:: 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 => (0x000014bfc4790000) libmkl_intel_lp64.so.1 => /net/nfs1/public/compilers/intel-2021.3/mkl/2021.3.0/lib/intel64/libmkl_intel_lp64.so.1 (0x000014bfc37d9000) libmkl_intel_thread.so.1 => /net/nfs1/public/compilers/intel-2021.3/mkl/2021.3.0/lib/intel64/libmkl_intel_thread.so.1 (0x000014bfbfebf000) libmkl_core.so.1 => /net/nfs1/public/compilers/intel-2021.3/mkl/2021.3.0/lib/intel64/libmkl_core.so.1 (0x000014bfbb850000) libiomp5.so => /net/nfs1/public/compilers/intel-2021.3/compiler/2021.3.0/linux/compiler/lib/intel64_lin/libiomp5.so (0x000014bfbb43b000) libimf.so => /net/nfs1/public/compilers/intel-2021.3/compiler/2021.3.0/linux/compiler/lib/intel64_lin/libimf.so (0x000014bfbadb3000) libmpi.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libmpi.so.40 (0x000014bfbaaa0000) libdl.so.2 => /lib64/libdl.so.2 (0x000014bfba89c000) libtbb.so.12 => /net/nfs1/public/compilers/intel-2021.3/tbb/2021.3.0/env/../lib/intel64/gcc4.8/libtbb.so.12 (0x000014bfba623000) libtiff.so.5 => /lib64/libtiff.so.5 (0x000014bfba3af000) libpng15.so.15 => /lib64/libpng15.so.15 (0x000014bfba184000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x000014bfb9f2f000) libstdc++.so.6 => /public/gcc/10_2_0/lib64/libstdc++.so.6 (0x000014bfb9b62000) libm.so.6 => /lib64/libm.so.6 (0x000014bfb9860000) libgcc_s.so.1 => /public/gcc/10_2_0/lib64/libgcc_s.so.1 (0x000014bfb9648000) libpthread.so.0 => /lib64/libpthread.so.0 (0x000014bfb942c000) libc.so.6 => /lib64/libc.so.6 (0x000014bfb905e000) librt.so.1 => /lib64/librt.so.1 (0x000014bfb8e56000) /lib64/ld-linux-x86-64.so.2 (0x000014bfc4571000) libintlc.so.5 => /net/nfs1/public/compilers/intel-2021.3/compiler/2021.3.0/linux/compiler/lib/intel64_lin/libintlc.so.5 (0x000014bfb8bde000) libopen-rte.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libopen-rte.so.40 (0x000014bfb8924000) libopen-pal.so.40 => /public/EM/OpenMPI/openmpi-4.0.1/build/lib/libopen-pal.so.40 (0x000014bfb8616000) libutil.so.1 => /lib64/libutil.so.1 (0x000014bfb8413000) libz.so.1 => /lib64/libz.so.1 (0x000014bfb81fd000) libjbig.so.2.0 => /lib64/libjbig.so.2.0 (0x000014bfb7ff1000) RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE: /public/EM/SIDESPLITTER/sidesplitter_wrapper.sh SIDESPLITTER: /public/EM/SIDESPLITTER/sidesplitter RUN STARTED AT Fri Dec 3 07:27:09 GMT 2021 TO KILL THIS JOB, RUN: scancel 255450 ------------------------------------------------------------------------------------ Creating a mask ... == Extending initial binary mask ... 000/??? sec ~~(,_,"> [oo] 0.02/1.98 min ~~(,_,"> 0.03/1.98 min .~~(,_,"> 0.05/1.98 min .~~(,_,"> 0.08/2.48 min ..~~(,_,"> 0.10/2.38 min ..~~(,_,"> 0.12/2.32 min ...~~(,_,"> 0.13/2.28 min ...~~(,_,"> 0.17/2.48 min ....~~(,_,"> 0.18/2.43 min ....~~(,_,"> 0.22/2.58 min .....~~(,_,"> 0.23/2.53 min .....~~(,_,"> 0.25/2.48 min ......~~(,_,"> 0.28/2.60 min ......~~(,_,"> 0.30/2.57 min .......~~(,_,"> 0.32/2.52 min .......~~(,_,"> 0.35/2.62 min ........~~(,_,"> 0.37/2.58 min ........~~(,_,"> 0.38/2.55 min .........~~(,_,"> 0.42/2.62 min .........~~(,_,"> 0.43/2.58 min ..........~~(,_,"> 0.45/2.57 min ..........~~(,_,"> 0.48/2.63 min ...........~~(,_,"> 0.50/2.60 min ...........~~(,_,"> 0.52/2.57 min ............~~(,_,"> 0.55/2.63 min ............~~(,_,"> 0.57/2.60 min .............~~(,_,"> 0.58/2.58 min .............~~(,_,"> 0.62/2.63 min ..............~~(,_,"> 0.63/2.62 min ..............~~(,_,"> 0.65/2.58 min ...............~~(,_,"> 0.67/2.57 min ...............~~(,_,"> 0.70/2.62 min ................~~(,_,"> 0.72/2.60 min ................~~(,_,"> 0.73/2.58 min .................~~(,_,"> 0.77/2.62 min .................~~(,_,"> 0.78/2.60 min ..................~~(,_,"> 0.80/2.58 min ..................~~(,_,"> 0.83/2.62 min ...................~~(,_,"> 0.85/2.60 min ...................~~(,_,"> 0.87/2.58 min ....................~~(,_,"> 0.90/2.63 min ....................~~(,_,"> 0.92/2.62 min .....................~~(,_,"> 0.93/2.60 min .....................~~(,_,"> 0.97/2.63 min ......................~~(,_,"> 0.98/2.62 min ......................~~(,_,"> 1.00/2.60 min .......................~~(,_,"> 1.02/2.58 min .......................~~(,_,"> 1.05/2.62 min ........................~~(,_,"> 1.07/2.60 min ........................~~(,_,"> 1.08/2.58 min .........................~~(,_,"> 1.12/2.62 min .........................~~(,_,"> 1.13/2.60 min ..........................~~(,_,"> 1.15/2.60 min ..........................~~(,_,"> 1.18/2.62 min ...........................~~(,_,"> 1.20/2.62 min ...........................~~(,_,"> 1.22/2.60 min ............................~~(,_,"> 1.25/2.62 min ............................~~(,_,"> 1.27/2.62 min .............................~~(,_,"> 1.28/2.60 min .............................~~(,_,"> 1.32/2.62 min ..............................~~(,_,"> 1.33/2.62 min ..............................~~(,_,"> 1.35/2.60 min ...............................~~(,_,"> 1.37/2.60 min ...............................~~(,_,"> 1.40/2.62 min ................................~~(,_,"> 1.42/2.60 min ................................~~(,_,"> 1.43/2.60 min .................................~~(,_,"> 1.47/2.62 min .................................~~(,_,"> 1.48/2.62 min ..................................~~(,_,"> 1.50/2.60 min ..................................~~(,_,"> 1.53/2.62 min ...................................~~(,_,"> 1.55/2.62 min ...................................~~(,_,"> 1.57/2.60 min ....................................~~(,_,"> 1.60/2.62 min ....................................~~(,_,"> 1.62/2.62 min .....................................~~(,_,"> 1.63/2.60 min .....................................~~(,_,"> 1.65/2.60 min ......................................~~(,_,"> 1.68/2.62 min ......................................~~(,_,"> 1.70/2.60 min .......................................~~(,_,"> 1.72/2.60 min .......................................~~(,_,"> 1.75/2.62 min ........................................~~(,_,"> 1.77/2.62 min ........................................~~(,_,"> 1.78/2.60 min .........................................~~(,_,"> 1.82/2.62 min .........................................~~(,_,"> 1.83/2.62 min ..........................................~~(,_,"> 1.85/2.60 min ..........................................~~(,_,"> 1.88/2.62 min ...........................................~~(,_,"> 1.90/2.62 min ...........................................~~(,_,"> 1.92/2.60 min ............................................~~(,_,"> 1.95/2.62 min ............................................~~(,_,"> 1.97/2.62 min .............................................~~(,_,"> 1.98/2.60 min .............................................~~(,_,"> 2.00/2.60 min ..............................................~~(,_,"> 2.03/2.62 min ..............................................~~(,_,"> 2.05/2.62 min ...............................................~~(,_,"> 2.07/2.60 min ...............................................~~(,_,"> 2.10/2.62 min ................................................~~(,_,"> 2.12/2.62 min ................................................~~(,_,"> 2.13/2.60 min .................................................~~(,_,"> 2.17/2.62 min .................................................~~(,_,"> 2.18/2.62 min ..................................................~~(,_,"> 2.20/2.60 min ..................................................~~(,_,"> 2.22/2.60 min ...................................................~~(,_,"> 2.25/2.62 min ...................................................~~(,_,"> 2.27/2.60 min ....................................................~~(,_,"> 2.28/2.60 min ....................................................~~(,_,"> 2.32/2.62 min .....................................................~~(,_,"> 2.33/2.62 min .....................................................~~(,_,"> 2.35/2.60 min ......................................................~~(,_,"> 2.38/2.62 min ......................................................~~(,_,"> 2.40/2.62 min .......................................................~~(,_,"> 2.42/2.60 min .......................................................~~(,_,"> 2.43/2.60 min ........................................................~~(,_,"> 2.47/2.62 min ........................................................~~(,_,"> 2.48/2.60 min .........................................................~~(,_,"> 2.50/2.60 min .........................................................~~(,_,"> 2.53/2.62 min ..........................................................~~(,_,"> 2.55/2.60 min ..........................................................~~(,_,"> 2.57/2.60 min ...........................................................~~(,_,"> 2.60/2.62 min ...........................................................~~(,_,"> 2.62/2.62 min ............................................................~~(,_,"> == Making a soft edge on the extended mask ... 000/??? sec ~~(,_,"> [oo] 0.02/1.98 min ~~(,_,"> 0.03/1.98 min .~~(,_,"> 0.05/1.98 min .~~(,_,"> 0.07/1.98 min ..~~(,_,"> 0.08/1.98 min ..~~(,_,"> 0.10/1.98 min ...~~(,_,"> 0.12/1.98 min ...~~(,_,"> 0.13/1.98 min ....~~(,_,"> 0.17/2.22 min ....~~(,_,"> 0.18/2.18 min .....~~(,_,"> 0.20/2.17 min .....~~(,_,"> 0.22/2.15 min ......~~(,_,"> 0.23/2.15 min ......~~(,_,"> 0.25/2.13 min .......~~(,_,"> 0.28/2.25 min .......~~(,_,"> 0.30/2.23 min ........~~(,_,"> 0.32/2.23 min ........~~(,_,"> 0.33/2.22 min .........~~(,_,"> 0.35/2.20 min .........~~(,_,"> 0.37/2.18 min ..........~~(,_,"> 0.38/2.18 min ..........~~(,_,"> 0.40/2.17 min ...........~~(,_,"> 0.43/2.25 min ...........~~(,_,"> 0.45/2.23 min ............~~(,_,"> 0.47/2.23 min ............~~(,_,"> 0.48/2.22 min .............~~(,_,"> 0.50/2.22 min .............~~(,_,"> 0.52/2.20 min ..............~~(,_,"> 0.53/2.20 min ..............~~(,_,"> 0.57/2.25 min ...............~~(,_,"> 0.58/2.25 min ...............~~(,_,"> 0.60/2.23 min ................~~(,_,"> 0.62/2.23 min ................~~(,_,"> 0.63/2.23 min .................~~(,_,"> 0.65/2.22 min .................~~(,_,"> 0.67/2.22 min ..................~~(,_,"> 0.68/2.20 min ..................~~(,_,"> 0.72/2.25 min ...................~~(,_,"> 0.73/2.25 min ...................~~(,_,"> 0.75/2.23 min ....................~~(,_,"> 0.77/2.23 min ....................~~(,_,"> 0.78/2.23 min .....................~~(,_,"> 0.80/2.22 min .....................~~(,_,"> 0.82/2.22 min ......................~~(,_,"> 0.83/2.22 min ......................~~(,_,"> 0.87/2.25 min .......................~~(,_,"> 0.88/2.25 min .......................~~(,_,"> 0.90/2.23 min ........................~~(,_,"> 0.92/2.23 min ........................~~(,_,"> 0.93/2.23 min .........................~~(,_,"> 0.95/2.23 min .........................~~(,_,"> 0.97/2.22 min ..........................~~(,_,"> 0.98/2.22 min ..........................~~(,_,"> 1.02/2.25 min ...........................~~(,_,"> 1.03/2.25 min ...........................~~(,_,"> 1.05/2.23 min ............................~~(,_,"> 1.07/2.23 min ............................~~(,_,"> 1.08/2.23 min .............................~~(,_,"> 1.10/2.23 min .............................~~(,_,"> 1.12/2.22 min ..............................~~(,_,"> 1.13/2.22 min ..............................~~(,_,"> 1.17/2.25 min ...............................~~(,_,"> 1.18/2.25 min ...............................~~(,_,"> 1.20/2.23 min ................................~~(,_,"> 1.22/2.23 min ................................~~(,_,"> 1.23/2.23 min .................................~~(,_,"> 1.25/2.23 min .................................~~(,_,"> 1.27/2.23 min ..................................~~(,_,"> 1.30/2.25 min ..................................~~(,_,"> 1.32/2.25 min ...................................~~(,_,"> 1.33/2.25 min ...................................~~(,_,"> 1.35/2.23 min ....................................~~(,_,"> 1.37/2.23 min ....................................~~(,_,"> 1.38/2.23 min .....................................~~(,_,"> 1.40/2.23 min .....................................~~(,_,"> 1.42/2.23 min ......................................~~(,_,"> 1.43/2.23 min ......................................~~(,_,"> 1.47/2.25 min .......................................~~(,_,"> 1.48/2.25 min .......................................~~(,_,"> 1.50/2.23 min ........................................~~(,_,"> 1.52/2.23 min ........................................~~(,_,"> 1.53/2.23 min .........................................~~(,_,"> 1.55/2.23 min .........................................~~(,_,"> 1.57/2.23 min ..........................................~~(,_,"> 1.60/2.25 min ..........................................~~(,_,"> 1.62/2.25 min ...........................................~~(,_,"> 1.63/2.25 min ...........................................~~(,_,"> 1.65/2.23 min ............................................~~(,_,"> 1.67/2.23 min ............................................~~(,_,"> 1.68/2.23 min .............................................~~(,_,"> 1.70/2.23 min .............................................~~(,_,"> 1.72/2.23 min ..............................................~~(,_,"> 1.75/2.25 min ..............................................~~(,_,"> 1.77/2.25 min ...............................................~~(,_,"> 1.78/2.25 min ...............................................~~(,_,"> 1.80/2.23 min ................................................~~(,_,"> 1.82/2.23 min ................................................~~(,_,"> 1.83/2.23 min .................................................~~(,_,"> 1.85/2.23 min .................................................~~(,_,"> 1.87/2.23 min ..................................................~~(,_,"> 1.88/2.23 min ..................................................~~(,_,"> 1.92/2.25 min ...................................................~~(,_,"> 1.93/2.25 min ...................................................~~(,_,"> 1.95/2.23 min ....................................................~~(,_,"> 1.97/2.23 min ....................................................~~(,_,"> 1.98/2.23 min .....................................................~~(,_,"> 2.00/2.23 min .....................................................~~(,_,"> 2.02/2.23 min ......................................................~~(,_,"> 2.03/2.23 min ......................................................~~(,_,"> 2.07/2.25 min .......................................................~~(,_,"> 2.08/2.25 min .......................................................~~(,_,"> 2.10/2.23 min ........................................................~~(,_,"> 2.12/2.23 min ........................................................~~(,_,"> 2.13/2.23 min .........................................................~~(,_,"> 2.15/2.23 min .........................................................~~(,_,"> 2.17/2.23 min ..........................................................~~(,_,"> 2.18/2.23 min ..........................................................~~(,_,"> 2.22/2.25 min ...........................................................~~(,_,"> 2.23/2.25 min ...........................................................~~(,_,"> 2.23/2.23 min ............................................................~~(,_,"> Done creating mask! Written out: MaskCreate/job113/mask.mrc ------------------------------------------------------------------------------------ RUN FINISHED AT Fri Dec 3 07:32:04 GMT 2021 ELAPSED WALL CLOCK TIME IN SECONDS: 295