[MOBY-l] java.lang.OutOfMemoryError: PermGen space from getJpegFromAnnotatedImage

Stian Soiland-Reyes soiland-reyes at cs.manchester.ac.uk
Mon Jun 29 15:32:39 UTC 2009 

Hi!

I am getting this exception from the BioMoby service:

http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage



As far as I understand this happens on server-side, I've tried
increasing the PermGen space in Taverna to be sure.

This happens with Taverna 1.7.1 and 2.1.x running the Fetch Dragon
Images workflow [2]

(I'm going through the example workflows[1]  before releasing Taverna
2.1b2 - we would very much have a BioMoby workflow included!)


[1] http://www.myexperiment.org/packs/14
[2] http://www.myexperiment.org/workflows/162


Do you know how to avoid this problem - or another similar workflow we
could put in instead?


ERROR 2009-06-29 16:24:24,682 java.lang.OutOfMemoryError: PermGen
space; nested exception is:
	java.lang.OutOfMemoryError: PermGen space
ERROR 2009-06-29 16:24:24,721 Error invoking biomoby service for
biomoby. A MobyException caught
org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[ns1:hostname: null]
Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is:
	java.lang.OutOfMemoryError: PermGen space
Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
Fault actor:  null
When calling:
	http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage
===========

	at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
	at org.biomoby.client.CentralImpl.call(CentralImpl.java:1549)
	at org.biomoby.client.taverna.plugin.BiomobyTask.executeMobyService(BiomobyTask.java:710)
	at org.biomoby.client.taverna.plugin.BiomobyTask.executeService(BiomobyTask.java:1226)
	at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:646)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:585)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:524)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:443)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingleIteration(ProcessorTask.java:962)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access$100(ProcessorTask.java:95)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run(ProcessorTask.java:835)
Caused by: java.lang.OutOfMemoryError: PermGen space; nested exception is:
	java.lang.OutOfMemoryError: PermGen space
	at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:222)
	at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:129)
	at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
	at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
	at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown
Source)
	at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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:375)
	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:435)
	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:2784)
	at org.apache.axis.client.Call.invoke(Call.java:2767)
	at org.apache.axis.client.Call.invoke(Call.java:2443)
	at org.apache.axis.client.Call.invoke(Call.java:2366)
	at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
	... 10 more
ERROR 2009-06-29 16:24:24,725 Task failed while iterating
Thread[Processor worker getJpegFromAnnotatedImage #0,6,main]
uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException:
Task failed due to problem invoking biomoby service.
===ERROR===
Fault details:
[ns1:hostname: null]
Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is:
	java.lang.OutOfMemoryError: PermGen space
Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
Fault actor:  null
When calling:
	http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage
===========

	at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:664)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:585)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:524)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:443)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingleIteration(ProcessorTask.java:962)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access$100(ProcessorTask.java:95)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run(ProcessorTask.java:835)
Caused by: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[ns1:hostname: null]
Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is:
	java.lang.OutOfMemoryError: PermGen space
Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
Fault actor:  null
When calling:
	http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage
===========

	at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
	at org.biomoby.client.CentralImpl.call(CentralImpl.java:1549)
	at org.biomoby.client.taverna.plugin.BiomobyTask.executeMobyService(BiomobyTask.java:710)
	at org.biomoby.client.taverna.plugin.BiomobyTask.executeService(BiomobyTask.java:1226)
	at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:646)
	... 6 more
Caused by: java.lang.OutOfMemoryError: PermGen space; nested exception is:
	java.lang.OutOfMemoryError: PermGen space
	at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:222)
	at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:129)
	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:375)
	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:435)
	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:2784)
	at org.apache.axis.client.Call.invoke(Call.java:2767)
	at org.apache.axis.client.Call.invoke(Call.java:2443)
	at org.apache.axis.client.Call.invoke(Call.java:2366)
	at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
	... 10 more


-- 
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester

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