NAMD

#!/bin/bash
#$ -S /bin/bash
#$ -N  mutm_ap-oxog
#$ -q  E5-2670gpuK20deb128
#$ -pe mpi_debian 16
#$ -cwd
#$ -V
 
# Loading modules to set up environment
module load NAMD/multicore+CUDA/2.12
 
# Setting up home and scratch directories
HOMEDIR=$SGE_O_WORKDIR
cd $HOMEDIR
 
SCRATCHDIR=/scratch/Chimie/$USER/$JOB_ID
# Using ramdisk as scratch instead
# SCRATCHDIR=/dev/shm/$USER/$JOB_ID/
 
/bin/mkdir -p $SCRATCHDIR
HOSTFILE=$TMPDIR/machines
cp $HOSTFILE .
sed -i -e 's/^/host\ /' machines
 
# Please provide the following files for namd
CONFIGFILE=run2.namd
TOPFILE=DDB2_CT_hmr.prmtop
PDBFILE=DDB2_CT_run1_0.coor
FIXFILE=DDB2_CT_new.fix
COLVARSFILE=dihedral_run1.in
LOGFILE=run2.out
 
# Copying files to scratchdir
rsync -c $CONFIGFILE $TOPFILE $PDBFILE $FIXFILE $COLVARSFILE machines runscript $SCRATCHDIR
 
# The executables for mpirun and namd2
MPIRUN=mpirun
 
# Go to scratch directory and run calculation there
cd $SCRATCHDIR
echo 'group main ++shell ssh' > nodelist
cat machines>>nodelist
 
namd2 +idlepoll +p $NSLOTS +devices 0,1 $CONFIGFILE> ${LOGFILE}
 
# Copy back data
rsync -c --exclude '$CONFIGFILE $TOPFILE $PDBFILE $COLVARSFILE' * $HOMEDIR
cd $HOMEDIR
 
# Cleaning up scratch directory and hostfile
rm -fr $SCRATCHDIR