chimie4psmn / submit / namd / sub_namd_bash @ 55
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| 1 | 23 | tjiang | # $Id$ |
|---|---|---|---|
| 2 | 23 | tjiang | #!/bin/bash |
| 3 | 23 | tjiang | #$ -S /bin/bash |
| 4 | 23 | tjiang | #$ -N NameOfYourJob |
| 5 | 23 | tjiang | #$ -q E5* |
| 6 | 23 | tjiang | #$ -pe mpi4_debian 4 |
| 7 | 23 | tjiang | #$ -cwd |
| 8 | 23 | tjiang | |
| 9 | 23 | tjiang | # Loading modules to set up environment |
| 10 | 23 | tjiang | source /usr/share/modules/init/bash |
| 11 | 23 | tjiang | module use /applis/PSMN/Modules |
| 12 | 23 | tjiang | module load Base/psmn |
| 13 | 23 | tjiang | module load NAMD/2.12-multicore |
| 14 | 23 | tjiang | |
| 15 | 23 | tjiang | HOMEDIR=$SGE_O_WORKDIR |
| 16 | 23 | tjiang | cd $HOMEDIR |
| 17 | 23 | tjiang | SCRATCHDIR=/scratch/$USER/$JOB_ID |
| 18 | 23 | tjiang | /bin/mkdir -p $SCRATCHDIR |
| 19 | 23 | tjiang | |
| 20 | 23 | tjiang | # Please provide the following files for namd |
| 21 | 23 | tjiang | CONFIGFILE=ubq_wb_eq.conf |
| 22 | 23 | tjiang | INPFILE=par_all27_prot_lipid.inp |
| 23 | 23 | tjiang | PDBFILE=ubq_wb.pdb |
| 24 | 23 | tjiang | PSFFILE=ubq_wb.psf |
| 25 | 23 | tjiang | LOGFILE=ubq_wb_eq.log |
| 26 | 23 | tjiang | |
| 27 | 23 | tjiang | # Copying files to scratchdir |
| 28 | 23 | tjiang | rsync -c $CONFIGFILE $INPFILE $PDBFILE $PSFFILE $SCRATCHDIR |
| 29 | 23 | tjiang | |
| 30 | 23 | tjiang | # The executables for mpirun and namd2 |
| 31 | 23 | tjiang | MPIRUN=mpirun |
| 32 | 23 | tjiang | COMMAND=`which namd2` |
| 33 | 23 | tjiang | |
| 34 | 23 | tjiang | # Go to scratch directory and run calculation there |
| 35 | 23 | tjiang | cd $SCRATCHDIR |
| 36 | 23 | tjiang | #charmrun namd2 +p$NSLOTS ++mpiexec ++remote-shell $MPIRUN $COMMAND $CONFIGFILE |
| 37 | 23 | tjiang | charmrun +p$NSLOTS $MPIRUN $COMMAND $CONFIGFILE> $LOGFILE |
| 38 | 23 | tjiang | |
| 39 | 23 | tjiang | # Copy back data |
| 40 | 23 | tjiang | rsync -c --exclude '$CONFIGFILE $INPFILE $PDBFILE $PSFFILE' * $HOMEDIR |
| 41 | 23 | tjiang | cd $HOMEDIR |
| 42 | 23 | tjiang | |
| 43 | 23 | tjiang | # Cleaning up scratch directory and hostfile |
| 44 | 23 | tjiang | rm -fr $SCRATCHDIR |