AMBER

#!/bin/bash
#$ -S /bin/bash
#$ -N amber17
#$ -cwd
#$ -V
#$ -o npt4.out
#$ -j y
##=====================
##Choose between cpu queues and gpu queues, default gpu queues
##cpu queues
##$ -q M6*,E5-2667*,E5-2697*,E5-2670deb*
##$ -pe mpi16_debian 16
##gpu queues
#$ -q E5-2670gpuK20deb128,r7x0deb128gpu
#$ -pe mpi_debian 1
##=====================
 
# PSMN: $Id$
#
 
export MODULEPATH=/home/tjiang/modules/lmod/:${MODULEPATH}
module use ${MODULEPATH}
 
#module file for gpu version of amber
module load amber/17_gcc5.4.0_cuda8.0ga2_openmpi1.6.4
 
#module file for cpu only version of amber
#module load amber/17_intel15.0.2_openmpi1.6.4
 
ambermod=$(basename $AMBERHOME)
echo $ambermod
if [ $ambermod = "gcc5.4.0_cuda8.0ga2_openmpi1.6.4" ]; then
    amberexe="pmemd.cuda"
else
    amberexe="pmemd"
fi
echo $amberexe
 
ulimit -v unlimited
ulimit -s unlimited
 
######################"
HOMEDIR=$SGE_O_WORKDIR
HOSTFILE=$TMPDIR/machines
 
cd $SGE_O_WORKDIR
 
echo NSLOTS=$NSLOTS
 
if [[ -d "/scratch/Chimie" ]]
then
    SCRATCHDIR=/scratch/Chimie/$USER/$JOB_ID/
elif [[ -d "/scratch/Lake" ]]
then
    SCRATCHDIR=/scratch/Lake/$USER/$JOB_ID/
elif [[ -d "/scratch/E5N" ]]
then
    SCRATCHDIR=/scratch/E5N/$USER/$JOB_ID/
elif [[ -d "/scratch/E5" ]]
then
    SCRATCHDIR=/scratch/E5/$USER/$JOB_ID/
else
    echo "/scratch not found, cannot create ${SCRATCHDIR}, fall back to current directory"
    SCRATCHDIR=${SGE_O_WORKDIR}
fi
# Using /tmp as scratch instead
# SCRATCHDIR=/tmp/$USER/$JOB_ID/
 
echo $SCRATCHDIR
/bin/mkdir -p $SCRATCHDIR
###################
Mac=`hostname | awk '{print substr($1,1,2)}' `
 
NbMac=`wc $PE_HOSTFILE | awk '{print $1}' `
rm ./machines
for i in `seq 1 $NbMac`
    do
        Mac=` head -n $i $PE_HOSTFILE | tail -1 | awk '{print $1}' `
        Nb=` head -n $i $PE_HOSTFILE | tail -1 | awk '{print $2}' `
        for j in `seq 1 $Nb`
             do
                 echo $Mac >> ./machines
                  done
                  done
 
                  cp $PE_HOSTFILE ./PE_HOSTFILE
 
                  cd $SCRATCHDIR
 
                  echo "start at"
                  date
 
                  echo -n "Starting Script at: "
                  date
                  $amberexe -O -i $HOMEDIR/min.in \
                                -o $HOMEDIR/min.out \
                                -p $HOMEDIR/dna_TT.prmtop \
                                -c $HOMEDIR/dna3_TT.inpcrd \
                                -r $HOMEDIR/dna_TT_min.rst \
                                -x $HOMEDIR/dna_TT_min.mdcrd
 
                  echo "done at"
                  date
                  cp -rf * $HOMEDIR