Re: [Opaltoolkit-users] problem launching opal jobs

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

Hi, Malcolm,

What version of PBS are you using, and what is the OS for the cluster?
We'll try to find something similar or set up a virtual cluster to check
out this issue with PBS.

Cheers,

Wilfred


-----Original Message-----
From: Malcolm Tobias [mailto:mt...@wu...] 
Sent: Tuesday, June 23, 2009 12:28 PM
To: opa...@li...
Subject: [Opaltoolkit-users] problem launching opal jobs


I'm attempting to set up our own local pdb2pqr Opal server following the
instructions at:

http://www.nbcr.net/software/opal/docs/2.0/installation.html

After customizing the XML configuration to point to our local pdb2pqr, I

deployed the service:

ant deploy -DserviceName=pdb2pqr -DappConfig=./pdb2pqr_config.xml 

I then tried to use the client to launch a job:

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

Reading command line arguments
Service URL: http://agave:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
Exception in thread "main" AxisFault
 faultCode:
{http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
 faultSubcode: 
 faultString: 
 faultActor: 
 faultNode: 
 faultDetail: 
        {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>
        
{http://xml.apache.org/axis/}exceptionName:edu.sdsc.nbcr.opal.FaultType
        {http://xml.apache.org/axis/}hostname:agave.wustl.edu

The job manager that I have specified in my pdb2pqr_config.xml file is:

<jobManagerFQCN>edu.sdsc.ncbr.opal.manager.DRMAAJobManager</jobManagerFQ
CN>

The corresponding job manager defined in my etc/opal.properties is:

   opal.jobmanager=edu.sdsc.ncbr.opal.manager.DRMAAJobManager

Any ideas on what might be wrong?


A second question that I'll need to address at some point is how to
customize 
the batch script that is used for launching the jobs.  We have an
existing 
cluster (running PBS/torque) and I'd like to define a property that
denotes 
that some special nodes are available for running Opal jobs.  If I were
doing 
this manually, instead of specifying:

qsub -I -lnodes=1

I'd do this by specifying:

qsub -I -lnodes=1:opal

Is there some way to customize how Opal talking to the queuing system
via 
DRMAA?

Thanks,
Malcolm


-- 
Malcolm Tobias
314.362.1594


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