On 12/01/2013 03:13 PM, Reuti wrote:
Hi,
Am 01.12.2013 um 22:20 schrieb David Dotson:
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
The scratch directory supplied by SGE, i.e. $TMPDIR is not sufficient? It's the one set
up in the queue definition "tmpdir".
I was not aware of this option. It shouldn't make a difference, but
could it? We may very well change our standard submission scripts to
reference $TMPDIR instead if that's the case.
function setup_workdir () {
echo "-- [$(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?
Yes, this might happen - how long does the copy process take to complete. It
should be recorded in the message for the node though (do you see a 90 sec
interval?).
The time it takes for the job to die during cleanup appears to vary. I
have had instances where it takes minutes, and others in which it takes
seconds. This has made it very frustrating to figure out, and it's why
I'm reaching out for some help.
As a note, I have tried sending SIGTERM as a notification instead, and setting
the `notify` queue configuration key to 24:00:00
And changed the signal in SGE's configuration ("NOTIFY_KILL=sigterm") and submitted with
"-notify"? This would be better than changing the "terminate_method" to something which
must be handled inside the script to kill itself.
Correct. I added this key to "execd_params" in the SGE configuration,
and submitted the job with the "-notify" flag. As I said, it seems to be
working in some quick tests I did today, but I do recall this failing in
the past when actually copying back large files (meaning the copy was
killed mid-copy).
(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.
What do you mean by failed - is was killed anyway?
-- Reuti
David
--
David L. Dotson
Center for Biological Physics
Arizona State University
Email:
[email protected]
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users mailing list
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--
David L. Dotson
Center for Biological Physics
Arizona State University
Email: [email protected]
_______________________________________________
users mailing list
[email protected]
https://gridengine.org/mailman/listinfo/users
