Re: [Opaltoolkit-users] problem launching opal jobs

[Malcolm T. <mt...@wu...>]

Luca,

On Tuesday 23 June 2009 04:46:55 pm Luca Clementi wrote:
> >         {http://nbcr.sdsc.edu/opal/types}opalFaultOutput:<message>Can't
> > instantiate Opal Job Manager - Job manager class
> > edu.sdsc.ncbr.opal.manager.DRMAAJobManager not found</message>
>
> Tobias,
> you have to typo, it's nbcr not ncbr.

Doh!  Sorry I didn't catch that.

After fixing it, I'm getting a different error when I try to submit a job:

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
sample.pdb output.pqr" -f samples/sample.pdb
Exception in thread "main" java.lang.NoClassDefFoundError: 
edu/sdsc/nbcr/opal/GenericServiceClient
Caused by: java.lang.ClassNotFoundException: 
edu.sdsc.nbcr.opal.GenericServiceClient
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
Could not find the main class: edu.sdsc.nbcr.opal.GenericServiceClient.  
Program will exit.

> > Is there some way to customize how Opal talking to the queuing system via
> > DRMAA?
>
> Not really. Unfortunately we use DRMAA so that we don't have to generate
>   submission scripts for each scheduler (DRMAA is an API library).
>
> On our machine we don't use PBS but SGE and to specify a default queue
> on our cluster we have used a SGE configuration file that can be placed
> in the home of the user called .sge_request.

I couldn't find a similar configuration file for PBS/Torque so I was thinking
about creating an alias for qsub.  This works for interactive logins, but I'm 
not sure if it will work with DRMAA.  Any reasons why this wouldn't work?  
Is there some log file that I should be check in case this doesn't work?

Cheers,
Malcolm


-- 
Malcolm Tobias
314.362.1594