AMBER11

TR-Grid sitesinden

Amber11 için örnek PBS dosyası aşağıdadır. Dosyayı ihtiyaçlarınız (node, ppn, çalışma dizini, input dosyaları v.s. ) doğrultusunda değitirmeyi unutmayın. İyi çalışmalar.

#!/bin/sh

#PBS -q trgridd@ce.ulakbim.gov.tr
#PBS -N amber11-test
#PBS -l nodes=2:ppn=2
## Export all my environment variables to the job
#PBS -V
#
## Change to my working directory
CALISMA_DIZINI=$HOMR/amber
cd $CALISMA_DIZINI 

## define AMBERBIN path
export AMBERBIN="/home_palamut1/software/tr-01-ulakbim/application/amber11/bin"
############################################################################### 

if [ "x$PBS_NODEFILE" != "x" ] ; then
  echo "PBS Nodefile: $PBS_NODEFILE"
  HOST_NODEFILE=$PBS_NODEFILE
fi 

if [ "x$LSB_HOSTS" != "x" ] ; then
  echo "LSF Hosts: $LSB_HOSTS"
  HOST_NODEFILE=`pwd`/lsf_nodefile.$$
  for host in ${LSB_HOSTS}
  do
    echo $host >> ${HOST_NODEFILE}
  done
fi

if [ "x$HOST_NODEFILE" = "x" ]; then
  echo "No hosts file defined.  Exiting..."
  exit
fi

CPU_NEEDED=`cat $HOST_NODEFILE | wc -l`
cat $HOST_NODEFILE >nodes

export DO_PARALLEL="mpirun -n $CPU_NEEDED"

/usr/mpi/gcc/mvapich2-1.2p1/bin/mpdboot --totalnum=`cat $HOST_NODEFILE |uniq|wc -l` --file=$HOST_NODEFILE 

########## AMBER 11 KULLANICI KOMUTLARI ##########################################

$DO_PARALLEL $AMBERBIN/pmemd.MPI -O -i $CALISMA_DIZINI/cellulose/mdin -o $CALISMA_DIZINI/cellulose/4cores-for-2nodes.mdout -p $CALISMA_DIZINI/cellulose/prmtop -c $CALISMA_DIZINI/cellulose/inpcrd
##################################################################################
/usr/mpi/gcc/mvapich2-1.2p1/bin/mpdallexit