Script examples - GridChem NWChem

#!/bin/sh 

#SBATCH -J iumtest2

#SBATCH -p development

#SBATCH -o iumtest2.o%j

##SBATCH -n 1

#SBATCH -N 1 -n 16

#SBATCH -t 0:30:0

#SBATCH --mail-user=ccg-admin@gridchem.uits.iu.edu

#SBATCH --mail-type=ALL

#SBATCH -A TG-CHE080068N

 # Application NWCHEM6.3 STAMPEDE

set -x

module load globus;

module load uberftp;

module load nwchem

export X509_USER_PROXY=

###2007/05/03 export LD_LIBRARY_PATH=/opt/apps/intel13/mvapich2/1.9/lib:/opt/apps/intel13/mvapich

2/1.9/lib/shared:/opt/apps/intel/13/composer_xe_2013.2.146/tbb/lib/intel64:/opt/apps/intel/13/com

poser_xe_2013.2.146/compiler/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic

/myo/lib:/opt/apps/intel/13/composer_xe_2013.2.146/mpirt/lib/intel64:/opt/apps/intel/13/composer_

xe_2013.2.146/ipp/../compiler/lib/intel64:/opt/apps/intel/13/composer_xe_2013.2.146/ipp/lib/intel

64:/opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64:/opt/apps/intel/13/composer_xe_

2013.2.146/mkl/lib/intel64:/opt/apps/intel/13/composer_xe_2013.2.146/tbb/lib/intel64:/opt/apps/xs

ede/gsi-openssh-5.7/lib64:/opt/apps/xsede/gsi-openssh-5.7/lib64   # NOT NEEDED

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

jobdir="iumtest2.stampede.tacc.utexas.edu.$jobid.141117"

export OutDir=/work/00421/ccguser/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 HOME_BATCH=/work/00421/ccguser/spamidig/spamidig_proj/$jobdir

export SCRATCH_BATCH=/scratch/00421/ccguser/$SLURM_JOBID

if [ ! -d $SCRATCH_BATCH ] ; then

    mkdir -p $SCRATCH_BATCH

fi

if [ ! -d $HOME_BATCH ] ; then 

  echo "Linking HOME_BATCH to SCRATCH_BATH: $HOME_BATCH -> $SCRATCH_BATCH"   ; 

  ln -s $SCRATCH_BATCH $HOME_BATCH  || exit 1;

fi

# change directory to SCRATCH_BATCH

cd $SCRATCH_BATCH

pwd

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

#/bin/ln -s  /work/00421/ccguser/spamidig/tempdirs/tempdirLdnzJQH $OutDir/

cp -p /work/00421/ccguser/spamidig/tempdirs/tempdirLdnzJQH/nwchem_sample0.nw .

Diskoutputfile_with_dir=$SCRATCH_BATCH/iumtest2.out

trap ". /work/00421/ccguser/spamidig/tempdirs/tempdirLdnzJQH/qsubin44102_cleanup ; exit 99 " XCPU

 INT TERM CHLD  

export NWCHEM_BASIS_LIBRARY=/opt/apps/intel13/mvapich2_1_9/nwchem/6.3/data/libraries/

/opt/apps/intel13/mvapich2_1_9/nwchem/6.3/bin/nwchem nwchem_sample0.nw >| $Diskoutputfile_with_di

r

. /work/00421/ccguser/spamidig/tempdirs/tempdirLdnzJQH/qsubin44102_cleanup