Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. lmbwide.login complete /public/xtal/CCP4/ccp4-64/Prerelease ccp4_base /public/xtal lmbbase +------------------------------------------------ LMB crystallography software CCP4 release 7.1 installed 23/04/2020 (DB) Type "ccp4i2" to get the new improved interface for new projects NOW IMPROVED WITH ACCESS TO ccp4i1 projects **** If you really want to use the older (7.0) version, edit your .login to "source /public/xtal/ccp4/xtal-7.0.login" and login again ------------------------------------------------------------------------------ phenix release 1.18 (3874) 20 5 20 (JL) "phenix &" for GUI ------------------------------------------------------------------------------ sharp server is on hal:8081, Sharp version 2.9.0 7/2/20 (DB) ------------------------------------------------------------------------------ XDS 4/2020 (DB), generate_XDS.INP / eiger_XDS.INP 5/2019 (JL) ------------------------------------------------------------------------------ MAIN 2019 JL 3/2019 ------------------------------------------------------------------------------ iMosflm will now read "master" hdf5 files, including the Eiger2 detector at DLS AGWL 5/2019 ------------------------------------------------------------------------------ Buster and autoPROC update 19/3/20 (DB) ------------------------------------------------------------------------------ MoRDa database updated to version 31 13/04/2020 (DB/JL) ------------------------------------------------------------------------------ ************************************************** MRC image processing programs have moved. You are using image2010 by default. If you wish to use the frozen image2000 you need to : source /public/EM/image2000/com/image.login and source /public/EM/image2000/com/image.cshrc Jude Short (F46 x2039 jms@mrc-lmb.cam.ac.uk) 09.03.2011 ************************************************** Path to mpiexec: /public/EM/OpenMPI/openmpi-2.0.1/build/bin/mpiexec Path to relion_refine_mpi: /lmb/home/tnakane/prog/relion-devel-lmb/build-test/bin/relion_refine_mpi Libraries for relion_refine_mpi: linux-vdso.so.1 => (0x00007ffda55e8000) libcufft.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcufft.so.9.0 (0x00002b23468c6000) libmpi.so.20 => /public/EM/OpenMPI/openmpi-2.0.1/build/lib/libmpi.so.20 (0x00002b234e967000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b234ec46000) libtiff.so.5 => /lib64/libtiff.so.5 (0x00002b234ee4a000) libfftw3.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3.so.3 (0x00002b234f0be000) libfftw3f.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3f.so.3 (0x00002b234f43d000) libcurand.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcurand.so.9.0 (0x00002b234f848000) libpng15.so.15 => /lib64/libpng15.so.15 (0x00002b23537ac000) libcudart.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcudart.so.9.0 (0x00002b23539d7000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002b2353c44000) libm.so.6 => /lib64/libm.so.6 (0x00002b2353f4c000) libgomp.so.1 => /lib64/libgomp.so.1 (0x00002b235424e000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b2354474000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b235468a000) libc.so.6 => /lib64/libc.so.6 (0x00002b23548a6000) librt.so.1 => /lib64/librt.so.1 (0x00002b2354c73000) libopen-rte.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-rte.so.20 (0x00002b2354e7b000) libopen-pal.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-pal.so.20 (0x00002b23550fa000) libutil.so.1 => /lib64/libutil.so.1 (0x00002b23553e0000) /lib64/ld-linux-x86-64.so.2 (0x00002b23466a2000) libjbig.so.2.0 => /lib64/libjbig.so.2.0 (0x00002b23555e3000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00002b23557ef000) libz.so.1 => /lib64/libz.so.1 (0x00002b2355a44000) RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE = /public/EM/SIDESPLITTER/sidesplitter_wrapper.sh SIDESPLITTER = /public/EM/SIDESPLITTER/sidesplitter RUN STARTED AT 1594080687 ----------------------------------------------------------- Reading in optimiser.star ... + Reading in mask ... + The subtracted particles will be re-centred on projections of 3D-coordinate: (84 , -41 , -3) + Calculating Fourier transforms of the maps ... + Subtracting all particles ... 000/??? sec ~~(,_,"> [oo] 0.01/1.27 hrs ~~(,_,"> 0.02/1.18 hrs ~~(,_,"> 0.03/1.16 hrs .~~(,_,"> 0.04/1.17 hrs .~~(,_,"> 0.05/1.17 hrs ..~~(,_,"> 0.06/1.18 hrs ..~~(,_,"> 0.07/1.18 hrs ...~~(,_,"> 0.08/1.16 hrs ...~~(,_,"> 0.09/1.17 hrs ....~~(,_,"> 0.10/1.18 hrs ....~~(,_,"> 0.11/1.18 hrs .....~~(,_,"> 0.12/1.18 hrs .....~~(,_,"> 0.13/1.20 hrs ......~~(,_,"> 0.14/1.21 hrs ......~~(,_,"> 0.15/1.21 hrs .......~~(,_,"> 0.16/1.21 hrs .......~~(,_,"> 0.18/1.24 hrs ........~~(,_,"> 0.19/1.29 hrs ........~~(,_,"> 0.21/1.32 hrs .........~~(,_,"> 0.22/1.35 hrs .........~~(,_,"> 0.24/1.38 hrs ..........~~(,_,"> 0.26/1.40 hrs ..........~~(,_,"> 0.27/1.42 hrs ...........~~(,_,"> 0.29/1.44 hrs ...........~~(,_,"> 0.30/1.46 hrs ............~~(,_,"> 0.32/1.47 hrs ............~~(,_,"> 0.33/1.49 hrs .............~~(,_,"> 0.35/1.50 hrs .............~~(,_,"> 0.37/1.51 hrs ..............~~(,_,"> 0.38/1.53 hrs ..............~~(,_,"> 0.40/1.54 hrs ...............~~(,_,"> 0.41/1.56 hrs ...............~~(,_,"> 0.43/1.56 hrs ................~~(,_,"> 0.44/1.57 hrs ................~~(,_,"> 0.46/1.58 hrs .................~~(,_,"> 0.47/1.58 hrs .................~~(,_,"> 0.49/1.58 hrs ..................~~(,_,"> 0.50/1.59 hrs ..................~~(,_,"> 0.52/1.59 hrs ...................~~(,_,"> 0.53/1.59 hrs ...................~~(,_,"> 0.54/1.59 hrs ....................~~(,_,"> 0.56/1.60 hrs ....................~~(,_,"> 0.57/1.60 hrs .....................~~(,_,"> 0.59/1.60 hrs .....................~~(,_,"> 0.60/1.61 hrs ......................~~(,_,"> 0.62/1.61 hrs ......................~~(,_,"> 0.63/1.62 hrs .......................~~(,_,"> 0.65/1.62 hrs .......................~~(,_,"> 0.67/1.63 hrs ........................~~(,_,"> 0.68/1.64 hrs ........................~~(,_,"> 0.70/1.64 hrs .........................~~(,_,"> 0.71/1.65 hrs .........................~~(,_,"> 0.73/1.65 hrs ..........................~~(,_,"> 0.75/1.66 hrs ..........................~~(,_,"> 0.77/1.68 hrs ...........................~~(,_,"> 0.78/1.68 hrs ...........................~~(,_,"> 0.80/1.68 hrs ............................~~(,_,"> 0.81/1.69 hrs ............................~~(,_,"> 0.83/1.69 hrs .............................~~(,_,"> 0.85/1.69 hrs .............................~~(,_,"> 0.86/1.70 hrs ..............................~~(,_,"> 0.88/1.70 hrs ..............................~~(,_,"> 0.89/1.70 hrs ...............................~~(,_,"> 0.91/1.71 hrs ...............................~~(,_,"> 0.92/1.71 hrs ................................~~(,_,"> 0.94/1.71 hrs ................................~~(,_,"> 0.95/1.71 hrs .................................~~(,_,"> 0.97/1.71 hrs .................................~~(,_,"> 0.98/1.71 hrs ..................................~~(,_,"> 1.00/1.71 hrs ..................................~~(,_,"> 1.01/1.71 hrs ...................................~~(,_,"> 1.03/1.72 hrs ...................................~~(,_,"> 1.04/1.72 hrs ....................................~~(,_,"> 1.06/1.72 hrs ....................................~~(,_,"> 1.08/1.72 hrs .....................................~~(,_,"> 1.09/1.72 hrs .....................................~~(,_,"> 1.10/1.72 hrs ......................................~~(,_,"> 1.12/1.72 hrs ......................................~~(,_,"> 1.13/1.72 hrs .......................................~~(,_,"> 1.14/1.71 hrs .......................................~~(,_,"> 1.16/1.71 hrs ........................................~~(,_,"> 1.17/1.71 hrs ........................................~~(,_,"> 1.18/1.71 hrs .........................................~~(,_,"> 1.19/1.71 hrs .........................................~~(,_,"> 1.21/1.71 hrs ..........................................~~(,_,"> 1.22/1.70 hrs ..........................................~~(,_,"> 1.23/1.70 hrs ...........................................~~(,_,"> 1.25/1.70 hrs ...........................................~~(,_,"> 1.26/1.70 hrs ............................................~~(,_,"> 1.27/1.70 hrs ............................................~~(,_,"> 1.29/1.70 hrs .............................................~~(,_,"> 1.30/1.69 hrs .............................................~~(,_,"> 1.31/1.69 hrs ..............................................~~(,_,"> 1.32/1.69 hrs ..............................................~~(,_,"> 1.34/1.69 hrs ...............................................~~(,_,"> 1.35/1.69 hrs ...............................................~~(,_,"> 1.36/1.69 hrs ................................................~~(,_,"> 1.38/1.69 hrs ................................................~~(,_,"> 1.39/1.68 hrs .................................................~~(,_,"> 1.40/1.68 hrs .................................................~~(,_,"> 1.41/1.68 hrs ..................................................~~(,_,"> 1.43/1.68 hrs ..................................................~~(,_,"> 1.44/1.68 hrs ...................................................~~(,_,"> 1.46/1.68 hrs ...................................................~~(,_,"> 1.47/1.68 hrs ....................................................~~(,_,"> 1.48/1.68 hrs ....................................................~~(,_,"> 1.50/1.68 hrs .....................................................~~(,_,"> 1.51/1.68 hrs .....................................................~~(,_,"> 1.52/1.67 hrs ......................................................~~(,_,"> 1.53/1.67 hrs ......................................................~~(,_,"> 1.54/1.67 hrs .......................................................~~(,_,"> 1.56/1.67 hrs .......................................................~~(,_,"> 1.57/1.67 hrs ........................................................~~(,_,"> 1.58/1.66 hrs ........................................................~~(,_,"> 1.59/1.66 hrs .........................................................~~(,_,"> 1.60/1.66 hrs .........................................................~~(,_,"> 1.62/1.66 hrs ..........................................................~~(,_,"> 1.63/1.65 hrs ..........................................................~~(,_,"> 1.64/1.65 hrs ...........................................................~~(,_,"> 1.65/1.65 hrs ...........................................................~~(,_,"> 1.65/1.65 hrs ............................................................~~(,_,"> + Saved STAR file with 403474 subtracted particles in Subtract/job447/particles_subtracted.star ----------------------------------------------------------- RUN FINISHED AT 1594086900 ELAPSED WALL CLOCK TIME: 6213 Running epilog script on fmb153.lmb.internal Tue 7 Jul 02:55:00 BST 2020 Removing files owned by mwilkin on /ssd Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. lmbwide.login complete /public/xtal/CCP4/ccp4-64/Prerelease ccp4_base /public/xtal lmbbase +------------------------------------------------ LMB crystallography software CCP4 release 7.1 installed 23/04/2020 (DB) updated 05/01/21 (DB) Type "ccp4i2" to get the new improved interface for new projects NOW IMPROVED WITH ACCESS TO ccp4i1 projects **** If you really want to use the older (7.0) version, edit your .login to "source /public/xtal/ccp4/xtal-7.0.login" and login again ------------------------------------------------------------------------------ phenix release 1.19.1 (4122) 1/21 JL "phenix &" for GUI ------------------------------------------------------------------------------ sharp server is on hal:8081, Sharp version 2.9.0 7/2/20 (DB) ------------------------------------------------------------------------------ XDS 01/10/2020 (DB), generate_XDS.INP / eiger_XDS.INP 5/2019 (JL) ------------------------------------------------------------------------------ MAIN 2020 JL 9/20 ------------------------------------------------------------------------------ iMosflm will now read "master" hdf5 files, including the Eiger2 detector at DLS AGWL 5/2019 ------------------------------------------------------------------------------ Buster and autoPROC update 02/10/20 (DB) ------------------------------------------------------------------------------ MoRDa database updated to version 40 05/01/2021 (DB) ------------------------------------------------------------------------------ ************************************************** MRC image processing programs have moved. You are using image2010 by default. If you wish to use the frozen image2000 you need to : source /public/EM/image2000/com/image.login and source /public/EM/image2000/com/image.cshrc Jude Short (F46 x2039 jms@mrc-lmb.cam.ac.uk) 09.03.2011 ************************************************** Path to mpiexec: /public/EM/OpenMPI/openmpi-2.0.1/build/bin/mpiexec Path to relion_refine_mpi: /lmb/home/tnakane/prog/relion-devel-lmb/build-test/bin/relion_refine_mpi Libraries for relion_refine_mpi: linux-vdso.so.1 => (0x00007ffc8136b000) libcufft.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcufft.so.9.0 (0x00002b841c0be000) libmpi.so.20 => /public/EM/OpenMPI/openmpi-2.0.1/build/lib/libmpi.so.20 (0x00002b842415f000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b842443e000) libtiff.so.5 => /lib64/libtiff.so.5 (0x00002b8424642000) libfftw3.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3.so.3 (0x00002b84248b6000) libfftw3f.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3f.so.3 (0x00002b8424c35000) libcurand.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcurand.so.9.0 (0x00002b8425040000) libpng15.so.15 => /lib64/libpng15.so.15 (0x00002b8428fa4000) libcudart.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcudart.so.9.0 (0x00002b84291cf000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002b842943c000) libm.so.6 => /lib64/libm.so.6 (0x00002b8429744000) libgomp.so.1 => /lib64/libgomp.so.1 (0x00002b8429a46000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b8429c6c000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b8429e82000) libc.so.6 => /lib64/libc.so.6 (0x00002b842a09e000) librt.so.1 => /lib64/librt.so.1 (0x00002b842a46b000) libopen-rte.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-rte.so.20 (0x00002b842a673000) libopen-pal.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-pal.so.20 (0x00002b842a8f2000) libutil.so.1 => /lib64/libutil.so.1 (0x00002b842abd8000) /lib64/ld-linux-x86-64.so.2 (0x00002b841be9a000) libjbig.so.2.0 => /lib64/libjbig.so.2.0 (0x00002b842addb000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00002b842afe7000) libz.so.1 => /lib64/libz.so.1 (0x00002b842b23c000) RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE = /public/EM/SIDESPLITTER/sidesplitter_wrapper.sh SIDESPLITTER = /public/EM/SIDESPLITTER/sidesplitter RUN STARTED AT 1613764268 ----------------------------------------------------------- Reading in optimiser.star ... + Reading in mask ... + The subtracted particles will be re-centred on projections of 3D-coordinate: (84 , -41 , -3) + Calculating Fourier transforms of the maps ... + Subtracting all particles ... 000/??? sec ~~(,_,"> [oo] 0.45/54.02 min ~~(,_,"> 0.88/53.02 min ~~(,_,"> 1.33/53.35 min .~~(,_,"> 1.78/53.52 min .~~(,_,"> 2.25/54.02 min ..~~(,_,"> 2.72/54.35 min ..~~(,_,"> 3.15/54.02 min ...~~(,_,"> 3.58/53.77 min ...~~(,_,"> 4.08/54.47 min ....~~(,_,"> 4.52/54.22 min ....~~(,_,"> 4.97/54.20 min .....~~(,_,"> 5.42/54.18 min .....~~(,_,"> 5.87/54.18 min ......~~(,_,"> 6.35/54.45 min ......~~(,_,"> 6.82/54.55 min .......~~(,_,"> 7.28/54.65 min .......~~(,_,"> 7.75/54.73 min ........~~(,_,"> 8.22/54.80 min ........~~(,_,"> 8.67/54.77 min .........~~(,_,"> 9.12/54.72 min .........~~(,_,"> 9.57/54.68 min ..........~~(,_,"> 10.00/54.57 min ..........~~(,_,"> 10.43/54.45 min ...........~~(,_,"> 10.88/54.43 min ...........~~(,_,"> 11.33/54.42 min ............~~(,_,"> 11.82/54.57 min ............~~(,_,"> 12.28/54.62 min .............~~(,_,"> 12.75/54.67 min .............~~(,_,"> 13.23/54.78 min ..............~~(,_,"> 13.70/54.82 min ..............~~(,_,"> 14.13/54.73 min ...............~~(,_,"> 14.62/54.83 min ...............~~(,_,"> 15.12/54.98 min ................~~(,_,"> 15.57/54.97 min ................~~(,_,"> 16.03/55.00 min .................~~(,_,"> 16.50/55.02 min .................~~(,_,"> 16.97/55.05 min ..................~~(,_,"> 17.43/55.07 min ..................~~(,_,"> 17.88/55.05 min ...................~~(,_,"> 18.33/55.02 min ...................~~(,_,"> 18.78/55.00 min ....................~~(,_,"> 19.28/55.12 min ....................~~(,_,"> 19.73/55.10 min .....................~~(,_,"> 20.20/55.12 min .....................~~(,_,"> 20.67/55.13 min ......................~~(,_,"> 21.12/55.12 min ......................~~(,_,"> 21.58/55.13 min .......................~~(,_,"> 22.07/55.18 min .......................~~(,_,"> 22.52/55.17 min ........................~~(,_,"> 22.98/55.18 min ........................~~(,_,"> 23.43/55.17 min .........................~~(,_,"> 23.88/55.13 min .........................~~(,_,"> 24.35/55.15 min ..........................~~(,_,"> 24.82/55.17 min ..........................~~(,_,"> 25.27/55.15 min ...........................~~(,_,"> 25.73/55.17 min ...........................~~(,_,"> 26.20/55.18 min ............................~~(,_,"> 26.73/55.33 min ............................~~(,_,"> 27.22/55.38 min .............................~~(,_,"> 27.68/55.38 min .............................~~(,_,"> 28.12/55.33 min ..............................~~(,_,"> 28.58/55.35 min ..............................~~(,_,"> 29.05/55.35 min ...............................~~(,_,"> 29.53/55.40 min ...............................~~(,_,"> 29.98/55.38 min ................................~~(,_,"> 30.43/55.35 min ................................~~(,_,"> 30.87/55.30 min .................................~~(,_,"> 31.30/55.25 min .................................~~(,_,"> 31.78/55.30 min ..................................~~(,_,"> 32.30/55.40 min ..................................~~(,_,"> 32.73/55.35 min ...................................~~(,_,"> 33.23/55.42 min ...................................~~(,_,"> 33.73/55.47 min ....................................~~(,_,"> 34.27/55.58 min ....................................~~(,_,"> 34.77/55.65 min .....................................~~(,_,"> 35.32/55.78 min .....................................~~(,_,"> 35.82/55.83 min ......................................~~(,_,"> 36.30/55.87 min ......................................~~(,_,"> 36.80/55.92 min .......................................~~(,_,"> 37.28/55.95 min .......................................~~(,_,"> 37.82/56.05 min ........................................~~(,_,"> 38.32/56.10 min ........................................~~(,_,"> 38.83/56.17 min .........................................~~(,_,"> 39.33/56.22 min .........................................~~(,_,"> 39.83/56.25 min ..........................................~~(,_,"> 40.33/56.30 min ..........................................~~(,_,"> 40.83/56.35 min ...........................................~~(,_,"> 41.35/56.42 min ...........................................~~(,_,"> 41.82/56.40 min ............................................~~(,_,"> 42.25/56.35 min ............................................~~(,_,"> 42.70/56.33 min .............................................~~(,_,"> 43.13/56.28 min .............................................~~(,_,"> 43.60/56.28 min ..............................................~~(,_,"> 44.05/56.25 min ..............................................~~(,_,"> 44.60/56.37 min ...............................................~~(,_,"> 45.12/56.42 min ...............................................~~(,_,"> 45.62/56.45 min ................................................~~(,_,"> 46.60/57.08 min ................................................~~(,_,"> 47.18/57.22 min .................................................~~(,_,"> 47.67/57.22 min .................................................~~(,_,"> 48.13/57.22 min ..................................................~~(,_,"> 48.63/57.23 min ..................................................~~(,_,"> 49.13/57.27 min ...................................................~~(,_,"> 49.60/57.25 min ...................................................~~(,_,"> 50.10/57.28 min ....................................................~~(,_,"> 50.57/57.27 min ....................................................~~(,_,"> 51.05/57.28 min .....................................................~~(,_,"> 51.52/57.27 min .....................................................~~(,_,"> 52.00/57.27 min ......................................................~~(,_,"> 52.48/57.28 min ......................................................~~(,_,"> 52.97/57.28 min .......................................................~~(,_,"> 53.45/57.28 min .......................................................~~(,_,"> 53.95/57.32 min ........................................................~~(,_,"> 54.43/57.32 min ........................................................~~(,_,"> 54.90/57.32 min .........................................................~~(,_,"> 55.37/57.30 min .........................................................~~(,_,"> 55.80/57.25 min ..........................................................~~(,_,"> 56.23/57.22 min ..........................................................~~(,_,"> 56.68/57.18 min ...........................................................~~(,_,"> 57.17/57.18 min ...........................................................~~(,_,"> 57.18/57.18 min ............................................................~~(,_,"> + Saved STAR file with 403474 subtracted particles in Subtract/job447/particles_subtracted.star ----------------------------------------------------------- RUN FINISHED AT 1613767774 ELAPSED WALL CLOCK TIME: 3506 USER=mwilkin Running epilog script on fmb236.lmb.internal Fri 19 Feb 20:49:34 GMT 2021 Removing files owned by mwilkin on /ssd Finished epilog script