script example - GridChem dmol3

#!/bin/sh

#PBS -m bae

#PBS -N dmol3 

#PBS -q debug 

#PBS -M ccg-admin@gridchem.uits.iu.edu

#PBS -j oe 

#PBS  -V 

#PBS -l walltime=0:30:0,ncpus=16

#PBS -l mem=1000mb

#PBS -A ch87lmp

set -x

. /usr/share/modules/init/bash

module load torque/2.3.13_psc

module load globus/5.0.4

module load mpt/2.04

module load DMol3

export X509_USER_PROXY=/brashear/gcommuni/spamidig/tempdirs/tempdirQouqrym/x509up_p20177.fileHelqfm.1

###2007/05/03 export LD_LIBRARY_PATH=/usr/psc/globus/5.2.5/lib64:/usr/psc/globus/5.2.5/lib:/opt/intel/composer_xe_20

13_sp1.0.080/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/mpirt/lib/intel64:/opt/intel/composer_xe_201

3_sp1.0.080/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/ipp/lib/intel64:/opt/intel/composer_xe

_2013_sp1.0.080/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/intel64:/opt/intel/composer_xe_20

13_sp1.0.080/tbb/lib/intel64/gcc4.1:/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64:/opt/intel/composer_x

e_2013_sp1.0.080/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/ipp/../compiler/lib/intel64:/opt/intel/comp

oser_xe_2013_sp1.0.080/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64:/opt/intel/compose

r_xe_2013_sp1.0.080/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/tbb/lib/intel64/gcc4.1:/opt/sgi/mpt/mpt-2.

04/lib:/opt/intel/composerxe-2011.3.174/mkl/lib/intel64   # NOT NEEDED

jobid=`echo $PBS_JOBID |sed 's/\..*//' `

jobdir="dmol3.blacklight.psc.teragrid.org.$jobid.141125"

export OutDir=/brashear/gcommuni/spamidig/spamidig_proj/$jobdir

if [ ! -d $OutDir ] ; then

  echo "Making dir: $OutDir"; 

  mkdir -p $OutDir || exit 1;  # let us stop if we can not make this dir - it is too important

fi

# we need to export SCRATCH_BATCH 

export SCRATCH_BATCH=/brashear/gcommuni/spamidig/spamidig_proj/$jobdir/batch_scratch

if [ ! -d $SCRATCH_BATCH ] ; then 

  echo "Making dir: $SCRATCH_BATCH"   ; 

  mkdir -p $SCRATCH_BATCH  || exit 1;

fi

# change directory to SCRATCH_BATCH

cd $SCRATCH_BATCH

# 2006/03/31 make a link of the Outdir into OutDir for convenience

/bin/ln -s  /brashear/gcommuni/spamidig/tempdirs/tempdirQouqrym $OutDir/

###which uberftp

###echo "DEBUG: TEMP01AAAAAA 20070301 skk ";  ls -l $X509_USER_PROXY

cp -p /brashear/gcommuni/spamidig/tempdirs/tempdirQouqrym/dmol3.* .

Diskoutputfile_with_dir=$SCRATCH_BATCH/dmol3.out

/bin/ln -sf $Diskoutputfile_with_dir $OutDir/dmol3.out

trap ". /brashear/gcommuni/spamidig/tempdirs/tempdirQouqrym/qsubin20181_cleanup ; exit 99 " XCPU INT TERM CHLD  

cp -p /brashear/gcommuni/spamidig/tempdirs/tempdirQouqrym/*.* /brashear/gcommuni/spamidig/spamidig_proj/$jobdir/batc

h_scratch

/usr/local/packages/DMOL3/etc/DMol3/bin/RunDMol3.sh -np 4 dmol3

. /brashear/gcommuni/spamidig/tempdirs/tempdirQouqrym/qsubin20181_cleanup