Ceci est une ancienne révision du document !
#!/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 ${SCRATCHDIR}" fi # Using /tmp as scratch instead # SCRATCHDIR=/dev/tmp/$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