[MOBY-l] java.lang.OutOfMemoryError: PermGen space from getJpegFromAnnotatedImage
Edward Kawas
edward.kawas at gmail.com
Mon Jun 29 16:14:49 UTC 2009
Hi Stian,
A workflow that excluded the service 'getJpegFromAnnotatedImage', but
included a parser to extract the jpeg content would work nicely. I am having
problems running the workbench at the moment, so I make the change at the
moment, but I have included (attached) a similar workflow that could replace
the one on myExperiment.
Thanks,
Eddie
-----Original Message-----
From: moby-l-bounces at lists.open-bio.org
[mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Stian Soiland-Reyes
Sent: June-29-09 8:33 AM
To: moby-l at biomoby.org
Subject: [MOBY-l] java.lang.OutOfMemoryError: PermGen space from
getJpegFromAnnotatedImage
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.jav
a:1226)
at
org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:646)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenera
teTemplates(ProcessorTask.java:585)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocation
WithRetryLogic(ProcessorTask.java:524)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(P
rocessorTask.java:443)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingleIter
ation(ProcessorTask.java:962)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access$100(P
rocessorTask.java:95)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run(Proces
sorTask.java:835)
Caused by: java.lang.OutOfMemoryError: PermGen space; nested exception is:
java.lang.OutOfMemoryError: PermGen space
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:2
22)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:12
9)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationCo
ntext.java:1087)
at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown
Source)
at
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc
her.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(MustUnderstandChe
cker.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.runAndGenera
teTemplates(ProcessorTask.java:585)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocation
WithRetryLogic(ProcessorTask.java:524)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(P
rocessorTask.java:443)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingleIter
ation(ProcessorTask.java:962)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access$100(P
rocessorTask.java:95)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run(Proces
sorTask.java:835)
Caused by: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[ns1:hostname: null]
Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception
is:
java.lang.OutOfMemoryError: PermGen space
Fault code:
{http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
Fault actor: null
When calling:
http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage
===========
at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
at org.biomoby.client.CentralImpl.call(CentralImpl.java:1549)
at
org.biomoby.client.taverna.plugin.BiomobyTask.executeMobyService(BiomobyTask
.java:710)
at
org.biomoby.client.taverna.plugin.BiomobyTask.executeService(BiomobyTask.jav
a:1226)
at
org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:646)
... 6 more
Caused by: java.lang.OutOfMemoryError: PermGen space; nested exception is:
java.lang.OutOfMemoryError: PermGen space
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:2
22)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:12
9)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationCo
ntext.java:1087)
at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown
Source)
at
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc
her.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(MustUnderstandChe
cker.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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