Re: [Opaltoolkit-users] Opal DRMAA with Torque

[Sriram K. <sr...@sd...>]

Hi Peter,

We have never had any luck getting DRMAA to work with PBS/Torque. The  
DRMAA implementation has only really been tested using SGE.

However, we now have a new PBSJobManager in SVN. If you can wait till  
around mid May, we are planning on a next release which will include  
this job manager - and some documentation for the same. If you would  
like to try it out beforehand, just update from SVN (and let us know  
if you have any comments). To use it, simply set opal.jobmanager to  
edu.sdsc.nbcr.opal.manager.PBSJobManager in your opal.properties. You  
also have to make sure that all of the Torque commands like qsub,  
qstat, etc are in your path before you restart Tomcat.

Cheers,
Sriram

On Apr 19, 2010, at 7:24 PM, Peter Scott wrote:

> Hi Opal Users,
>
> I am  trying to get Opal working as part of the Meme Suite. I am  
> trying to use Opal to dispatch jobs to our cluster running Torque  
> PBS using DRMAA.
> I believe that the Torque implementation of DRMAA differs from the  
> SGE implementation, especially concerning the return value of  
> drmaa_wait().
> With Torque this causes errors even with the Torque DRMAA build test  
> code (described in OGF DRMAA v 1.0 - PBS/Torque Experience).
> I suspect that that the return value is preventing completion of the  
> job and am starting to look at hacking away at the Torque DRMAA  
> source code.
> One alternative that I see is to use Globus instead of DRMAA however  
> this would require an overhaul of the cluster infrastructure and  
> strikes me as a heavy handed approach. Another option would be to  
> write a new job interface using the Opal libs but ideally I would  
> like to use the native Opal DRMAA interface.
> Does anyone have any experience getting Opal to dispatch jobs to PBS  
> Torque (We are using Maui as the scheduler) ?
> Can anyone advise on how the DRMAA interface is implemented within  
> Opal (what parameters are passed to DRMAA and where they come from  
> etc).
>
> Regards,
>
> Peter Scott
>
> Peter Scott
> Queensland Facility for Advanced Bioinformatics
> Institute for Molecular Bioscience
> Queensland Bioscience Precinct
> University of Queensland
> St Lucia QLD 4072
>
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