Gromacs

Sample job file for running a gromacs serial job for single CPU:

File Name : gromacs.cmd

#!/bin/bash

#@ output = test.out

#@ error = test.err

#@ job_type = serial

#@ class = Small

#@ environment = COPY_ALL

#@ queue

Jobid=`echo $LOADL_STEP_ID | cut -f 6 -d .`

tmpdir=$HOME/scratch/job$Jobid

mkdir -p $tmpdir; cd $tmpdir

cp -R $LOADL_STEP_INITDIR/* $tmpdir

/sware/gromacs455/bin/mdrun -v -s cetp-2ob-pcw-full.tpr

mv ../job$Jobid $LOADL_STEP_INITDIR

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