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Re: [Opaltoolkit-users] problem launching opal jobs
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From: Luca C. <lcl...@uc...> - 2009-06-24 20:42:35
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Malcolm Tobias wrote:
> 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
>
Tobias,
there is a space between the . and etc/classpath.sh
. etc/classpath.sh
if you write ./etc/classpath.sh it is going to work.
I guess that if you properly load the classpath.sh the errors should
disapear.
Sincerely,
Luca
> [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
>
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