Gromacs

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

File Name : gromacs.cmd

#!/bin/bash

#@ output = test.out

#@ error = test.err

#@ job_type = MPICH

#@ class = Long

#@ node = 1

#@ tasks_per_node = 16

#@ 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

mpirun -np 16 /sware/gromacs455/bin/mdrun_mpi -v -s cetp-2ob-pcw-full.tpr -deffnm

cetp_full

mv ../job$Jobid $LOADL_STEP_INITDIR

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