Chimie Théorique » scripts_chimie4psmn

# $Id$

#!/bin/bash

#$ -S /bin/bash

#$ -N  NameOfYourJob

#$ -q  E5*

#$ -pe mpi4_debian 4

#$ -cwd

# Loading modules to set up environment

source /usr/share/modules/init/bash

module use /applis/PSMN/Modules

module load Base/psmn

module load NAMD/2.12-multicore

HOMEDIR=$SGE_O_WORKDIR

cd $HOMEDIR

SCRATCHDIR=/scratch/$USER/$JOB_ID

/bin/mkdir -p $SCRATCHDIR

# Please provide the following files for namd

CONFIGFILE=ubq_wb_eq.conf

INPFILE=par_all27_prot_lipid.inp

PDBFILE=ubq_wb.pdb

PSFFILE=ubq_wb.psf

LOGFILE=ubq_wb_eq.log

# Copying files to scratchdir

rsync -c $CONFIGFILE $INPFILE $PDBFILE $PSFFILE $SCRATCHDIR

# The executables for mpirun and namd2

MPIRUN=mpirun

COMMAND=`which namd2`

# Go to scratch directory and run calculation there

cd $SCRATCHDIR

#charmrun namd2 +p$NSLOTS ++mpiexec ++remote-shell $MPIRUN  $COMMAND $CONFIGFILE

charmrun +p$NSLOTS  $MPIRUN  $COMMAND $CONFIGFILE> $LOGFILE

# Copy back data

rsync -c --exclude '$CONFIGFILE $INPFILE $PDBFILE $PSFFILE' * $HOMEDIR

cd $HOMEDIR

# Cleaning up scratch directory and hostfile

rm -fr $SCRATCHDIR