Re: [Opaltoolkit-users] problem launching opal jobs

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Luca,

On Wednesday 24 June 2009 01:02:42 pm Luca Clementi wrote:
> > 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.

I thought running the shell script would set the CLASSPATH, but for some weird 
reason it doesn't.  It just prints out the list of directories:

[root@agave opal-ws-2.0]# ./etc/classpath.sh 

[root@agave opal-ws-2.0]# echo $CLASSPATH

[root@agave opal-ws-2.0]# printenv | grep CLASS
[root@agave opal-ws-2.0]# 

It probably doesn't matter why it's failing.  I manually set it.
Here's what I see now:

[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

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.userException
 faultSubcode: 
 faultString: java.lang.reflect.InvocationTargetException
 faultActor: 
 faultNode: 
 faultDetail: 
        {http://xml.apache.org/axis/}hostname:agave.wustl.edu

java.lang.reflect.InvocationTargetException
        at 
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:221)
        at 
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:128)
        at 
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
        at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        at 
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227)
        at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
        at org.apache.axis.Message.getSOAPEnvelope(Message.java:424)
        at 
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62)
        at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
        at org.apache.axis.client.Call.invokeEngine(Call.java:2765)
        at org.apache.axis.client.Call.invoke(Call.java:2748)
        at org.apache.axis.client.Call.invoke(Call.java:2424)
        at org.apache.axis.client.Call.invoke(Call.java:2347)
        at org.apache.axis.client.Call.invoke(Call.java:1804)
        at 
edu.sdsc.nbcr.opal.AppServicePortTypeSoapBindingStub.launchJob(AppServicePortTypeSoapBindingStub.java:551)
        at 
edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.java:311)

At least it appears to be talking to Tomcat.  Here are the Tomcat logs:

2009-06-24 13:39:55,205 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
called
2009-06-24 13:39:55,308 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
2009-06-24 13:49:21,483 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchJob(AppServiceImpl.java:237) - called
2009-06-24 13:49:21,485 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java:1038) - 
called
2009-06-24 13:49:21,487 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java:944) - 
called
2009-06-24 13:49:21,500 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's DN: Unknown 
client
2009-06-24 13:49:21,502 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's IP: 
127.0.0.1
2009-06-24 13:49:21,504 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
called
2009-06-24 13:49:21,509 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager

I think I'm getting close ;-)

Thanks again for your help.

Malcolm

-- 
Malcolm Tobias
314.362.1594