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Namd

Sample job file for running Namd serial job for single CPU:

File Name : namd.cmd

#!/bin/bash

#@ output = test.out

#@ error = test.err

#@ job_type = MPICH

#@ class = Medium128

#@ node = 2

#@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

cat $LOADL_HOSTFILE > ./host.list

export LD_LIBRARY_PATH=/sware/openmpi1.6/lib:$LD_LIBRARY_PATH

/sware/openmpi1.6/bin/mpirun --mca btl openib,self -np 32 -hostfile

$LOADL_HOSTFILE /sware/NAMD_2.9_Source/Linux-x86_64-g++/namd2 inputfile >

outfile/logfile

mv ../job$Jobid $LOADL_STEP_INITDIR

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