script example - GridChem Lammps_DS

#!/bin/sh 

#SBATCH -J default_job

#SBATCH -p development

#SBATCH -o default_job.o%j

#SBATCH -n 128

#SBATCH -t 0:30:0

#SBATCH --mail-user=ccg-admin@ccg-mw2.ncsa.uiuc.edu

#SBATCH --mail-type=ALL

#SBATCH -A TG-CHE080068N

set -x

export X509_USER_PROXY=/work/00421/ccguser/mvanmoer/tempdirs/tempdirXhPapVc/x509up_p14595.fileIqTlFB.1

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

ntel/13/composer_xe_2013.2.146/tbb/lib/intel64:/opt/apps/intel/13/composer_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/intel64:/opt/apps/in

tel/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/xsede/gsi-openssh-6.2p1/lib64:/opt/apps/xsede/gsi-openssh-6.2p1/lib64   #

 NOT NEEDED

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

jobdir="default_job.stampede.tacc.utexas.edu.$jobid.140123"

export OutDir=/work/00421/ccguser/mvanmoer/mvanmoer_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/mvanmoer/mvanmoer_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/mvanmoer/tempdirs/tempdirXhPapVc $OutDir/

###which uberftp

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

# 20140115:MVM - not sure where the best place to do this is

# need to copy files from ds_lammps/data to working directory to avoid having

# to upload them through Gridchem

# also not sure if there's a variable containig this path

cp /home1/00421/ccguser/apps/ds_lammps/data/* .

cp -p /work/00421/ccguser/mvanmoer/tempdirs/tempdirXhPapVc/* .

Diskoutputfile_with_dir=$SCRATCH_BATCH/default_job.out

trap ". /work/00421/ccguser/mvanmoer/tempdirs/tempdirXhPapVc/qsubin14607_cleanup ; exit 99 " XCPU INT TERM CHLD  

ibrun ~/apps/ds_lammps/bin/lmp_stampede < a_0001_300K.in > default_job.out

Ndumps=`find . -type f -name \*dump | wc -l`

if [ $Ndumps -eq "0" ] 

then

 echo "No dump files were generated, skipping Gordon job." ;

else

 echo "dump files generated, creating Gordon job."

 export jobdir=$jobdir

        export OutDir=$OutDir

 sed -i "s/export/export jobdir=$jobdir \nexport/" /work/00421/ccguser/mvanmoer/tempdirs/tempdirXhPapVc/ssh14607_gordo

n_sh   

 sed -i "s%export%export OutDir=$OutDir \nexport%" /work/00421/ccguser/mvanmoer/tempdirs/tempdirXhPapVc/ssh14607_gordo

n_sh  

 ssh login1.stampede.tacc.utexas.edu /work/00421/ccguser/mvanmoer/tempdirs/tempdirXhPapVc/ssh14607_gordon_sh > ssh_gor

don.out 2>&1

fi #end of Ndump conditional

. /work/00421/ccguser/mvanmoer/tempdirs/tempdirXhPapVc/qsubin14607_cleanup

# Qsubin CleanUp will be done in Qsubin_Vis