[GE users] Setting OMP_NUM_THREADS automatically

Reuti reuti at staff.uni-marburg.de
Fri Jul 25 17:32:52 BST 2008


Am 25.07.2008 um 18:06 schrieb Chris Rudge:

>
> Ah, spoke too soon.
>
> Things seem to break when an MPI job runs in the same queue. I'm  
> using tight
> integration and end up with errors like:
> /usr/local/sge6.0/openmp/startomp.sh: line 5: exec: cd: not found

Which type of MPI? This was done by Myrinet in the past and also  
broke Tight Integration as the second command after the ";" (i.e. the  
command to start slave tasks was: cd balbla; pgmname ...) created a  
subshell.

-- Reuti


> I've not delved too far to work out exactly where this comes from  
> but it
> does suggest that it would be better to have a solution to setting the
> number of threads which can be implemented within the PE rather  
> than for the
> queue.
>
> Chris
>
>
>> -----Original Message-----
>> From: Chris Rudge [mailto:chris.rudge at astro.le.ac.uk]
>> Sent: 25 July 2008 13:46
>> To: users at gridengine.sunsource.net
>> Subject: Re: [GE users] Setting OMP_NUM_THREADS automatically
>>
>>
>> Great, that seems to work. Obviously it now gets set for all
>> jobs that run in that queue, and has to be set for all queues
>> that run OpenMP jobs, but I can live with that.
>>
>> Chris
>>
>> On Fri, 2008-07-25 at 13:51 +0200, Reuti wrote:
>>> you could setup a custom starter_method like:
>>>
>>> #!/bin/sh
>>> export OMP_NUM_THREADS=$NSLOTS
>>> exec "$@"
>>>
>>> and set it in the queue definition just:
>>>
>>> starter_method /usr/sge/cluster/startup.sh
>>>
>>> -- Reuti
>> --
>> Dr Chris Rudge
>> chris.rudge at astro.le.ac.uk
>>
>> Research Computing Manager
>> Dept of Physics & Astronomy
>> University of Leicester
>> LE1 7RH
>>
>> web.  www.ukaff.ac.uk
>> Tel.  +44 (0)116 2523331
>> Fax.  +44 (0)116 2231283
>> Mob.  +44 (0)794 1379420
>>
>>
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>
>
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