Chimie Théorique » scripts_chimie4psmn

#!/bin/bash

#$ -S /bin/bash

#$ -N  mutm_ap-oxog

#$ -q  E5-2670gpuK20deb128

#$ -l  h=!c82gpgpu33

#$ -pe mpi_debian 16

#$ -cwd

#$ -V

# Loading modules to set up environment

export MODULEPATH=/home/tjiang/modules/lmod/:${MODULEPATH}

module use ${MODULEPATH}

module load NAMD/multicore+CUDA/2.12

# Setting up home and scratch directories

HOMEDIR=$SGE_O_WORKDIR

cd $HOMEDIR

SCRATCHDIR=/scratch/$USER/$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

#CONFIGFILE=run1.namd

#TOPFILE=ap-oxog3go8.prmtop

#PDBFILE=mutm_ap-oxog.coor

#COLVARSFILE=dihedral_run1.in

#LOGFILE=run1.out

# Copying files to scratchdir

rsync -c $CONFIGFILE $TOPFILE $PDBFILE $FIXFILE $COLVARSFILE machines runscript $SCRATCHDIR

# The executables for mpirun and namd2

MPIRUN=mpirun

COMMAND=`which namd2`

# Go to scratch directory and run calculation there

cd $SCRATCHDIR

echo 'group main ++shell ssh' > nodelist 

cat machines>>nodelist

#/applis/PSMN/generic/NAMD/2.12/NAMD_2.12_Linux-x86_64-ibverbs-smp-CUDA/charmrun ++p $NSLOTS ++ppn 8 ++nodelist nodelist ++remote-shell ssh /applis/PSMN/generic/NAMD/2.12/NAMD_2.12_Linux-x86_64-ibverbs-smp-CUDA/namd2 +setcpuaffinity +idlepoll $CONFIGFILE> ${LOGFILE}_2nodes

#/applis/PSMN/generic/NAMD/2.12/NAMD_2.12_Linux-x86_64-ibverbs-smp-CUDA/charmrun +p${NSLOTS} ++ppn 8 ++nodelist nodelist ++remote-shell ssh /applis/PSMN/generic/NAMD/2.12/NAMD_2.12_Linux-x86_64-ibverbs-smp-CUDA/namd2 +setcpuaffinity +idlepoll $CONFIGFILE> ${LOGFILE}_2nodes

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

#namd2 +p 16  $CONFIGFILE> $LOGFILE

namd2 +idlepoll +p $NSLOTS +devices 0,1 $CONFIGFILE> ${LOGFILE}_${NSLOTS}cpu_2gpu_node31

# Copy back data

rsync -c --exclude '$CONFIGFILE $TOPFILE $PDBFILE $COLVARSFILE' * $HOMEDIR

cd $HOMEDIR

# Cleaning up scratch directory and hostfile

rm -fr $SCRATCHDIR