[GE users] prolog/epilog

Wheeler, Dr M.D. mdw10 at leicester.ac.uk
Thu Oct 28 11:13:34 BST 2004

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Dear All,

Sorry if this seems a simple/naive request.

I am new to SGE (I have used PBS in the past).  I would like to set up prolog/epilog scripts to set up temporary directories where output is written during execution and then to rmove them upon completion/deletion of the job (these temp files can contain up to60 GB of data so it is imperative taht they are always removed).  I used to do something similar in PBS

Essentially the prolog file contains

#create temporary directories
/bin/mkdir /state/partition1/$JOB_ID
/bin/chmod 700 /state/partition1/$JOB_ID
/bin/chown $LOGNAME /state/partition1/$JOB_ID
/bin/mkdir /state/partition2/$JOB_ID
/bin/chmod 700 /state/partition2/$JOB_ID
/bin/chown $LOGNAME /state/partition2/$JOB_ID

export TMPDIR=/state/partition1/$JOB_ID
export TMPDIR2=/state/partition2/$JOB_ID

and the epilog file contains

#remove temporary directories
/bin/rm -rf /state/partition1/$JOB_ID
/bin/rm -rf /state/partition2/$JOB_ID

I ahve tried putting these commands into script files and referencing them via the qconf -mconf command

however, it causes my SGE installation to stop working....

Does anyone have any advice on how this can be achieved?

Thanks in advance,

Dr. Martyn D. Wheeler
Department of Chemistry
University of Leicester
University Road
Leicester, LE1 7RH, UK.
Tel (office): +44 (0)116 252 3985
Tel (lab):    +44 (0)116 252 2115
Fax:          +44 (0)116 252 3789
Email:        martyn.wheeler at le.ac.uk

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