[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,
Martyn


----------------------------------------------
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
http://www.le.ac.uk/chemistry/staff/mdw10.html
 

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