submit

#!/bin/sh

## Default parameters
MAX_DURATION="${MAX_DURATION:-20:00}"
MAX_MEMORY="${MAX_MEMORY:-16GB}"
OMP_NUM_THREADS="${OMP_NUM_THREADS:-1}"
MC_CORES="${MC_CORES:-1}"

## Additional parameters
QWAIT="${QWAIT:-0}"
## NOTIFICATION="${NOTIFICATION:-a}"
QUEUE="${QUEUE:-hpc}"

# Message
echo "Job parameters"
echo "=============="
echo
echo "MAX_DURATION    = $MAX_DURATION  (hh:mm)"
echo "MAX_MEMORY      = $MAX_MEMORY"
echo "OMP_NUM_THREADS = $OMP_NUM_THREADS"
echo "MC_CORES        = $MC_CORES"
echo

JOB_INFO=`
echo "
### -- embedded options to bsub - start with #BSUB
#BSUB -J Job
#BSUB -W $MAX_DURATION
### -- specify memory per core/slot (FIXME?)
#BSUB -R "rusage[mem=$MAX_MEMORY]"
#BSUB -n $(( $OMP_NUM_THREADS * $MC_CORES ))
#BSUB -R "span[hosts=1]"
### -- Deprecated #PBS -m $NOTIFICATION
#BSUB -q $QUEUE

### -- run in the current working (submission) directory --
### -- cd $PBS_O_WORKDIR <--- didn't work !
cd $PWD

## Reduce time spent in gc
export R_GC_MEM_GROW=3

# here follow the commands you want to execute
export OMP_NUM_THREADS=$OMP_NUM_THREADS
export MC_CORES=$MC_CORES
export QUEUE=$QUEUE

cat /proc/cpuinfo
env

$*
" | bsub
`

## echo $JOB_INFO
JOBID=`echo $JOB_INFO | sed 's/Job..//g' | sed 's/>.*//g'`
## echo $JOBID

if [ $QWAIT == 1 ]
then
  echo "Waiting for $JOBID"
  while true
  do
    if ! `bstat | grep -q $JOBID`
    then
      echo "completed $JOBID"
      exit 0
    fi
    sleep 1
  done
fi