chimie4psmn / submit / namd / sub_namd_bash @ 23
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# $Id$ |
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#!/bin/bash |
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#$ -S /bin/bash |
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#$ -N NameOfYourJob |
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#$ -q E5* |
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#$ -pe mpi4_debian 4 |
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#$ -cwd |
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# Loading modules to set up environment |
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source /usr/share/modules/init/bash |
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module use /applis/PSMN/Modules |
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module load Base/psmn |
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module load NAMD/2.12-multicore |
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HOMEDIR=$SGE_O_WORKDIR |
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cd $HOMEDIR |
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SCRATCHDIR=/scratch/$USER/$JOB_ID |
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/bin/mkdir -p $SCRATCHDIR |
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# Please provide the following files for namd |
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CONFIGFILE=ubq_wb_eq.conf |
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INPFILE=par_all27_prot_lipid.inp |
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PDBFILE=ubq_wb.pdb |
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PSFFILE=ubq_wb.psf |
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LOGFILE=ubq_wb_eq.log |
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# Copying files to scratchdir |
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rsync -c $CONFIGFILE $INPFILE $PDBFILE $PSFFILE $SCRATCHDIR |
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# The executables for mpirun and namd2 |
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MPIRUN=mpirun |
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COMMAND=`which namd2` |
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# Go to scratch directory and run calculation there |
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cd $SCRATCHDIR |
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#charmrun namd2 +p$NSLOTS ++mpiexec ++remote-shell $MPIRUN $COMMAND $CONFIGFILE |
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charmrun +p$NSLOTS $MPIRUN $COMMAND $CONFIGFILE> $LOGFILE |
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# Copy back data |
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rsync -c --exclude '$CONFIGFILE $INPFILE $PDBFILE $PSFFILE' * $HOMEDIR |
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cd $HOMEDIR |
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# Cleaning up scratch directory and hostfile |
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rm -fr $SCRATCHDIR |