Gromacs

Sample job file for running a gromacs serial job :

File Name : gromacs.cmd

#!/bin/bash

#PBS -l cput=02:00:00

#PBS -e errorfile.err

#PBS -o logfile.log

#PBS -l select=1:ncpus=4

tpdir=`echo $PBS_JOBID | cut -f 1 -d .`

tempdir=$HOME/work/job$tpdir

mkdir -p $tempdir

cd $tempdir

cp -R $PBS_O_WORKDIR/* .

mdrun -s test.tpr >> output

mv ../job$tpdir $PBS_O_WORKDIR/.

In the command prompt, type the command, qsub gromacs.cmd

Sample job file for running a gromacs parallel job within one node :

File Name : gromacs.cmd

#!/bin/bash

#PBS -l cput=200:00:00

#PBS -e errorfile.err

#PBS -o logfile.log

#PBS -l select=1:ncpus=16

tpdir=`echo $PBS_JOBID | cut -f 1 -d .`

tempdir=$HOME/work/job$tpdir

mkdir -p $tempdir

cd $tempdir

cp -R $PBS_O_WORKDIR/* .

mpirun -np 16 -hostfile `which mdrun_mpi` -s -v -deffnm test.tpr

mv ../job$tpdir $PBS_O_WORKDIR/.

In the command prompt, type the command, qsub gromacs.cmd

Sample job file for running a gromacs parallel job multiple nodes :

File Name : gromacs.cmd

#!/bin/bash

#PBS -l cput=400:00:00

#PBS -e errorfile.err

#PBS -o logfile.log

#PBS -l select=2:ncpus=16

tpdir=`echo $PBS_JOBID | cut -f 1 -d .`

tempdir=$HOME/work/job$tpdir

mkdir -p $tempdir

cd $tempdir

cp -R $PBS_O_WORKDIR/* .

mpirun -np 32 -hostfile $PBS_NODEFILE `which mdrun_mpi` -s -v -deffnm test.tpr

mv ../job$tpdir $PBS_O_WORKDIR/.

In the command prompt, type the command, qsub gromacs.cmd