Re: [Opaltoolkit-users] problem launching opal jobs

[Luca C. <lcl...@uc...>]

Malcolm Tobias wrote:
> 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.
> 

Tobias,
you have to set the classpath properly before you can use the Opal 
client. Please run
. etc/classpath.sh
if you are using bash.


>>> 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?  

DRMAA uses APIs to talk with the scheduler, it doesn't use any command 
line. My guess is that it shouldn't work.

> Is there some log file that I should be check in case this doesn't work?
> 

All the log of Opal are in $CATALINA_HOME/logs/catalina.out

Tobias I would keep on looking in PBS documentation how to default a 
user to a particular queue.

Sincerely,
Luca