[gridengine users] prolog-like script for qrsh

Reuti reuti at staff.uni-marburg.de
Tue May 14 16:52:10 UTC 2013


Am 14.05.2013 um 18:17 schrieb Riccardo Murri:

> Hi,
> 
> On 14 May 2013 09:05, Reuti <reuti at staff.uni-marburg.de> wrote:
>> 
>> Am 14.05.2013 um 01:26 schrieb Riccardo Murri:
>> 
>>> is there a prolog-like script that gets executed before a task spawned
>>> by qrsh (as part of a parallel job) is run?  The usual prolog is only
>>> run on the master node at the start of the job, but I'm trying to
>>> intercept instances of `qrsh -V` spawned by OpenMPI's `mpiexec`.
>> 
>> Why?
> 
> To workaround the multi-line environment variables bug that's still
> present in OGE 6.2u8.
> (But I ended up using QRSH_WRAPPER for that purpose.)

Why is it necessary to run the prolog as root for this purpose?

-- Reuti


>> In the prolog of the PE you could program a loop across all granted nodes by using a `qrsh -inherit -V ...` to all nodes therein to make some preparations.
> 
> I'm now doing this:
> 
>        HOSTS=$( cut -d' ' -f1 $PE_HOSTFILE | fgrep -v $(hostname -s) )
> 	for host in $HOSTS; do
> 	    qrsh -inherit -V $host $RUNSCRIPT | grep -q "failed"
>            # ... react on failure
>        done
> 
> but apparently `execd` does not allow me to qrsh from the prolog:
> 
>    error: executing task of job 2648607 failed: execution daemon on
> host "r01c04b04n02" didn't accept task
> 
> anything wrong with my use of `qrsh`?
> 
> Thanks,
> Riccardo
> 
> --
> Riccardo Murri
> http://www.gc3.uzh.ch/people/rm
> 
> Grid Computing Competence Centre
> University of Zurich
> Winterthurerstrasse 190, CH-8057 Zürich (Switzerland)
> Tel: +41 44 635 4222
> Fax: +41 44 635 6888
> 





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