=== RELION MPI setup === + Number of MPI processes = 6 + Leader (0) runs on host = hex.lmb.internal + Follower 1 runs on host = hex.lmb.internal + Follower 2 runs on host = hex.lmb.internal + Follower 3 runs on host = hex.lmb.internal + Follower 4 runs on host = hex.lmb.internal + Follower 5 runs on host = hex.lmb.internal ================= + Reading Refine3D/job019/run_data.star... + Using movie pixel size from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.824 A + Using coord. pixel size from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.824 A + Using dose per frame from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.98 e/A^2 + Reading references ... + The names of the reference half maps and the mask were taken from the PostProcess STAR file. - Half map 1: Refine3D/job019/run_half1_class001_unfil.mrc - Half map 2: Refine3D/job019/run_half2_class001_unfil.mrc - Mask: MaskCreate/job015/mask.mrc + Masking references ... + Transforming references ... + Initializing motion estimator ... + Performing loop over micrographs ... 000/??? sec ~~(,_,"> [oo]-------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 0 on node hex exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- === RELION MPI setup === + Number of MPI processes = 6 + Leader (0) runs on host = hex.lmb.internal + Follower 1 runs on host = hex.lmb.internal ================= + Follower 2 runs on host = hex.lmb.internal + Follower 3 runs on host = hex.lmb.internal + Follower 4 runs on host = hex.lmb.internal + Follower 5 runs on host = hex.lmb.internal + Reading Refine3D/job019/run_data.star... + Using movie pixel size from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.824 A + Using coord. pixel size from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.824 A + Using dose per frame from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.98 e/A^2 - Will estimate motion for all 286 micrographs - none are finished - Will recombine frames for all 286 micrographs - none are finished + Reading references ... + The names of the reference half maps and the mask were taken from the PostProcess STAR file. - Half map 1: Refine3D/job019/run_half1_class001_unfil.mrc - Half map 2: Refine3D/job019/run_half2_class001_unfil.mrc - Mask: MaskCreate/job015/mask.mrc + Masking references ... + Transforming references ... + Initializing motion estimator ... + Performing loop over micrographs ... 000/??? sec ~~(,_,"> [oo] 0.22/10.40 min .~~(,_,"> 0.95/22.80 min ..~~(,_,"> 1.53/24.53 min ...~~(,_,"> exiting with an abort ... ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[12239,1],4] Exit code: 2 -------------------------------------------------------------------------- :: initializing oneAPI environment ... slurm_script: BASH_VERSION = 4.2.46(2)-release :: advisor -- latest :: ccl -- latest :: clck -- latest :: compiler -- latest :: dal -- latest :: debugger -- latest :: dev-utilities -- latest :: dnnl -- latest :: dpcpp-ct -- latest :: dpl -- latest :: inspector -- latest :: intelpython -- latest :: ipp -- latest :: ippcp -- latest :: ipp -- latest :: itac -- latest :: mkl -- latest :: mpi -- latest :: tbb -- latest :: vtune -- latest :: oneAPI environment initialized :: * RELION 4.0 CPU JOB ENVIRONMENT * PATH TO mpiexec: /public/EM/OpenMPI/openmpi-4.0.1/build/bin/mpiexec PATH TO relion_refine_mpi: /public/EM/RELION/relion-4.0-dev/build-cpu/bin/relion_refine_mpi LIBRARIES FOR relion_refine_mpi: linux-vdso.so.1 => (0x00007ffe9df6f000) libmkl_intel_lp64.so.1 => /net/nfs1/public/compilers/intel-2021.3/mkl/2021.3.0/lib/intel64/libmkl_intel_lp64.so.1 (0x000014b3c3261000) libmkl_intel_thread.so.1 => /net/nfs1/public/compilers/intel-2021.3/mkl/2021.3.0/lib/intel64/libmkl_intel_thread.so.1 (0x000014b3bf947000) libmkl_core.so.1 => /net/nfs1/public/compilers/intel-2021.3/mkl/2021.3.0/lib/intel64/libmkl_core.so.1 (0x000014b3bb2d8000) libiomp5.so => /net/nfs1/public/compilers/intel-2021.3/compiler/2021.3.0/linux/compiler/lib/intel64_lin/libiomp5.so (0x000014b3baec3000) libimf.so => /net/nfs1/public/compilers/intel-2021.3/compiler/2021.3.0/linux/compiler/lib/intel64_lin/libimf.so (0x000014b3ba83b000) libmpi.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libmpi.so.40 (0x000014b3ba528000) libdl.so.2 => /lib64/libdl.so.2 (0x000014b3ba324000) libtbb.so.12 => /net/nfs1/public/compilers/intel-2021.3/tbb/2021.3.0/env/../lib/intel64/gcc4.8/libtbb.so.12 (0x000014b3ba0ab000) libtiff.so.5 => /lib64/libtiff.so.5 (0x000014b3b9e37000) libpng15.so.15 => /lib64/libpng15.so.15 (0x000014b3b9c0c000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x000014b3b99b7000) libstdc++.so.6 => /public/gcc/10_2_0/lib64/libstdc++.so.6 (0x000014b3b95ea000) libm.so.6 => /lib64/libm.so.6 (0x000014b3b92e8000) libgcc_s.so.1 => /public/gcc/10_2_0/lib64/libgcc_s.so.1 (0x000014b3b90d0000) libpthread.so.0 => /lib64/libpthread.so.0 (0x000014b3b8eb4000) libc.so.6 => /lib64/libc.so.6 (0x000014b3b8ae6000) librt.so.1 => /lib64/librt.so.1 (0x000014b3b88de000) /lib64/ld-linux-x86-64.so.2 (0x000014b3c3ff9000) libintlc.so.5 => /net/nfs1/public/compilers/intel-2021.3/compiler/2021.3.0/linux/compiler/lib/intel64_lin/libintlc.so.5 (0x000014b3b8666000) libopen-rte.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libopen-rte.so.40 (0x000014b3b83ac000) libopen-pal.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libopen-pal.so.40 (0x000014b3b809e000) libutil.so.1 => /lib64/libutil.so.1 (0x000014b3b7e9b000) libz.so.1 => /lib64/libz.so.1 (0x000014b3b7c85000) libjbig.so.2.0 => /lib64/libjbig.so.2.0 (0x000014b3b7a79000) RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE: /public/EM/SIDESPLITTER/sidesplitter_wrapper.sh SIDESPLITTER: /public/EM/SIDESPLITTER/sidesplitter RUN STARTED AT Wed Jan 12 21:21:25 GMT 2022 TO KILL THIS JOB, RUN: scancel 268405 ------------------------------------------------------------------------------------ === RELION MPI setup === + Number of MPI processes = 4 + Leader (0) runs on host = fmb385.lmb.internal + Follower 1 runs on host = fmb385.lmb.internal ================= + Follower 2 runs on host = fmb385.lmb.internal + Follower 3 runs on host = fmb385.lmb.internal + Reading Refine3D/job019/run_data.star... + Using movie pixel size from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.824 A + Using coord. pixel size from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.824 A + Using dose per frame from MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.star: 0.98 e/A^2 - Will only estimate motion for 266 unfinished micrographs - Will recombine frames for all 286 micrographs - none are finished + Reading references ... + The names of the reference half maps and the mask were taken from the PostProcess STAR file. - Half map 1: Refine3D/job019/run_half1_class001_unfil.mrc - Half map 2: Refine3D/job019/run_half2_class001_unfil.mrc - Mask: MaskCreate/job015/mask.mrc + Masking references ... + Transforming references ... + Initializing motion estimator ... + Performing loop over micrographs ... 000/??? sec ~~(,_,"> [oo] 0.23/15.63 min ~~(,_,"> 0.70/23.45 min .~~(,_,"> 0.97/21.58 min ..~~(,_,"> 1.25/20.93 min ...~~(,_,"> 1.52/20.32 min ....~~(,_,"> 1.93/21.58 min .....~~(,_,"> 2.22/21.22 min ......~~(,_,"> 2.47/20.65 min .......~~(,_,"> 2.68/19.97 min ........~~(,_,"> 2.98/19.98 min ........~~(,_,"> 3.25/19.78 min .........~~(,_,"> 3.97/22.13 min ..........~~(,_,"> 4.25/21.90 min ...........~~(,_,"> 4.47/21.37 min ............~~(,_,"> 5.07/22.62 min .............~~(,_,"> 5.72/23.93 min ..............~~(,_,"> 6.70/26.40 min ...............~~(,_,"> 7.35/27.35 min ................~~(,_,"> 7.73/27.27 min .................~~(,_,"> 8.32/27.85 min .................~~(,_,"> 8.90/28.38 min ..................~~(,_,"> 9.63/29.33 min ...................~~(,_,"> 10.30/30.00 min ....................~~(,_,"> 10.98/30.65 min .....................~~(,_,"> 11.37/30.45 min ......................~~(,_,"> 11.78/30.35 min .......................~~(,_,"> 12.08/29.98 min ........................~~(,_,"> 12.40/29.67 min .........................~~(,_,"> 12.78/29.53 min .........................~~(,_,"> 13.95/31.15 min ..........................~~(,_,"> 14.27/30.83 min ...........................~~(,_,"> 14.60/30.57 min ............................~~(,_,"> 14.95/30.35 min .............................~~(,_,"> 15.18/29.92 min ..............................~~(,_,"> 15.88/30.40 min ...............................~~(,_,"> 16.90/31.45 min ................................~~(,_,"> 17.20/31.13 min .................................~~(,_,"> 17.42/30.70 min ..................................~~(,_,"> 17.72/30.43 min ..................................~~(,_,"> 18.50/30.98 min ...................................~~(,_,"> 19.48/31.83 min ....................................~~(,_,"> 19.85/31.65 min .....................................~~(,_,"> 20.63/32.13 min ......................................~~(,_,"> 21.62/32.90 min .......................................~~(,_,"> 22.07/32.85 min ........................................~~(,_,"> 22.77/33.15 min .........................................~~(,_,"> 23.38/33.33 min ..........................................~~(,_,"> 23.70/33.07 min ..........................................~~(,_,"> 24.08/32.92 min ...........................................~~(,_,"> 24.35/32.62 min ............................................~~(,_,"> 24.57/32.27 min .............................................~~(,_,"> 25.13/32.38 min ..............................................~~(,_,"> 25.58/32.33 min ...............................................~~(,_,"> 26.12/32.40 min ................................................~~(,_,"> 26.37/32.12 min .................................................~~(,_,"> 26.57/31.78 min ..................................................~~(,_,"> 26.85/31.55 min ...................................................~~(,_,"> 27.18/31.40 min ...................................................~~(,_,"> 27.62/31.35 min ....................................................~~(,_,"> 27.93/31.18 min .....................................................~~(,_,"> 28.68/31.50 min ......................................................~~(,_,"> 28.97/31.30 min .......................................................~~(,_,"> 29.23/31.08 min ........................................................~~(,_,"> 29.55/30.93 min .........................................................~~(,_,"> 29.87/30.78 min ..........................................................~~(,_,"> 30.35/30.80 min ...........................................................~~(,_,"> 30.98/30.98 min ............................................................~~(,_,"> + Fitting B/k-factors for optics-group-1 using FCCs from all particles between 15 and 118 pixels, or 20 and 2.68149 Angstrom ... + Combining frames for micrographs ... 000/??? sec ~~(,_,"> [oo] 0.25/18.00 min ~~(,_,"> 0.83/30.00 min .~~(,_,"> 1.32/31.60 min ..~~(,_,"> 1.63/29.40 min ...~~(,_,"> 2.08/30.00 min ....~~(,_,"> 2.38/28.60 min ....~~(,_,"> 2.72/27.93 min .....~~(,_,"> 3.03/27.30 min ......~~(,_,"> 3.50/28.00 min .......~~(,_,"> 3.83/27.60 min ........~~(,_,"> 4.13/27.05 min .........~~(,_,"> 4.38/26.30 min ..........~~(,_,"> 4.78/26.48 min ..........~~(,_,"> 5.12/26.30 min ...........~~(,_,"> 5.97/28.63 min ............~~(,_,"> 6.27/28.20 min .............~~(,_,"> 6.52/27.60 min ..............~~(,_,"> 7.23/28.93 min ...............~~(,_,"> 8.00/30.30 min ...............~~(,_,"> 9.08/32.70 min ................~~(,_,"> 9.78/33.53 min .................~~(,_,"> 10.18/33.32 min ..................~~(,_,"> 10.98/34.37 min ...................~~(,_,"> 11.60/34.80 min ...................~~(,_,"> 12.37/35.60 min ....................~~(,_,"> 13.10/36.27 min .....................~~(,_,"> 13.87/36.97 min ......................~~(,_,"> 14.27/36.68 min .......................~~(,_,"> 14.78/36.70 min ........................~~(,_,"> 15.12/36.27 min .........................~~(,_,"> 15.50/36.00 min .........................~~(,_,"> 15.97/35.92 min ..........................~~(,_,"> 17.18/37.48 min ...........................~~(,_,"> 17.43/36.92 min ............................~~(,_,"> 17.88/36.78 min .............................~~(,_,"> 18.33/36.67 min ..............................~~(,_,"> 18.63/36.25 min ..............................~~(,_,"> 19.48/36.90 min ...............................~~(,_,"> 20.67/38.15 min ................................~~(,_,"> 21.00/37.80 min .................................~~(,_,"> 21.25/37.32 min ..................................~~(,_,"> 21.60/37.02 min ...................................~~(,_,"> 22.42/37.53 min ...................................~~(,_,"> 23.40/38.28 min ....................................~~(,_,"> 23.83/38.13 min .....................................~~(,_,"> 24.73/38.70 min ......................................~~(,_,"> 25.82/39.53 min .......................................~~(,_,"> 26.32/39.47 min ........................................~~(,_,"> 26.95/39.60 min ........................................~~(,_,"> 27.20/39.17 min .........................................~~(,_,"> 27.47/38.77 min ..........................................~~(,_,"> 27.72/38.37 min ...........................................~~(,_,"> 28.55/38.78 min ............................................~~(,_,"> 29.30/39.07 min .............................................~~(,_,"> 29.67/38.83 min .............................................~~(,_,"> 30.20/38.82 min ..............................................~~(,_,"> 30.52/38.53 min ...............................................~~(,_,"> 30.75/38.17 min ................................................~~(,_,"> 31.43/38.35 min .................................................~~(,_,"> 31.95/38.33 min ..................................................~~(,_,"> 32.62/38.48 min ..................................................~~(,_,"> 32.92/38.22 min ...................................................~~(,_,"> 33.17/37.90 min ....................................................~~(,_,"> 33.50/37.68 min .....................................................~~(,_,"> 33.93/37.58 min ......................................................~~(,_,"> 34.52/37.65 min .......................................................~~(,_,"> 34.93/37.53 min .......................................................~~(,_,"> 35.87/37.97 min ........................................................~~(,_,"> 36.20/37.77 min .........................................................~~(,_,"> 36.53/37.57 min ..........................................................~~(,_,"> 36.92/37.43 min ...........................................................~~(,_,"> 37.35/37.35 min ............................................................~~(,_,"> + Aligning and combining frames for micrographs ... + Combining all EPS and STAR files ... + Pixel size for optics group 1: 0.824 + Done! + Written logfile in Polish/job022/logfile.pdf + Written new particle STAR file in Polish/job022/shiny.star ------------------------------------------------------------------------------------ RUN FINISHED AT Wed Jan 12 22:37:49 GMT 2022 ELAPSED WALL CLOCK TIME IN SECONDS: 4584