[GE users] prolog/epilog

Wheeler, Dr M.D. mdw10 at leicester.ac.uk
Thu Oct 28 12:05:52 BST 2004


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Hi Joe,
I'd already encountered this and done an ad hoc fix, the cluster-fork method looks neater though

-----Original Message-----
From: Joe Landman [mailto:landman at scalableinformatics.com]
Sent: 28 October 2004 12:03
To: users at gridengine.sunsource.net; martyn.wheeler at leicester.ac.uk
Subject: Re: [GE users] prolog/epilog


Hi Martyn:

  An issue that you may wish to deal with is the permissions on the 
directory /state/partition* .  As you are using ROCKS, the 
/state/partition* directories generally start up with incorrect 
permissions/ownership for end users to read/write to.

  You wil need to look at this, and if they are incorrect, try

    cluster-fork chmod -R a+rwx /state/partition*

to enable them to work.

Joe

Wheeler, Dr M.D. wrote:

>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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-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 612 4615


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