Wrapper ScriptΒΆ

#!/bin/sh
#
#  Run command in batch on stoomboot
#
#  Usage bsub [ -J <jobname> ] <cmdline>
#

if [ $# -eq 0 ] ; then
  echo "usage: bsub <command> [<arg>,...]"
  exit 1
fi

NAME="bsub_$$"
if [ "$1" == "-J" ] ; then
  NAME=$2 ;
  shift 2
fi


SCRIPT=/tmp/bsub_$$
cat >> $SCRIPT << EOF
#!/bin/sh
echo "--- PBS job configuration ---"
echo "PBS_O_HOST = " \$PBS_O_HOST
echo "PBS_O_QUEUE = " \$PBS_O_QUEUE
echo "PBS_O_WORKDIR = " \$PBS_O_WORKDIR
echo "PBS_ENVIRONMENT = " \$PBS_ENVIRONMENT
echo "PBS_JOBID = " \$PBS_JOBID
echo "PBS_JOBNAME = " \$PBS_JOBNAME
echo "PBS_NODEFILE = " \$PBS_NODEFILE
echo "PBS_QUEUE = " \$PBS_QUEUE
echo "-----------------------------"

export PATH=\${PBS_O_PATH}
cd $PWD
$*
EOF
#chmod +x $SCRIPT

BQUEUE=${BSUBQUEUE:-stbcq}

unset TMPDIR
qsub -N ${NAME} -q $BQUEUE -V -j oe -d $PWD $SCRIPT

rm $SCRIPT