Greetings,
We have the terminate_method for our queue set to SIGTERM, so that when
the following submission script runs, it should copy back all the files
generated to the original directory. The signal is indeed caught, and
the copy-back takes place, but it often dies without completing after a
short amount of time.
# BEGIN SCRIPT
#============
# standard gridengine script with automatic copying back of data
#$ -S /bin/bash
#$ -N grid_job
#$ -pe singlenode 16
#$ -cwd
#$ -j y
#$ -R y -r n
# set up scratch directory
WORK=/scratch/${USER}/WORK/${JOB_ID}
ORIG=$PWD
function setup_workdir() {
echo "-- [$(date)] setting up$WORK"
mkdir -p $WORK
test -d $WORK || { echo "EE ERROR: Failed to make tmpdir";exit 1;}
cp $TPR $DEFFNM.cpt$DEFFNM.xtc$DEFFNM.trr$DEFFNM.edr$DEFFNM.log$WORK
copy_success="True"
}
function cleanup_exit() {
# ensure that we don't overwrite complete files with partial ones if job
killed mid-copy
echo "-- [$(date)] cleaning up:$WORK -->$ORIG"
cp $WORK/* $ORIG || { echo "EE ERROR: Did not copy$WORK --- check
manually!";exit 1;}
cd $ORIG
rm -r $WORK
exit 0
}
# make sure that killing the job copies back everything; won't copy back if job
# killed while copying to workstation (a good thing!)
# (GE must be configured to use SIGTERM for killing jobs!)
trap cleanup_exit TERM
setup_workdir
cd $WORK || { echo "EE ERROR: failed to cd$WORK";exit 2;}
# MAIN COMPUTATION RUNS HERE
cleanup_exit
#============
# END SCRIPT
What is happening here? Is a second SIGTERM sent by gridengine after
some time? If so, what is the best way to ensure this copy-back
completes on qdel?
As a note, I have tried sending SIGTERM as a notification instead, and
setting the `notify` queue configuration key to 24:00:00 (basically,
REALLY LONG). This seems to work in some of my tests, but it has failed
in actual use when copying back large data files.
David
--
David L. Dotson
Center for Biological Physics
Arizona State University
Email:[email protected]
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