOVED: 100s cloud-init* python3-configobj* python3-debconf* 100s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 100s After this operation, 3256 kB disk space will be freed. 100s (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 ... 52170 files and directories currently installed.) 100s Removing cloud-init (24.1.2-0ubuntu1) ... 101s Removing python3-configobj (5.0.8-3) ... 101s Removing python3-debconf (1.5.86) ... 101s Processing triggers for man-db (2.12.0-3) ... 101s (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 ... 51781 files and directories currently installed.) 101s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 102s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 102s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 102s invoke-rc.d: policy-rc.d denied execution of try-restart. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s linux-generic is already the newest version (6.8.0-11.11+1). 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s autopkgtest [09:47:19]: rebooting testbed after setup commands that affected boot 121s autopkgtest [09:47:34]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 124s autopkgtest [09:47:37]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 129s Get:1 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (dsc) [2135 B] 129s Get:2 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (tar) [2345 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (diff) [12.0 kB] 129s gpgv: Signature made Sat Feb 4 12:33:57 2023 UTC 129s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 129s gpgv: Can't check signature: No public key 129s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3build1.dsc: no acceptable signature found 129s autopkgtest [09:47:42]: testing package relion version 3.1.3-3build1 130s autopkgtest [09:47:43]: build not needed 133s autopkgtest [09:47:46]: test command1: preparing testbed 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Starting pkgProblemResolver with broken count: 0 134s Starting 2 pkgProblemResolver with broken count: 0 134s Done 135s The following additional packages will be installed: 135s libatomic1 libdeflate0 libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 135s libfftw3-single3 libgomp1 libhwloc-plugins libhwloc15 libjbig0 135s libjpeg-turbo8 libjpeg8 libmunge2 libopenmpi3 libpciaccess0 libpmix2 135s librdmacm1t64 libsharpyuv0 libtiff6 libwebp7 libxnvctrl0 ocl-icd-libopencl1 135s openmpi-bin openmpi-common relion 135s Suggested packages: 135s libfftw3-bin libfftw3-dev opencl-icd gfortran | fortran-compiler 135s The following NEW packages will be installed: 135s autopkgtest-satdep libatomic1 libdeflate0 libevent-pthreads-2.1-7 libfabric1 135s libfftw3-double3 libfftw3-single3 libgomp1 libhwloc-plugins libhwloc15 135s libjbig0 libjpeg-turbo8 libjpeg8 libmunge2 libopenmpi3 libpciaccess0 135s libpmix2 librdmacm1t64 libsharpyuv0 libtiff6 libwebp7 libxnvctrl0 135s ocl-icd-libopencl1 openmpi-bin openmpi-common relion 135s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 135s Need to get 19.3 MB/19.3 MB of archives. 135s After this operation, 101 MB of additional disk space will be used. 135s Get:1 /tmp/autopkgtest.9XCL93/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 135s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240303-1ubuntu1 [9392 B] 135s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 135s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libevent-pthreads-2.1-7 s390x 2.1.12-stable-9 [7692 B] 135s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x librdmacm1t64 s390x 50.0-2 [74.1 kB] 135s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libfabric1 s390x 1.17.0-3build1 [566 kB] 136s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 136s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libfftw3-double3 s390x 3.3.10-1ubuntu1 [465 kB] 136s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libfftw3-single3 s390x 3.3.10-1ubuntu1 [449 kB] 136s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x libhwloc15 s390x 2.10.0-1 [174 kB] 136s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 136s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 136s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x libmunge2 s390x 0.5.15-3ubuntu1 [17.3 kB] 136s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libpciaccess0 s390x 0.17-3 [18.5 kB] 136s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu1 [11.7 kB] 136s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1 [39.1 kB] 136s Get:17 http://ftpmaster.internal/ubuntu noble/universe s390x libhwloc-plugins s390x 2.10.0-1 [16.1 kB] 136s Get:18 http://ftpmaster.internal/ubuntu noble/universe s390x libpmix2 s390x 5.0.1-4 [722 kB] 137s Get:19 http://ftpmaster.internal/ubuntu noble/universe s390x libopenmpi3 s390x 4.1.6-5ubuntu1 [3024 kB] 137s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 137s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 137s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 137s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 137s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x openmpi-common all 4.1.6-5ubuntu1 [178 kB] 137s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x openmpi-bin s390x 4.1.6-5ubuntu1 [92.5 kB] 137s Get:26 http://ftpmaster.internal/ubuntu noble/universe s390x relion s390x 3.1.3-3build1 [12.6 MB] 139s Fetched 19.3 MB in 4s (4333 kB/s) 139s Selecting previously unselected package libatomic1:s390x. 139s (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 ... 51726 files and directories currently installed.) 139s Preparing to unpack .../00-libatomic1_14-20240303-1ubuntu1_s390x.deb ... 139s Unpacking libatomic1:s390x (14-20240303-1ubuntu1) ... 139s Selecting previously unselected package libdeflate0:s390x. 139s Preparing to unpack .../01-libdeflate0_1.19-1_s390x.deb ... 139s Unpacking libdeflate0:s390x (1.19-1) ... 139s Selecting previously unselected package libevent-pthreads-2.1-7:s390x. 139s Preparing to unpack .../02-libevent-pthreads-2.1-7_2.1.12-stable-9_s390x.deb ... 139s Unpacking libevent-pthreads-2.1-7:s390x (2.1.12-stable-9) ... 139s Selecting previously unselected package librdmacm1t64:s390x. 139s Preparing to unpack .../03-librdmacm1t64_50.0-2_s390x.deb ... 139s Unpacking librdmacm1t64:s390x (50.0-2) ... 139s Selecting previously unselected package libfabric1:s390x. 139s Preparing to unpack .../04-libfabric1_1.17.0-3build1_s390x.deb ... 139s Unpacking libfabric1:s390x (1.17.0-3build1) ... 139s Selecting previously unselected package libgomp1:s390x. 139s Preparing to unpack .../05-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 139s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 139s Selecting previously unselected package libfftw3-double3:s390x. 139s Preparing to unpack .../06-libfftw3-double3_3.3.10-1ubuntu1_s390x.deb ... 139s Unpacking libfftw3-double3:s390x (3.3.10-1ubuntu1) ... 139s Selecting previously unselected package libfftw3-single3:s390x. 139s Preparing to unpack .../07-libfftw3-single3_3.3.10-1ubuntu1_s390x.deb ... 139s Unpacking libfftw3-single3:s390x (3.3.10-1ubuntu1) ... 139s Selecting previously unselected package libhwloc15:s390x. 139s Preparing to unpack .../08-libhwloc15_2.10.0-1_s390x.deb ... 139s Unpacking libhwloc15:s390x (2.10.0-1) ... 139s Selecting previously unselected package libjpeg-turbo8:s390x. 140s Preparing to unpack .../09-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 140s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 140s Selecting previously unselected package libjpeg8:s390x. 140s Preparing to unpack .../10-libjpeg8_8c-2ubuntu11_s390x.deb ... 140s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 140s Selecting previously unselected package libmunge2:s390x. 140s Preparing to unpack .../11-libmunge2_0.5.15-3ubuntu1_s390x.deb ... 140s Unpacking libmunge2:s390x (0.5.15-3ubuntu1) ... 140s Selecting previously unselected package libpciaccess0:s390x. 140s Preparing to unpack .../12-libpciaccess0_0.17-3_s390x.deb ... 140s Unpacking libpciaccess0:s390x (0.17-3) ... 140s Selecting previously unselected package libxnvctrl0:s390x. 140s Preparing to unpack .../13-libxnvctrl0_510.47.03-0ubuntu1_s390x.deb ... 140s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu1) ... 140s Selecting previously unselected package ocl-icd-libopencl1:s390x. 140s Preparing to unpack .../14-ocl-icd-libopencl1_2.3.2-1_s390x.deb ... 140s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1) ... 140s Selecting previously unselected package libhwloc-plugins:s390x. 140s Preparing to unpack .../15-libhwloc-plugins_2.10.0-1_s390x.deb ... 140s Unpacking libhwloc-plugins:s390x (2.10.0-1) ... 140s Selecting previously unselected package libpmix2:s390x. 140s Preparing to unpack .../16-libpmix2_5.0.1-4_s390x.deb ... 140s Unpacking libpmix2:s390x (5.0.1-4) ... 140s Selecting previously unselected package libopenmpi3:s390x. 140s Preparing to unpack .../17-libopenmpi3_4.1.6-5ubuntu1_s390x.deb ... 140s Unpacking libopenmpi3:s390x (4.1.6-5ubuntu1) ... 140s Selecting previously unselected package libsharpyuv0:s390x. 140s Preparing to unpack .../18-libsharpyuv0_1.3.2-0.4_s390x.deb ... 140s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 140s Selecting previously unselected package libjbig0:s390x. 140s Preparing to unpack .../19-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 140s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 140s Selecting previously unselected package libwebp7:s390x. 140s Preparing to unpack .../20-libwebp7_1.3.2-0.4_s390x.deb ... 140s Unpacking libwebp7:s390x (1.3.2-0.4) ... 140s Selecting previously unselected package libtiff6:s390x. 140s Preparing to unpack .../21-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 140s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 140s Selecting previously unselected package openmpi-common. 140s Preparing to unpack .../22-openmpi-common_4.1.6-5ubuntu1_all.deb ... 140s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 140s Selecting previously unselected package openmpi-bin. 140s Preparing to unpack .../23-openmpi-bin_4.1.6-5ubuntu1_s390x.deb ... 140s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 140s Selecting previously unselected package relion. 140s Preparing to unpack .../24-relion_3.1.3-3build1_s390x.deb ... 140s Unpacking relion (3.1.3-3build1) ... 140s Selecting previously unselected package autopkgtest-satdep. 140s Preparing to unpack .../25-1-autopkgtest-satdep.deb ... 140s Unpacking autopkgtest-satdep (0) ... 140s Setting up libsharpyuv0:s390x (1.3.2-0.4) ... 140s Setting up libpciaccess0:s390x (0.17-3) ... 140s Setting up libdeflate0:s390x (1.19-1) ... 140s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 140s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... 140s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu1) ... 140s Setting up libmunge2:s390x (0.5.15-3ubuntu1) ... 140s Setting up libhwloc15:s390x (2.10.0-1) ... 140s Setting up libatomic1:s390x (14-20240303-1ubuntu1) ... 140s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 140s Setting up libfftw3-double3:s390x (3.3.10-1ubuntu1) ... 140s Setting up libwebp7:s390x (1.3.2-0.4) ... 140s Setting up ocl-icd-libopencl1:s390x (2.3.2-1) ... 140s Setting up openmpi-common (4.1.6-5ubuntu1) ... 140s Setting up librdmacm1t64:s390x (50.0-2) ... 140s Setting up libevent-pthreads-2.1-7:s390x (2.1.12-stable-9) ... 140s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 140s Setting up libfabric1:s390x (1.17.0-3build1) ... 140s Setting up libfftw3-single3:s390x (3.3.10-1ubuntu1) ... 140s Setting up libhwloc-plugins:s390x (2.10.0-1) ... 140s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 140s Setting up libpmix2:s390x (5.0.1-4) ... 140s Setting up libopenmpi3:s390x (4.1.6-5ubuntu1) ... 140s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 140s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 140s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 140s Setting up relion (3.1.3-3build1) ... 140s Setting up autopkgtest-satdep (0) ... 140s Processing triggers for man-db (2.12.0-3) ... 141s Processing triggers for libc-bin (2.39-0ubuntu6) ... 143s (Reading database ... 52290 files and directories currently installed.) 143s Removing autopkgtest-satdep (0) ... 144s autopkgtest [09:47:57]: test command1: /usr/bin/relion_refine 144s autopkgtest [09:47:57]: test command1: [----------------------- 144s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 144s ====== General options ===== 144s --i () : Input images (in a star-file) 144s --o () : Output rootname 144s --iter (50) : Maximum number of iterations to perform 144s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 144s --K (1) : Number of references to be refined 144s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 144s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 144s --flatten_solvent (false) : Perform masking on the references as well? 144s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 144s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 144s --lowpass_mask (None) : User-provided mask for low-pass filtering 144s --lowpass (0) : User-provided cutoff for region specified above 144s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 144s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 144s --split_random_halves (false) : Refine two random halves of the data completely separately 144s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 144s ====== Initialisation ===== 144s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 144s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 144s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 144s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 144s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 144s ====== Orientations ===== 144s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 144s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 144s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 144s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 144s --sym (c1) : Symmetry group 144s --relax_sym () : Symmetry to be relaxed 144s --offset_range (6) : Search range for origin offsets (in pixels) 144s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 144s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 144s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 144s --auto_refine (false) : Perform 3D auto-refine procedure? 144s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 144s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 144s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 144s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 144s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 144s --skip_align (false) : Skip orientational assignment (only classify)? 144s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 144s --bimodal_psi (false) : Do bimodal searches of psi angle? 144s ====== Helical reconstruction (in development...) ===== 144s --helix (false) : Perform 3D classification or refinement for helices? 144s --ignore_helical_symmetry (false) : Ignore helical symmetry? 144s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 144s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 144s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 144s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 144s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 144s --helical_rise_initial (0.) : Helical rise (in Angstroms) 144s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 144s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 144s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 144s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 144s --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 144s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 144s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 144s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 144s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 144s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 144s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 144s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 144s ====== Corrections ===== 144s --ctf (false) : Perform CTF correction? 144s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 144s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 144s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 144s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 144s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 144s --norm (false) : Perform normalisation-error correction? 144s --scale (false) : Perform intensity-scale corrections on image groups? 144s --no_norm (false) : Switch off normalisation-error correction? 144s --no_scale (false) : Switch off intensity-scale corrections on image groups? 144s ====== Stochastic Gradient Descent ===== 144s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 144s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 144s --sgd_ini_iter (50) : Number of initial SGD iterations 144s --sgd_fin_iter (50) : Number of final SGD iterations 144s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 144s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 144s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 144s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 144s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 144s --mu (0.9) : Momentum parameter for SGD updates 144s --sgd_stepsize (0.5) : Step size parameter for SGD updates 144s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 144s --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) 144s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 144s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 144s ====== Computation ===== 144s --pool (1) : Number of images to pool for each thread task 144s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 144s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 144s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 144s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 144s --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! 144s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 144s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 144s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 144s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 144s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 144s --gpu (false) : Use available gpu resources for some calculations 144s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 144s ====== Expert options ===== 144s --pad (2) : Oversampling factor for the Fourier transforms of the references 144s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 144s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 144s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 144s --verb (1) : Verbosity (1=normal, 0=silent) 144s --random_seed (-1) : Number for the random seed generator 144s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 144s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 144s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 144s --fix_sigma_noise (false) : Fix the experimental noise spectra? 144s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 144s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 144s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 144s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 144s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 144s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 144s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 144s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 144s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 144s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 144s --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). 144s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 144s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 144s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 144s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 144s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 144s --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 144s --maxsig (-1) : Maximum number of poses & translations to consider 144s --skip_gridding (false) : Skip gridding in the M step 144s --version : Print RELION version and exit 144s autopkgtest [09:47:57]: test command1: -----------------------] 145s command1 PASS (superficial) 145s autopkgtest [09:47:58]: test command1: - - - - - - - - - - results - - - - - - - - - - 145s autopkgtest [09:47:58]: @@@@@@@@@@@@@@@@@@@@ summary 145s command1 PASS (superficial) 159s Creating nova instance adt-noble-s390x-relion-20240326-094533-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240326.img (UUID c527e0e4-2e65-4e86-ad63-05d7f665f2fb)...