Re: [Opaltoolkit-users] problem launching opal jobs

[Wilfred L. <wi...@sd...>]

Looking at your opal.properties file, I'd suggest that you use the ForkJobManager for now to debug your installation, since we haven't figured out how to configure the DRMAAJobManager with PBS yet. We used PBS 4 or 5 years ago, but switched to SGE for a number of reasons. You can do this by adding the appConfig entry 

<jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>, or edit your current entry for DRMAAJobmanager. 

I've attached the pdb2pqr appConfig file that we have. I suspect that with Opal 2.0, the application version number is supposed to be part of the URL. That's explicitly specified in the appConfig file. But Luca can clarify on that.

Our plan is to include the appConfig files that we use as a template in future distributions of Opal.

Cheers,

Wilfred


-----Original Message-----
From: Malcolm Tobias [mailto:mt...@wu...] 
Sent: Thursday, June 25, 2009 9:07 AM
To: Wilfred Li
Cc: opa...@li...
Subject: Re: [Opaltoolkit-users] problem launching opal jobs


Wilfred,

On Thursday 25 June 2009 10:30:45 am Wilfred Li wrote:
> I got the same error when I tried your service using the Opal Client, 
> whereas the ws.nbcr.net pdb2pqr service returned a successful launch. 
> My guess is still an configuration issue. Could you please send me 
> your opal.properties file and your app config file for pdb2pqr?

Sure.  They're attached.

> [wilfred@rocks-32 opal-ws-2.0]$ java
> edu.sdsc.nbcr.opal.GenericServiceClient -l 
> http://ws.nbcr.net/opal2/services/pdb2pqr_1.4.0 -r launchJob -a 
> "--ff=amber sample.pdb output.pqr" -f samples/sample.pdb

FWIW, I verified I could also use your server, which I guess rules out problems with my client.

I should mention that I do expect jobs to fail at some point with our server.
The user running Tomcat doesn't have permission to run jobs on the default queue.  I'm still trying to figure out how to have a different default queue for this specific user.  Luca mentioned that you use .sge_request for SGE but I can't find any equivalent configuration file for PBS.  I'm guessing the server would tell the client that it has accepted the job, and then it would fail to run.  I'm not sure if that is responsible for the current error.  

Malcolm

--
Malcolm Tobias
314.362.1594