Re: [Opaltoolkit-users] problem launching opal jobs

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

Could you try using the FQDN of agave on your command line?

Best regards,

Wilfred

Sent from my FUZE™

-----Original Message-----
From: Malcolm Tobias <mt...@wu...>
Sent: 2009年6月25日 上午 06:03
To: Luca Clementi <lcl...@uc...>
Cc: opa...@li... <opa...@li...>
Subject: Re: [Opaltoolkit-users] problem launching opal jobs


Luca,

On Wednesday 24 June 2009 03:40:18 pm Luca Clementi wrote:
> 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.

Even with the CLASSPATH set:

[root@agave opal-ws-2.0]# printenv | grep CLASS
CLASSPATH=/usr/local/src/opal-ws-2.0:/usr/local/src/opal-ws-2.0/build/classes:/usr/local/src/opal-ws-2.0/lib:/usr/local/src/opal-ws-2.0/etc:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/axis-ant.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/axis.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/commons-discovery-0.2.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/commons-logging-1.0.4.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/jaxrpc.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/saaj.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/wsdl4j-1.5.1.jar:/usr/local/src/opal-ws-2.0/lib/activation-1_0_2.jar:/usr/local/src/opal-ws-2.0/lib/antlr-2.7.6.jar:/usr/local/src/opal-ws-2.0/lib/cglib-2.1.3.jar:/usr/local/src/opal-ws-2.0/lib/cog-axis.jar:/usr/local/src/opal-ws-2.0/lib/cog-jglobus.jar:/usr/local/src/opal-ws-2.0/lib/cog-tomcat.jar:/usr/local/src/opal-ws-2.0/lib/cog-url.jar:/usr/local/src/opal-ws-2.0/lib/commons-cl!
 i-2.0.jar:/usr/local/src/opal-ws-2.0/lib/commons-collections-3.1.jar:/usr/local/src/opal-ws-2.0/lib/cryptix32.jar:/usr/local/src/opal-ws-2.0/lib/cryptix-asn1.jar:/usr/local/src/opal-ws-2.0/lib/cryptix.jar:/usr/local/src/opal-ws-2.0/lib/dom4j-1.6.1.jar:/usr/local/src/opal-ws-2.0/lib/drmaa.jar:/usr/local/src/opal-ws-2.0/lib/hibernate3.jar:/usr/local/src/opal-ws-2.0/lib/hsqldb.jar:/usr/local/src/opal-ws-2.0/lib/javassist-3.4.GA.jar:/usr/local/src/opal-ws-2.0/lib/jce-jdk13-125.jar:/usr/local/src/opal-ws-2.0/lib/jcommon-1.0.12.jar:/usr/local/src/opal-ws-2.0/lib/jdom-1.1.jar:/usr/local/src/opal-ws-2.0/lib/jfreechart-1.0.8.jar:/usr/local/src/opal-ws-2.0/lib/jgss.jar:/usr/local/src/opal-ws-2.0/lib/jta-1.1.jar:/usr/local/src/opal-ws-2.0/lib/junit-4.4.jar:/usr/local/src/opal-ws-2.0/lib/log4j-1.2.15.jar:/usr/local/src/opal-ws-2.0/lib/mailapi-1_3_1.jar:/usr/local/src/opal-ws-2.0/lib/postgresql-8.2-506.jdbc3.jar:/usr/local/src/opal-ws-2.0/lib/puretls.jar:/usr/local/src/opal-ws-2.0/lib/r!
 ome-1.0RC1.jar:/usr/local/src/opal-ws-2.0/lib/servlet-api-2_4.jar:/usr
/local/src/opal-ws-2.0/lib/slf4j-api-1.5.2.jar:/usr/local/src/opal-ws-2.0/lib/slf4j-log4j12-1.5.2.jar:/usr/local/src/opal-ws-2.0/lib/xercesImpl.jar

I'm getting the error:

[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)

Malcolm


-- 
Malcolm Tobias
314.362.1594


------------------------------------------------------------------------------
_______________________________________________
Opaltoolkit-users mailing list
Opa...@li...
https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users