Re: [Opaltoolkit-users] Opaltoolkit on Rocks

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

Hello Rakesh,

Answers inline -

> I am really sorry to bother you, but didn't get any reply from  
> mailing list thus writing to you.

The mailing list is only open for posting to subscribers. Please sign  
up at - https://lists.sourceforge.net/lists/listinfo/opaltoolkit- 
users. It is fairly low traffic.


> We have rocks cluster and we are trying to use Opal Toolkit for job  
> submission for some of our applications. Opal-Toolkit is installed  
> successfully and working. As Rocks uses SGE by default we have set  
> the opal.properties to DRMAA.
> opal.jobmanager=edu.sdsc.nbcr.opal.manager.DRMAAJobManager
>
> Secondly, we would using OpenMpi thus have used the configuration
> drmaa.pe=orte (Could u advise, if this is ok)

We have personally never used it with OpenMpi, but there is no reason  
why it shouldn't work. Is "orte" the the PE that you use when you run  
SGE scripts from the command-line? If so, you should use that value.  
Also make sure that the mpi.run property is set correctly to run MPI  
programs correctly.

> This cluster is primarily being used for BLAST, I would appreciate  
> if your could advise me on the config.xml file for blast.

If you don't need advanced features such as automatic interface  
generation, I would start with the configs/date_config.xml and modify  
the "binaryLocation" and "parallel" values. If you want to try  
automatic interface generation, you could look at configs/ 
pdb2pqr_config.xml for an example.

Hope that helps,
Sriram