Namd

NAMD

Sample job file for running a namd serial job :

File Name : namd.cmd

#!/bin/bash

#PBS -o logfile.log

#PBS -e errorfile.err

#PBS -l cput=240:00:00

#PBS -l select=1:ncpus=1

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

tempdir=$HOME/work/job$tpdir

mkdir -p $tempdir

cd $tempdir

cp -R $PBS_O_WORKDIR/* .

LD_LIBRARY_PATH=/sfs1/sware/namd/tcl8.5.5/unix/lib:$LD_LIBRARY_PATH

charmrun /sfs1/sware/namd/NAMD_2.6_Linux-amd64/namd2 inputfile >

outfile

mv ../job$tpdir $PBS_O_WORKDIR/.

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

Sample job file for running a namd parallel job :

File Name : namd.cmd

#!/bin/bash

#PBS -l cput=240:00:00

#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/* .

NODELIST=/tmp/charmrun-nodelist.$PBS_JOBID

cat $PBS_NODEFILE | sed -e 's/^/host /' > $NODELIST

export CONV_RSH=ssh

charmrun +p32 ++remote-shell ssh ++nodelist $NODELIST

/sware/namd/NAMD_2.9b1_Linux-x86_64-ibverbs/namd2 inputfile > output

file

mv ../job$tpdir $PBS_O_WORKDIR/.

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