Am 13.07.2012 um 09:44 schrieb William Hay:
> On 13 July 2012 07:37, Joseph A. Farran <[email protected]> wrote:
>> Hi.
>>
>> I am trying to set OMP_NUM_THREADS to the number of slots in my .sge_request
>> with
>>
>> -v OMP_NUM_THREADS=$NSLOTS
>> But GE is not setting the variable to the value of $NSLOTS. It does a
>> literal set of "$NSLOTS".
>>
>> Can this be done with .sge_request to set OMP_NUM_THREADS with say 8 if
>> $NSLOTS is equal to 8?
>
> No that gets set when the job is submitted and $NSLOTS isn't set until
> runtime(because you can request a
> PE range). You could put instructions to do this in shell
> initialization scripts and/or set ENV/BASH_ENV
> scripts via .sge_request to point to a shell fragment that does this.
Besides using the "starter_method" we discussed last week, it's also possible
to use a job prolog to change the value in the environment file:
$ cat prolog.sh
#!/bin/sh
sed -i "/^OMP_NUM_THREADS/d;\$aOMP_NUM_THREADS=$NSLOTS"
$SGE_JOB_SPOOL_DIR/environment
$ qconf -sq all.q
...
prolog sgeadmin@/usr/sge/cluster/prolog.sh
$ cat job.sh
#!/bin/sh
echo $OMP_NUM_THREADS
$ qsub -q all.q -pe openmpi 4 job.sh
Your job 4489 ("job.sh") has been submitted
$ cat job.sh.o4489
4
-- Reuti
> William
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