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LIBRA NAMD

Sample job file for running a NAMD job :

File Name : namd.cmd

#!/bin/bash

#PBS -o logfile.log

#PBS -e errorfile.err

#PBS -l cput=750:00:00

#PBS -l select=1:ncpus=2:ngpus=1

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

tempdir=$HOME/work/job$tpdir

mkdir -p $tempdir

cd $tempdir

cp -R $PBS_O_WORKDIR/* .

/gpuusers/sware/NAMD_2.7b2_Linux-x86_64-CUDA/charmrun

/gpuusers/sware/NAMD_2.7b2_Linux-x86_64-CUDA/namd2 ++local +p2 +devices 0,1,2

+idlepoll inputfile > outfile

mv ../job$tpdir $PBS_O_WORKDIR/.

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