Gromacs

TR-Grid sitesinden

Gromacs-4.0.7'nin paralel ve seri versiyonlarını çalıştırmak için aşağıdaki PBS betikleri kullanılabilir.

Paralel versiyon:

#!/bin/bash 
#PBS -q trgridb@ce.ulakbim.gov.tr
#PBS -N gromacs_parallel
#PBS -l nodes=2:ppn=4
#PBS -V

. /usr/share/Modules/init/sh
module load tr-01-ulakbim/application/gromacs-4.0.7_parallel/intel

export CALISMA_DIZINI=$HOME/gromacs_test

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

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

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

cd $CALISMA_DIZINI
rm -rf ./err ./out
mpirun -np $CPU_NEEDED -machinefile $HOST_NODEFILE  /home_palamut1/sefa/programs/gromacs /gromacs-4.0.7_mpi/bin/mdrun -v -deffnm em >out 2>out2

Seri versiyon:

#!/bin/bash 
#PBS -q trgridb@ce.ulakbim.gov.tr
#PBS -N gromacs_serial
#PBS -l nodes=1:ppn=1
#PBS -V

. /usr/share/Modules/init/sh
module load tr-01-ulakbim/application/gromacs-4.0.7_serial/intel

export CALISMA_DIZINI=$HOME/gromacs_test

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

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

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

cd $CALISMA_DIZINI

/home_palamut1/sefa/programs/gromacs/gromacs-4.0.7_serial/bin/mdrun -v -deffnm em >out 2>out2