[#TAV-480] Raven class loader problems - LinkageError / IllegalArgumentException - myGrid

Details

Type: Bug
Status: Resolved
Priority: Major
Resolution: Fixed
Affects Version/s: 1.5.1.6
Fix Version/s: after 2.0
Component/s: Raven
Labels:
None

Description

~~TAV-221~~ is remanifesting itself when running Taverna from the command line:

: stain@mira ~/Desktop;/Applications/Taverna.app/Contents/MacOS/executeworkflow.sh -input sequence sequence.txt -outputdoc blah.xml blast.xml 
java.lang.IllegalArgumentException: uk.ac.soton.itinnovation.taverna.enactor.entities
        at java.lang.ClassLoader.definePackage(ClassLoader.java:1418)
        at java.net.URLClassLoader.definePackage(URLClassLoader.java:325)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:242)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:168)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:221)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:174)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:221)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:174)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:144)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
        at java.lang.Class.getDeclaredConstructors0(Native Method)
        at java.lang.Class.privateGetDeclaredConstructors(Class.java:2328)
        at java.lang.Class.getConstructor0(Class.java:2640)
        at java.lang.Class.newInstance0(Class.java:321)
        at java.lang.Class.newInstance(Class.java:303)
        at org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor.<init>(LocalServiceProcessor.java:64)
        at org.embl.ebi.escience.scuflworkers.java.LocalServiceXMLHandler.loadProcessorFromXML(LocalServiceXMLHandler.java:63)
        at org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML(ProcessorHelper.java:322)
        at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.java:479)
Could not load workflow file:blast.xml: org.embl.ebi.escience.scufl.ProcessorCreationException: Unable to instantiate processor for local service class org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter

: stain@mira ~/Desktop;/Applications/Taverna.app/Contents/MacOS/executeworkflow.sh -input sequence sequence.txt blast.xml 
ERROR 2007-05-16 09:30:29,632 Error finding class uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException ACL=loader{uk.org.mygrid.taverna.scufl:scufl-model:1.5.1} from 10451601
java.lang.LinkageError: duplicate class definition: uk/ac/soton/itinnovation/taverna/enactor/entities/TaskExecutionException
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:168)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:221)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:174)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:221)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:174)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:221)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:174)
        at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:144)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
        at java.lang.Class.getDeclaredConstructors0(Native Method)
        at java.lang.Class.privateGetDeclaredConstructors(Class.java:2328)
        at java.lang.Class.getConstructor0(Class.java:2640)
        at java.lang.Class.newInstance0(Class.java:321)
        at java.lang.Class.newInstance(Class.java:303)
        at org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor.<init>(LocalServiceProcessor.java:88)
        at org.embl.ebi.escience.scuflworkers.java.LocalServiceXMLHandler.loadProcessorFromXML(LocalServiceXMLHandler.java:61)
        at org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML(ProcessorHelper.java:322)
        at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.java:479)
Exception in thread "Thread-14" java.lang.NoClassDefFoundError: uk/ac/soton/itinnovation/taverna/enactor/entities/TaskExecutionException
        at java.lang.Class.getDeclaredConstructors0(Native Method)
        at java.lang.Class.privateGetDeclaredConstructors(Class.java:2328)
        at java.lang.Class.getConstructor0(Class.java:2640)
        at java.lang.Class.newInstance0(Class.java:321)
        at java.lang.Class.newInstance(Class.java:303)
        at org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor.<init>(LocalServiceProcessor.java:88)
        at org.embl.ebi.escience.scuflworkers.java.LocalServiceXMLHandler.loadProcessorFromXML(LocalServiceXMLHandler.java:61)
        at org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML(ProcessorHelper.java:322)
        at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.java:479)
Could not load workflow file:blast.xml: org.embl.ebi.escience.scufl.ProcessorCreationException: The workflow processor 'checkStatusWorkflow' caused an exception :
Unable to locate processor with name 'Fail_if_false'
 during creation. The exception had type :
class org.embl.ebi.escience.scufl.UnknownProcessorException

Using attached blast.xml and sequence.txt (Note that the sequence.txt is not really a sequence, but anyway the service should fail at a deeper level, as evidenced by running this in the GUI instead) on a Macbook Pro.

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Attachments

blast.xml

2007-05-16 09:55

9 kB

Stian Soiland-Reyes
sequence.txt

2007-05-16 09:55

0.0 kB

Stian Soiland-Reyes

Issue Links

Depends

This issue has dependent:
~~T2-552~~ Sometimes default services do not load

Duplicate

This issue is duplicated by:
~~TAV-221~~ Raven ArtifactClassLoader.findClass(*) not syncronized

This issue related to:
TAV-773 Raven LinkageError: violates loader constraints
~~T2-276~~ Activity palette sometimes does not show all the loaded activities (i.e. there are some missing activities)

Activity

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Stian Soiland-Reyes added a comment - 2007-05-16 10:09

This might or might not occur, it seems to happen more easily with the launcher because it kick-loads the workflow's classes faster than if you are slow and waiting for the GUI to load - at least the classes load in a different order.

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Stian Soiland-Reyes added a comment - 2007-05-16 10:09 This might or might not occur, it seems to happen more easily with the launcher because it kick-loads the workflow's classes faster than if you are slow and waiting for the GUI to load - at least the classes load in a different order.

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June Finch added a comment - 2007-05-25 10:22

Stian,

Can you comment on whether this has been reported by any users (or just by us internally). I think it should be considered for the next release; but a lot of this depends on how easy it is to reproduce. I'm a bit confused by your last comment - I think you mean it is reproduced only some times - did you only see it once? June.

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June Finch added a comment - 2007-05-25 10:22 Stian, Can you comment on whether this has been reported by any users (or just by us internally). I think it should be considered for the next release; but a lot of this depends on how easy it is to reproduce. I'm a bit confused by your last comment - I think you mean it is reproduced only some times - did you only see it once? June.

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Stian Soiland-Reyes added a comment - 2007-08-08 12:19

Back-assigning to Tom (as T2 project lead) until they are prioritised up for actual implementation

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Stian Soiland-Reyes added a comment - 2007-08-08 12:19 Back-assigning to Tom (as T2 project lead) until they are prioritised up for actual implementation

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Stian Soiland-Reyes added a comment - 2008-03-20 15:12

I don't believe this is a problem anymore in 1.7

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Stian Soiland-Reyes added a comment - 2008-03-20 15:12 I don't believe this is a problem anymore in 1.7

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Stian Soiland-Reyes added a comment - 2008-04-14 11:57

Just reproduced this:

: stain@mira ~/Desktop;rm -rf blast.xml_output && /Applications/Taverna.app/Contents/MacOS/executeworkflow.sh blast.xml -input sequence sequence.txt 
ERROR 2008-04-14 11:55:03,863 Error finding class uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException ACL=loader{uk.org.mygrid.taverna.scufl:scufl-model:1.7.1.0} from 2145862
java.lang.LinkageError: duplicate class definition: uk/ac/soton/itinnovation/taverna/enactor/entities/TaskExecutionException
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:178)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:231)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:184)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:231)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:184)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:154)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
	at java.lang.Class.getDeclaredConstructors0(Native Method)
	at java.lang.Class.privateGetDeclaredConstructors(Class.java:2357)
	at java.lang.Class.getConstructor0(Class.java:2671)
	at java.lang.Class.newInstance0(Class.java:321)
	at java.lang.Class.newInstance(Class.java:303)
	at org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor.<init>(LocalServiceProcessor.java:64)
	at org.embl.ebi.escience.scuflworkers.java.LocalServiceXMLHandler.loadProcessorFromXML(LocalServiceXMLHandler.java:63)
	at org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML(ProcessorHelper.java:322)
	at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.java:480)
ERROR 2008-04-14 11:55:07,326 Failure while executing task Fail_if_false
uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException: Test matches, aborting downstream processors
	at org.embl.ebi.escience.scuflworkers.java.FailIfTrue.execute(FailIfTrue.java:51)
	at org.embl.ebi.escience.scuflworkers.java.LocalServiceTask.execute(LocalServiceTask.java:31)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280)
	at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
ERROR 2008-04-14 11:55:38,459 Failure while executing task Fail_if_false
uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException: Test matches, aborting downstream processors
	at org.embl.ebi.escience.scuflworkers.java.FailIfTrue.execute(FailIfTrue.java:51)
	at org.embl.ebi.escience.scuflworkers.java.LocalServiceTask.execute(LocalServiceTask.java:31)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280)
	at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)

Using sequence.txt:

MKFLVLLFNILCLFPILGAD

Show

Stian Soiland-Reyes added a comment - 2008-04-14 11:57 Just reproduced this:

: stain@mira ~/Desktop;rm -rf blast.xml_output && /Applications/Taverna.app/Contents/MacOS/executeworkflow.sh blast.xml -input sequence sequence.txt 
ERROR 2008-04-14 11:55:03,863 Error finding class uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException ACL=loader{uk.org.mygrid.taverna.scufl:scufl-model:1.7.1.0} from 2145862
java.lang.LinkageError: duplicate class definition: uk/ac/soton/itinnovation/taverna/enactor/entities/TaskExecutionException
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:178)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:231)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:184)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:231)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:184)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:154)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
	at java.lang.Class.getDeclaredConstructors0(Native Method)
	at java.lang.Class.privateGetDeclaredConstructors(Class.java:2357)
	at java.lang.Class.getConstructor0(Class.java:2671)
	at java.lang.Class.newInstance0(Class.java:321)
	at java.lang.Class.newInstance(Class.java:303)
	at org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor.<init>(LocalServiceProcessor.java:64)
	at org.embl.ebi.escience.scuflworkers.java.LocalServiceXMLHandler.loadProcessorFromXML(LocalServiceXMLHandler.java:63)
	at org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML(ProcessorHelper.java:322)
	at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.java:480)
ERROR 2008-04-14 11:55:07,326 Failure while executing task Fail_if_false
uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException: Test matches, aborting downstream processors
	at org.embl.ebi.escience.scuflworkers.java.FailIfTrue.execute(FailIfTrue.java:51)
	at org.embl.ebi.escience.scuflworkers.java.LocalServiceTask.execute(LocalServiceTask.java:31)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280)
	at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
ERROR 2008-04-14 11:55:38,459 Failure while executing task Fail_if_false
uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException: Test matches, aborting downstream processors
	at org.embl.ebi.escience.scuflworkers.java.FailIfTrue.execute(FailIfTrue.java:51)
	at org.embl.ebi.escience.scuflworkers.java.LocalServiceTask.execute(LocalServiceTask.java:31)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353)
	at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280)
	at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)

Using sequence.txt:

MKFLVLLFNILCLFPILGAD

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Stian Soiland-Reyes added a comment - 2008-07-17 11:46

Probably fixed in latest 1.7-SNAPSHOT of Raven, it avoids multiple calls to findClass by using a lock from the map findClassLocks - also it will do this bit in the end:

synchronized (classMap) {
			if (!classMap.containsKey(name)) {
				classMap.put(name, loadedClass);
			} else {
				Class otherClass = classMap.get(name);
				if (otherClass != loadedClass) {
					logger.error("Duplicate class loading of " + otherClass);
					logger.error("Returning cached " + otherClass
							+ " instead of loaded " + loadedClass);
					loadedClass = otherClass;
				}
			}
		}

Show

Stian Soiland-Reyes added a comment - 2008-07-17 11:46 Probably fixed in latest 1.7-SNAPSHOT of Raven, it avoids multiple calls to findClass by using a lock from the map findClassLocks - also it will do this bit in the end:

synchronized (classMap) {
			if (!classMap.containsKey(name)) {
				classMap.put(name, loadedClass);
			} else {
				Class otherClass = classMap.get(name);
				if (otherClass != loadedClass) {
					logger.error("Duplicate class loading of " + otherClass);
					logger.error("Returning cached " + otherClass
							+ " instead of loaded " + loadedClass);
					loadedClass = otherClass;
				}
			}
		}

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Stian Soiland-Reyes added a comment - 2008-09-12 14:21

It happened again:

java.lang.LinkageError: duplicate class definition: net/sf/taverna/t2/partition/AbstractActivityItem
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:310)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:229)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:317)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:270)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:310)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:270)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
	at net.sf.taverna.t2.activities.beanshell.query.BeanshellQuery.doQuery(BeanshellQuery.java:33)
	at net.sf.taverna.t2.workbench.ui.activitypalette.ActivityTree$2.run(ActivityTree.java:135)

Show

Stian Soiland-Reyes added a comment - 2008-09-12 14:21 It happened again:

java.lang.LinkageError: duplicate class definition: net/sf/taverna/t2/partition/AbstractActivityItem
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:310)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:229)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:317)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:270)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:310)
	at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:270)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
	at net.sf.taverna.t2.activities.beanshell.query.BeanshellQuery.doQuery(BeanshellQuery.java:33)
	at net.sf.taverna.t2.workbench.ui.activitypalette.ActivityTree$2.run(ActivityTree.java:135)

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Permalink

Stian Soiland-Reyes added a comment - 2009-05-11 21:11

I think I got a deadlock on this old bug today:

Notice the last line from Java:

Found 1 deadlock.

: stain@mira ~/Downloads/taverna-2.1-beta-1;sh run.sh
WARN 2009-05-11 21:03:14,995 (org.hibernate.util.JDBCExceptionReporter:54) - SQL Warning: 10000, SQLState: 01J01
WARN 2009-05-11 21:03:14,998 (org.hibernate.util.JDBCExceptionReporter:55) - Database '/tmp/t2platform-29772.db/database' not created, connection made to existing database instead.
WARN 2009-05-11 21:03:16,454 (net.sf.taverna.raven.plugins.PluginManager:85) - HTTP status 404 while getting plugins http://www.mygrid.org.uk/taverna/updates/2.1-SNAPSHOT/plugins/pluginlist.xml

^\Full thread dump Java HotSpot(TM) Client VM (1.5.0_16-133 mixed mode, sharing):

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a5690 nid=0x49008c00 in Object.wait() [0xb3386000..0xb3386d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c80068> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a53a0 nid=0x49007e00 in Object.wait() [0xb3305000..0xb3305d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c800e0> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a4ec0 nid=0x4900c800 in Object.wait() [0xb2df8000..0xb2df8d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c80158> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a4b90 nid=0x4900ba00 in Object.wait() [0xb2d77000..0xb2d77d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c801d0> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a4570 nid=0x4900ac00 in Object.wait() [0xb2cf6000..0xb2cf6d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c80248> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a3c20 nid=0x49009e00 in Object.wait() [0xb2c75000..0xb2c75d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c802c0> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a3170 nid=0xf94a00 in Object.wait() [0xb2bf4000..0xb2bf4d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a35ecc8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a2b30 nid=0xf93c00 in Object.wait() [0xb2b73000..0xb2b73d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a35ed40> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a2540 nid=0x49007000 in Object.wait() [0xb2af2000..0xb2af2d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3594f8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a21b0 nid=0x49006200 in Object.wait() [0xb2a71000..0xb2a71d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a356108> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a1d10 nid=0x49005400 in Object.wait() [0xb29f0000..0xb29f0d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a351bb8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a19d0 nid=0x49004600 in Object.wait() [0xb296f000..0xb296fd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a350b70> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a1360 nid=0x49003800 in Object.wait() [0xb28ee000..0xb28eed90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a34ad38> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a0f90 nid=0x49002a00 in Object.wait() [0xb286d000..0xb286dd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a33f760> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a0ae0 nid=0x49001c00 in Object.wait() [0xb27ec000..0xb27ecd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a33f7d8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a0740 nid=0x49000e00 in Object.wait() [0xb276b000..0xb276bd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a33f850> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a00e0 nid=0x49000000 in Object.wait() [0xb26ea000..0xb26ead90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a338b78> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109fd20 nid=0xf9c000 in Object.wait() [0xb2669000..0xb2669d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a337e40> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109f850 nid=0xf9b200 in Object.wait() [0xb25e8000..0xb25e8d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a331350> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109f4c0 nid=0xf9a400 in Object.wait() [0xb2567000..0xb2567d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3313c8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109eeb0 nid=0xf99600 in Object.wait() [0xb2465000..0xb2465d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a32b018> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109eaa0 nid=0xf98800 in Object.wait() [0xb23e4000..0xb23e4d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a32b090> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109e3f0 nid=0xf97a00 in Object.wait() [0xb2363000..0xb2363d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a325f38> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109dfb0 nid=0xf96c00 in Object.wait() [0xb22e2000..0xb22e2d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a325fb0> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109d930 nid=0xf27a00 in Object.wait() [0xb2261000..0xb2261d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a31ddd0> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109d500 nid=0xf26c00 in Object.wait() [0xb21e0000..0xb21e0d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3169a8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109cdc0 nid=0xf25e00 in Object.wait() [0xb215f000..0xb215fd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a313500> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109cc40 nid=0xf25000 in Object.wait() [0xb20de000..0xb20ded90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a304fd8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109c550 nid=0xf24200 in Object.wait() [0xb205d000..0xb205dd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a305050> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109c2d0 nid=0xf23400 in Object.wait() [0xb1fdc000..0xb1fdcd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3050c8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109ba60 nid=0xf22600 in Object.wait() [0xb1f5b000..0xb1f5bd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a305140> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109b810 nid=0xf21800 in Object.wait() [0xb1eda000..0xb1edad90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3051b8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109b4c0 nid=0xf20a00 in Object.wait() [0xb1e59000..0xb1e59d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2fcd18> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109b1e0 nid=0xf1fc00 in Object.wait() [0xb1dd8000..0xb1dd8d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2fbfe0> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109ad80 nid=0xf30a00 in Object.wait() [0xb1d57000..0xb1d57d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2f5488> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109aa50 nid=0xf2fc00 in Object.wait() [0xb1cd6000..0xb1cd6d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2f4750> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109a220 nid=0xf92e00 in Object.wait() [0xb1c55000..0xb1c55d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2e94f8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x01099f80 nid=0xf92000 in Object.wait() [0xb1bd4000..0xb1bd4d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2e7df8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x01099ae0 nid=0xf32a00 in Object.wait() [0xb1b53000..0xb1b53d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2e4418> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010993e0 nid=0xf31c00 in Object.wait() [0xb18ce000..0xb18ced90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2e2f10> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Timer-5" daemon prio=6 tid=0x01098ee0 nid=0xf2aa00 in Object.wait() [0xb184d000..0xb184dd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2dcc48> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x01098bb0 nid=0xf29c00 in Object.wait() [0xb16ca000..0xb16cad90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2da608> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x01098650 nid=0xefa600 in Object.wait() [0xb13c4000..0xb13c4d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2be2e0> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Opening dataflow(s) [/Users/stain/Desktop/wei.t2flow]" prio=6 tid=0x01097fd0 nid=0xf28e00 waiting for monitor entry [0xb0db0000..0xb0db0d90]
at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity.parseWSDL(WSDLActivity.java:189)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity.configure(WSDLActivity.java:96)
at net.sf.taverna.t2.activities.wsdl.WSDLActivity.configure(WSDLActivity.java:62)
at net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer.deserializeActivity(ActivityXMLDeserializer.java:82)
at net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer.deserializeActivity(ActivityXMLDeserializer.java:110)
at net.sf.taverna.t2.workflowmodel.serialization.xml.ProcessorXMLDeserializer.deserializeProcessor(ProcessorXMLDeserializer.java:55)
at net.sf.taverna.t2.workflowmodel.serialization.xml.DataflowXMLDeserializer.deserializeDataflow(DataflowXMLDeserializer.java:66)
at net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializerImpl.deserializeDataflow(XMLDeserializerImpl.java:56)
at net.sf.taverna.t2.workbench.file.impl.T2DataflowOpener.openDataflowStream(T2DataflowOpener.java:136)
at net.sf.taverna.t2.workbench.file.impl.T2DataflowOpener.openDataflow(T2DataflowOpener.java:101)
at net.sf.taverna.t2.workbench.file.impl.FileManagerImpl.openDataflow(FileManagerImpl.java:327)
at net.sf.taverna.t2.workbench.file.impl.actions.OpenWorkflowAction.openWorkflows(OpenWorkflowAction.java:154)
at net.sf.taverna.t2.workbench.file.impl.actions.OpenWorkflowAction$FileOpenerThread.run(OpenWorkflowAction.java:348)

"Timer-4" daemon prio=6 tid=0x01089610 nid=0x8b3a00 in Object.wait() [0xb1ad2000..0xb1ad2d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x19b12740> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"RunnableQueue-0" daemon prio=6 tid=0x01082750 nid=0xf17000 in Object.wait() [0xb1a51000..0xb1a51d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at org.apache.batik.util.RunnableQueue.run(RunnableQueue.java:222)

locked <0x19b17ea8> (a org.apache.batik.util.DoublyLinkedList)
at java.lang.Thread.run(Thread.java:613)

"Batik CleanerThread" daemon prio=1 tid=0x010821c0 nid=0xee3600 in Object.wait() [0xb12c2000..0xb12c2d90]
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:120)

locked <0x19b12848> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:136)
at org.apache.batik.util.CleanerThread.run(CleanerThread.java:106)

"DestroyJavaVM" prio=5 tid=0x010015e0 nid=0xb0801000 waiting on condition [0x00000000..0xb0800060]

"Timer-3" daemon prio=6 tid=0x01077710 nid=0x8b2c00 in Object.wait() [0xb1547000..0xb1547d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x19959b78> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Timer-2" daemon prio=6 tid=0x0106ff20 nid=0xfe2000 in Object.wait() [0xb1343000..0xb1343d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x198dd2b8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"GraphAutoScrollTimer" daemon prio=6 tid=0x0106e350 nid=0xff2e00 in Object.wait() [0xb0f33000..0xb0f33d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x198c2200> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Find service descriptions from Biomoby service http://moby.ucalgary.ca/moby/MOBY-Central.pl" prio=1 tid=0x0106a3d0 nid=0xfc4a00 waiting for monitor entry [0xb17cb000..0xb17ccd90]
at java.lang.ClassLoader.checkCerts(ClassLoader.java:806)

waiting to lock <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.preDefineClass(ClassLoader.java:542)
at java.lang.ClassLoader.defineClass(ClassLoader.java:669)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:326)
locked <0x1987ab40> (a java.lang.Object)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:229)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:333)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
locked <0x18e0aaf0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
locked <0x18e0aaf0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.<init>(BiomobyQueryHelper.java:78)
at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:49)
at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)

"Find service descriptions from WSDL service http://www.ebi.ac.uk/ws/services/urn:Dbfetch?wsdl" prio=1 tid=0x01069b20 nid=0xfc9400 waiting for monitor entry [0xb1649000..0xb1649d90]
at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144)
at net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider.findServiceDescriptionsAsync(WSDLServiceProvider.java:63)
at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)

"Find service descriptions from Soaplab service http://www.ebi.ac.uk/soaplab/services/" prio=1 tid=0x010697d0 nid=0xfc8600 waiting for monitor entry [0xb15c7000..0xb15c8d90]
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:325)

waiting to lock <0x1987ab40> (a java.lang.Object)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
locked <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
locked <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at org.apache.axis.client.Service.getAxisClient(Service.java:104)
at org.apache.axis.client.Service.<init>(Service.java:113)
at net.sf.taverna.t2.activities.soaplab.query.Soap.callWebService(Soap.java:75)
at net.sf.taverna.t2.activities.soaplab.query.Soap.callWebService(Soap.java:49)
at net.sf.taverna.t2.activities.soaplab.query.SoaplabScavengerAgent.loadCategories(SoaplabScavengerAgent.java:99)
at net.sf.taverna.t2.activities.soaplab.query.SoaplabScavengerAgent.load(SoaplabScavengerAgent.java:79)
at net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider.findSoaplabServices(SoaplabServiceProvider.java:141)
at net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider.findServiceDescriptionsAsync(SoaplabServiceProvider.java:43)
at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)

"Find service descriptions from WSDL service http://soap.genome.jp/KEGG.wsdl" prio=1 tid=0x01068f70 nid=0xfc5c00 waiting for monitor entry [0xb1445000..0xb1445d90]
at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144)
at net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider.findServiceDescriptionsAsync(WSDLServiceProvider.java:63)
at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)

"Clear status line" prio=6 tid=0x01067b60 nid=0xfb7e00 in Object.wait() [0xb1241000..0xb1241d90]
at java.lang.Object.wait(Native Method)

waiting on <0x19847480> (a java.util.TaskQueue)
at java.util.TimerThread.mainLoop(Timer.java:509)
locked <0x19847480> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"Timer-1" prio=6 tid=0x01067770 nid=0xfb7000 in Object.wait() [0xb11c0000..0xb11c0d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x19847528> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"derby.rawStoreDaemon" daemon prio=6 tid=0x01054fd0 nid=0xf38000 in Object.wait() [0xb10be000..0xb10bed90]
at java.lang.Object.wait(Native Method)

waiting on <0x194972e8> (a org.apache.derby.impl.services.daemon.BasicDaemon)
at org.apache.derby.impl.services.daemon.BasicDaemon.rest(Unknown Source)
locked <0x194972e8> (a org.apache.derby.impl.services.daemon.BasicDaemon)
at org.apache.derby.impl.services.daemon.BasicDaemon.run(Unknown Source)
at java.lang.Thread.run(Thread.java:613)

"Timer-0" daemon prio=6 tid=0x01054680 nid=0xb99e00 in Object.wait() [0xb103d000..0xb103dd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x19487840> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)

"derby.antiGC" daemon prio=1 tid=0x01053c80 nid=0xb99000 in Object.wait() [0xb0fbc000..0xb0fbcd90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at org.apache.derby.impl.services.monitor.AntiGC.run(Unknown Source)

locked <0x19472998> (a org.apache.derby.impl.services.monitor.AntiGC)
at java.lang.Thread.run(Thread.java:613)

"TimerQueue" daemon prio=5 tid=0x01015800 nid=0x831000 in Object.wait() [0xb0eb2000..0xb0eb2d90]
at java.lang.Object.wait(Native Method)

waiting on <0x1822cdf0> (a javax.swing.TimerQueue)
at javax.swing.TimerQueue.run(TimerQueue.java:236)
locked <0x1822cdf0> (a javax.swing.TimerQueue)
at java.lang.Thread.run(Thread.java:613)

"AWT-EventQueue-0" prio=6 tid=0x01012270 nid=0x823000 in Object.wait() [0xb0e31000..0xb0e31d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.awt.EventQueue.getNextEvent(EventQueue.java:345)

locked <0x180ed320> (a java.awt.EventQueue)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:216)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

"Java2D Disposer" daemon prio=10 tid=0x01010030 nid=0x92ac00 in Object.wait() [0xb0d14000..0xb0d14d90]
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:120)

locked <0x180e25e8> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:136)
at sun.java2d.Disposer.run(Disposer.java:125)
at java.lang.Thread.run(Thread.java:613)

"AWT-Shutdown" prio=5 tid=0x0100f260 nid=0x8f9000 in Object.wait() [0xb0c8a000..0xb0c8ad90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:259)

locked <0x180e2678> (a java.lang.Object)
at java.lang.Thread.run(Thread.java:613)

"AWT-AppKit" daemon prio=5 tid=0x0100edf0 nid=0xa06a9720 runnable [0x00000000..0xbfffe928]

"Low Memory Detector" daemon prio=5 tid=0x010095a0 nid=0x84e800 runnable [0x00000000..0x00000000]

"CompilerThread0" daemon prio=9 tid=0x01008b90 nid=0x84a200 waiting on condition [0x00000000..0xb0b077d8]

"Signal Dispatcher" daemon prio=9 tid=0x01008640 nid=0x849400 waiting on condition [0x00000000..0x00000000]

"Finalizer" daemon prio=8 tid=0x01007ae0 nid=0x815800 in Object.wait() [0xb0a05000..0xb0a05d90]
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:120)

locked <0x180a9398> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:136)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=10 tid=0x01007720 nid=0x814000 in Object.wait() [0xb0984000..0xb0984d90]
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:474)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)

locked <0x180a9420> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=9 tid=0x01006e70 nid=0x80b800 runnable

"VM Periodic Task Thread" prio=9 tid=0x0100a180 nid=0x84f600 waiting on condition

"Exception Catcher Thread" prio=10 tid=0x01001830 nid=0x809800 runnable

Found one Java-level deadlock:
=============================
"Find service descriptions from Soaplab service http://www.ebi.ac.uk/soaplab/services/":
waiting to lock monitor 0x0081511c (object 0x1987ab40, a java.lang.Object),
which is held by "Find service descriptions from Biomoby service http://moby.ucalgary.ca/moby/MOBY-Central.pl"
"Find service descriptions from Biomoby service http://moby.ucalgary.ca/moby/MOBY-Central.pl":
waiting to lock monitor 0x008150d4 (object 0x18d152b0, a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader),
which is held by "Find service descriptions from Soaplab service http://www.ebi.ac.uk/soaplab/services/"

Java stack information for the threads listed above:
===================================================
"Find service descriptions from Soaplab service http://www.ebi.ac.uk/soaplab/services/":
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:325)

waiting to lock <0x1987ab40> (a java.lang.Object)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
locked <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
locked <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at org.apache.axis.client.Service.getAxisClient(Service.java:104)
at org.apache.axis.client.Service.<init>(Service.java:113)
at net.sf.taverna.t2.activities.soaplab.query.Soap.callWebService(Soap.java:75)
at net.sf.taverna.t2.activities.soaplab.query.Soap.callWebService(Soap.java:49)
at net.sf.taverna.t2.activities.soaplab.query.SoaplabScavengerAgent.loadCategories(SoaplabScavengerAgent.java:99)
at net.sf.taverna.t2.activities.soaplab.query.SoaplabScavengerAgent.load(SoaplabScavengerAgent.java:79)
at net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider.findSoaplabServices(SoaplabServiceProvider.java:141)
at net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider.findServiceDescriptionsAsync(SoaplabServiceProvider.java:43)
at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)
"Find service descriptions from Biomoby service http://moby.ucalgary.ca/moby/MOBY-Central.pl":
at java.lang.ClassLoader.checkCerts(ClassLoader.java:806)
waiting to lock <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.preDefineClass(ClassLoader.java:542)
at java.lang.ClassLoader.defineClass(ClassLoader.java:669)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:326)
locked <0x1987ab40> (a java.lang.Object)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:229)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:333)
at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
locked <0x18e0aaf0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
locked <0x18e0aaf0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.<init>(BiomobyQueryHelper.java:78)
at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:49)
at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)

Found 1 deadlock.

Show

Stian Soiland-Reyes added a comment - 2009-05-11 21:11 I think I got a deadlock on this old bug today: Notice the last line from Java: Found 1 deadlock. : stain@mira ~/Downloads/taverna-2.1-beta-1;sh run.sh WARN 2009-05-11 21:03:14,995 (org.hibernate.util.JDBCExceptionReporter:54) - SQL Warning: 10000, SQLState: 01J01 WARN 2009-05-11 21:03:14,998 (org.hibernate.util.JDBCExceptionReporter:55) - Database '/tmp/t2platform-29772.db/database' not created, connection made to existing database instead. WARN 2009-05-11 21:03:16,454 (net.sf.taverna.raven.plugins.PluginManager:85) - HTTP status 404 while getting plugins http://www.mygrid.org.uk/taverna/updates/2.1-SNAPSHOT/plugins/pluginlist.xml ^\Full thread dump Java HotSpot(TM) Client VM (1.5.0_16-133 mixed mode, sharing): "ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a5690 nid=0x49008c00 in Object.wait() [0xb3386000..0xb3386d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c80068> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a53a0 nid=0x49007e00 in Object.wait() [0xb3305000..0xb3305d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c800e0> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a4ec0 nid=0x4900c800 in Object.wait() [0xb2df8000..0xb2df8d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c80158> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a4b90 nid=0x4900ba00 in Object.wait() [0xb2d77000..0xb2d77d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c801d0> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a4570 nid=0x4900ac00 in Object.wait() [0xb2cf6000..0xb2cf6d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c80248> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a3c20 nid=0x49009e00 in Object.wait() [0xb2c75000..0xb2c75d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x16c802c0> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a3170 nid=0xf94a00 in Object.wait() [0xb2bf4000..0xb2bf4d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a35ecc8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a2b30 nid=0xf93c00 in Object.wait() [0xb2b73000..0xb2b73d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a35ed40> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a2540 nid=0x49007000 in Object.wait() [0xb2af2000..0xb2af2d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3594f8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a21b0 nid=0x49006200 in Object.wait() [0xb2a71000..0xb2a71d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a356108> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a1d10 nid=0x49005400 in Object.wait() [0xb29f0000..0xb29f0d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a351bb8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a19d0 nid=0x49004600 in Object.wait() [0xb296f000..0xb296fd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a350b70> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a1360 nid=0x49003800 in Object.wait() [0xb28ee000..0xb28eed90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a34ad38> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a0f90 nid=0x49002a00 in Object.wait() [0xb286d000..0xb286dd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a33f760> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a0ae0 nid=0x49001c00 in Object.wait() [0xb27ec000..0xb27ecd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a33f7d8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010a0740 nid=0x49000e00 in Object.wait() [0xb276b000..0xb276bd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a33f850> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x010a00e0 nid=0x49000000 in Object.wait() [0xb26ea000..0xb26ead90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a338b78> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109fd20 nid=0xf9c000 in Object.wait() [0xb2669000..0xb2669d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a337e40> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109f850 nid=0xf9b200 in Object.wait() [0xb25e8000..0xb25e8d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a331350> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109f4c0 nid=0xf9a400 in Object.wait() [0xb2567000..0xb2567d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3313c8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109eeb0 nid=0xf99600 in Object.wait() [0xb2465000..0xb2465d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a32b018> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109eaa0 nid=0xf98800 in Object.wait() [0xb23e4000..0xb23e4d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a32b090> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109e3f0 nid=0xf97a00 in Object.wait() [0xb2363000..0xb2363d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a325f38> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109dfb0 nid=0xf96c00 in Object.wait() [0xb22e2000..0xb22e2d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a325fb0> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109d930 nid=0xf27a00 in Object.wait() [0xb2261000..0xb2261d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a31ddd0> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109d500 nid=0xf26c00 in Object.wait() [0xb21e0000..0xb21e0d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3169a8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109cdc0 nid=0xf25e00 in Object.wait() [0xb215f000..0xb215fd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a313500> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109cc40 nid=0xf25000 in Object.wait() [0xb20de000..0xb20ded90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a304fd8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109c550 nid=0xf24200 in Object.wait() [0xb205d000..0xb205dd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a305050> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109c2d0 nid=0xf23400 in Object.wait() [0xb1fdc000..0xb1fdcd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3050c8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109ba60 nid=0xf22600 in Object.wait() [0xb1f5b000..0xb1f5bd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a305140> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109b810 nid=0xf21800 in Object.wait() [0xb1eda000..0xb1edad90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a3051b8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109b4c0 nid=0xf20a00 in Object.wait() [0xb1e59000..0xb1e59d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2fcd18> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109b1e0 nid=0xf1fc00 in Object.wait() [0xb1dd8000..0xb1dd8d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2fbfe0> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109ad80 nid=0xf30a00 in Object.wait() [0xb1d57000..0xb1d57d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2f5488> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x0109aa50 nid=0xf2fc00 in Object.wait() [0xb1cd6000..0xb1cd6d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2f4750> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x0109a220 nid=0xf92e00 in Object.wait() [0xb1c55000..0xb1c55d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2e94f8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x01099f80 nid=0xf92000 in Object.wait() [0xb1bd4000..0xb1bd4d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2e7df8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x01099ae0 nid=0xf32a00 in Object.wait() [0xb1b53000..0xb1b53d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2e4418> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x010993e0 nid=0xf31c00 in Object.wait() [0xb18ce000..0xb18ced90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2e2f10> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Timer-5" daemon prio=6 tid=0x01098ee0 nid=0xf2aa00 in Object.wait() [0xb184d000..0xb184dd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2dcc48> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"ErrorBounce layer state cleanup" daemon prio=6 tid=0x01098bb0 nid=0xf29c00 in Object.wait() [0xb16ca000..0xb16cad90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2da608> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Parallelize layer state cleanup" daemon prio=6 tid=0x01098650 nid=0xefa600 in Object.wait() [0xb13c4000..0xb13c4d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x1a2be2e0> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Opening dataflow(s) [/Users/stain/Desktop/wei.t2flow]" prio=6 tid=0x01097fd0 nid=0xf28e00 waiting for monitor entry [0xb0db0000..0xb0db0d90] at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144) at net.sf.taverna.t2.activities.wsdl.WSDLActivity.parseWSDL(WSDLActivity.java:189) at net.sf.taverna.t2.activities.wsdl.WSDLActivity.configure(WSDLActivity.java:96) at net.sf.taverna.t2.activities.wsdl.WSDLActivity.configure(WSDLActivity.java:62) at net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer.deserializeActivity(ActivityXMLDeserializer.java:82) at net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer.deserializeActivity(ActivityXMLDeserializer.java:110) at net.sf.taverna.t2.workflowmodel.serialization.xml.ProcessorXMLDeserializer.deserializeProcessor(ProcessorXMLDeserializer.java:55) at net.sf.taverna.t2.workflowmodel.serialization.xml.DataflowXMLDeserializer.deserializeDataflow(DataflowXMLDeserializer.java:66) at net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializerImpl.deserializeDataflow(XMLDeserializerImpl.java:56) at net.sf.taverna.t2.workbench.file.impl.T2DataflowOpener.openDataflowStream(T2DataflowOpener.java:136) at net.sf.taverna.t2.workbench.file.impl.T2DataflowOpener.openDataflow(T2DataflowOpener.java:101) at net.sf.taverna.t2.workbench.file.impl.FileManagerImpl.openDataflow(FileManagerImpl.java:327) at net.sf.taverna.t2.workbench.file.impl.actions.OpenWorkflowAction.openWorkflows(OpenWorkflowAction.java:154) at net.sf.taverna.t2.workbench.file.impl.actions.OpenWorkflowAction$FileOpenerThread.run(OpenWorkflowAction.java:348) "Timer-4" daemon prio=6 tid=0x01089610 nid=0x8b3a00 in Object.wait() [0xb1ad2000..0xb1ad2d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x19b12740> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"RunnableQueue-0" daemon prio=6 tid=0x01082750 nid=0xf17000 in Object.wait() [0xb1a51000..0xb1a51d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at org.apache.batik.util.RunnableQueue.run(RunnableQueue.java:222)

locked <0x19b17ea8> (a org.apache.batik.util.DoublyLinkedList) at java.lang.Thread.run(Thread.java:613)

"Batik CleanerThread" daemon prio=1 tid=0x010821c0 nid=0xee3600 in Object.wait() [0xb12c2000..0xb12c2d90] at java.lang.Object.wait(Native Method) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:120)

locked <0x19b12848> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:136) at org.apache.batik.util.CleanerThread.run(CleanerThread.java:106)

"pool-2-thread-1" prio=5 tid=0x01087d80 nid=0xf1ee00 waiting on condition [0xb19d0000..0xb19d0d90] at sun.misc.Unsafe.park(Native Method) at java.util.concurrent.locks.LockSupport.park(LockSupport.java:118) at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1841) at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:359) at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:470) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:674) at java.lang.Thread.run(Thread.java:613) "DestroyJavaVM" prio=5 tid=0x010015e0 nid=0xb0801000 waiting on condition [0x00000000..0xb0800060] "Timer-3" daemon prio=6 tid=0x01077710 nid=0x8b2c00 in Object.wait() [0xb1547000..0xb1547d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x19959b78> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Timer-2" daemon prio=6 tid=0x0106ff20 nid=0xfe2000 in Object.wait() [0xb1343000..0xb1343d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x198dd2b8> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"GraphAutoScrollTimer" daemon prio=6 tid=0x0106e350 nid=0xff2e00 in Object.wait() [0xb0f33000..0xb0f33d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x198c2200> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Find service descriptions from WSDL service http://soap.bind.ca/wsdl/bind.wsdl" prio=1 tid=0x0106acc0 nid=0xfcbe00 waiting for monitor entry [0xb194f000..0xb194fd90] at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144) at net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider.findServiceDescriptionsAsync(WSDLServiceProvider.java:63) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480) "Find service descriptions from Biomoby service http://moby.ucalgary.ca/moby/MOBY-Central.pl" prio=1 tid=0x0106a3d0 nid=0xfc4a00 waiting for monitor entry [0xb17cb000..0xb17ccd90] at java.lang.ClassLoader.checkCerts(ClassLoader.java:806)

waiting to lock <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at java.lang.ClassLoader.preDefineClass(ClassLoader.java:542) at java.lang.ClassLoader.defineClass(ClassLoader.java:669) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124) at java.net.URLClassLoader.defineClass(URLClassLoader.java:260) at java.net.URLClassLoader.access$100(URLClassLoader.java:56) at java.net.URLClassLoader$1.run(URLClassLoader.java:195) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:326)
locked <0x1987ab40> (a java.lang.Object) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:229) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:333) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276) at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
locked <0x18e0aaf0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
locked <0x18e0aaf0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.<init>(BiomobyQueryHelper.java:78) at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:49) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)

"Find service descriptions from WSDL service http://www.ebi.ac.uk/xembl/XEMBL.wsdl" prio=1 tid=0x0106a0e0 nid=0xfc3c00 waiting for monitor entry [0xb174b000..0xb174bd90] at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144) at net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider.findServiceDescriptionsAsync(WSDLServiceProvider.java:63) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480) "Find service descriptions from WSDL service http://www.ebi.ac.uk/ws/services/urn:Dbfetch?wsdl" prio=1 tid=0x01069b20 nid=0xfc9400 waiting for monitor entry [0xb1649000..0xb1649d90] at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144) at net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider.findServiceDescriptionsAsync(WSDLServiceProvider.java:63) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480) "Find service descriptions from Soaplab service http://www.ebi.ac.uk/soaplab/services/" prio=1 tid=0x010697d0 nid=0xfc8600 waiting for monitor entry [0xb15c7000..0xb15c8d90] at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:325)

waiting to lock <0x1987ab40> (a java.lang.Object) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276) at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
locked <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
locked <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at org.apache.axis.client.Service.getAxisClient(Service.java:104) at org.apache.axis.client.Service.<init>(Service.java:113) at net.sf.taverna.t2.activities.soaplab.query.Soap.callWebService(Soap.java:75) at net.sf.taverna.t2.activities.soaplab.query.Soap.callWebService(Soap.java:49) at net.sf.taverna.t2.activities.soaplab.query.SoaplabScavengerAgent.loadCategories(SoaplabScavengerAgent.java:99) at net.sf.taverna.t2.activities.soaplab.query.SoaplabScavengerAgent.load(SoaplabScavengerAgent.java:79) at net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider.findSoaplabServices(SoaplabServiceProvider.java:141) at net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider.findServiceDescriptionsAsync(SoaplabServiceProvider.java:43) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)

"Find service descriptions from WSDL service http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl" prio=1 tid=0x01069240 nid=0xfc6a00 waiting for monitor entry [0xb14c6000..0xb14c6d90] at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144) at net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider.findServiceDescriptionsAsync(WSDLServiceProvider.java:63) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480) "Find service descriptions from WSDL service http://soap.genome.jp/KEGG.wsdl" prio=1 tid=0x01068f70 nid=0xfc5c00 waiting for monitor entry [0xb1445000..0xb1445d90] at net.sf.taverna.wsdl.parser.WSDLParser.<init>(WSDLParser.java:144) at net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProvider.findServiceDescriptionsAsync(WSDLServiceProvider.java:63) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480) "Clear status line" prio=6 tid=0x01067b60 nid=0xfb7e00 in Object.wait() [0xb1241000..0xb1241d90] at java.lang.Object.wait(Native Method)

waiting on <0x19847480> (a java.util.TaskQueue) at java.util.TimerThread.mainLoop(Timer.java:509)
locked <0x19847480> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Timer-1" prio=6 tid=0x01067770 nid=0xfb7000 in Object.wait() [0xb11c0000..0xb11c0d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x19847528> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"Check for updates thread" daemon prio=6 tid=0x010645d0 nid=0xf38e00 waiting on condition [0xb113f000..0xb113fd90] at java.lang.Thread.sleep(Native Method) at net.sf.taverna.raven.plugins.ui.UpdatesAvailableIcon$1.run(UpdatesAvailableIcon.java:137) "derby.rawStoreDaemon" daemon prio=6 tid=0x01054fd0 nid=0xf38000 in Object.wait() [0xb10be000..0xb10bed90] at java.lang.Object.wait(Native Method)

waiting on <0x194972e8> (a org.apache.derby.impl.services.daemon.BasicDaemon) at org.apache.derby.impl.services.daemon.BasicDaemon.rest(Unknown Source)
locked <0x194972e8> (a org.apache.derby.impl.services.daemon.BasicDaemon) at org.apache.derby.impl.services.daemon.BasicDaemon.run(Unknown Source) at java.lang.Thread.run(Thread.java:613)

"Timer-0" daemon prio=6 tid=0x01054680 nid=0xb99e00 in Object.wait() [0xb103d000..0xb103dd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.util.TimerThread.mainLoop(Timer.java:483)

locked <0x19487840> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462)

"derby.antiGC" daemon prio=1 tid=0x01053c80 nid=0xb99000 in Object.wait() [0xb0fbc000..0xb0fbcd90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at org.apache.derby.impl.services.monitor.AntiGC.run(Unknown Source)

locked <0x19472998> (a org.apache.derby.impl.services.monitor.AntiGC) at java.lang.Thread.run(Thread.java:613)

"TimerQueue" daemon prio=5 tid=0x01015800 nid=0x831000 in Object.wait() [0xb0eb2000..0xb0eb2d90] at java.lang.Object.wait(Native Method)

waiting on <0x1822cdf0> (a javax.swing.TimerQueue) at javax.swing.TimerQueue.run(TimerQueue.java:236)
locked <0x1822cdf0> (a javax.swing.TimerQueue) at java.lang.Thread.run(Thread.java:613)

"AWT-EventQueue-0" prio=6 tid=0x01012270 nid=0x823000 in Object.wait() [0xb0e31000..0xb0e31d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.awt.EventQueue.getNextEvent(EventQueue.java:345)

locked <0x180ed320> (a java.awt.EventQueue) at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:216) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176) at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

"Java2D Disposer" daemon prio=10 tid=0x01010030 nid=0x92ac00 in Object.wait() [0xb0d14000..0xb0d14d90] at java.lang.Object.wait(Native Method) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:120)

locked <0x180e25e8> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:136) at sun.java2d.Disposer.run(Disposer.java:125) at java.lang.Thread.run(Thread.java:613)

"AWT-Shutdown" prio=5 tid=0x0100f260 nid=0x8f9000 in Object.wait() [0xb0c8a000..0xb0c8ad90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:259)

locked <0x180e2678> (a java.lang.Object) at java.lang.Thread.run(Thread.java:613)

"AWT-AppKit" daemon prio=5 tid=0x0100edf0 nid=0xa06a9720 runnable [0x00000000..0xbfffe928] "Low Memory Detector" daemon prio=5 tid=0x010095a0 nid=0x84e800 runnable [0x00000000..0x00000000] "CompilerThread0" daemon prio=9 tid=0x01008b90 nid=0x84a200 waiting on condition [0x00000000..0xb0b077d8] "Signal Dispatcher" daemon prio=9 tid=0x01008640 nid=0x849400 waiting on condition [0x00000000..0x00000000] "Finalizer" daemon prio=8 tid=0x01007ae0 nid=0x815800 in Object.wait() [0xb0a05000..0xb0a05d90] at java.lang.Object.wait(Native Method) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:120)

locked <0x180a9398> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:136) at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=10 tid=0x01007720 nid=0x814000 in Object.wait() [0xb0984000..0xb0984d90] at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:474) at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)

locked <0x180a9420> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=9 tid=0x01006e70 nid=0x80b800 runnable "VM Periodic Task Thread" prio=9 tid=0x0100a180 nid=0x84f600 waiting on condition "Exception Catcher Thread" prio=10 tid=0x01001830 nid=0x809800 runnable Found one Java-level deadlock: ============================= "Find service descriptions from Soaplab service http://www.ebi.ac.uk/soaplab/services/": waiting to lock monitor 0x0081511c (object 0x1987ab40, a java.lang.Object), which is held by "Find service descriptions from Biomoby service http://moby.ucalgary.ca/moby/MOBY-Central.pl" "Find service descriptions from Biomoby service http://moby.ucalgary.ca/moby/MOBY-Central.pl": waiting to lock monitor 0x008150d4 (object 0x18d152b0, a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader), which is held by "Find service descriptions from Soaplab service http://www.ebi.ac.uk/soaplab/services/" Java stack information for the threads listed above: =================================================== "Find service descriptions from Soaplab service http://www.ebi.ac.uk/soaplab/services/": at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:325)

waiting to lock <0x1987ab40> (a java.lang.Object) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276) at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
locked <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
locked <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at org.apache.axis.client.Service.getAxisClient(Service.java:104) at org.apache.axis.client.Service.<init>(Service.java:113) at net.sf.taverna.t2.activities.soaplab.query.Soap.callWebService(Soap.java:75) at net.sf.taverna.t2.activities.soaplab.query.Soap.callWebService(Soap.java:49) at net.sf.taverna.t2.activities.soaplab.query.SoaplabScavengerAgent.loadCategories(SoaplabScavengerAgent.java:99) at net.sf.taverna.t2.activities.soaplab.query.SoaplabScavengerAgent.load(SoaplabScavengerAgent.java:79) at net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider.findSoaplabServices(SoaplabServiceProvider.java:141) at net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider.findServiceDescriptionsAsync(SoaplabServiceProvider.java:43) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480) "Find service descriptions from Biomoby service http://moby.ucalgary.ca/moby/MOBY-Central.pl": at java.lang.ClassLoader.checkCerts(ClassLoader.java:806)
waiting to lock <0x18d152b0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at java.lang.ClassLoader.preDefineClass(ClassLoader.java:542) at java.lang.ClassLoader.defineClass(ClassLoader.java:669) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124) at java.net.URLClassLoader.defineClass(URLClassLoader.java:260) at java.net.URLClassLoader.access$100(URLClassLoader.java:56) at java.net.URLClassLoader$1.run(URLClassLoader.java:195) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:326)
locked <0x1987ab40> (a java.lang.Object) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:229) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:333) at net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276) at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
locked <0x18e0aaf0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
locked <0x18e0aaf0> (a net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader) at net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.<init>(BiomobyQueryHelper.java:78) at net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:49) at net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:480)

Found 1 deadlock.

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Stian Soiland-Reyes added a comment - 2009-05-28 12:43

Fixed for 2.1 snapshot (should go in for beta 1)

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Stian Soiland-Reyes added a comment - 2009-05-28 12:43 Fixed for 2.1 snapshot (should go in for beta 1)

People

Assignee:

Tom Oinn

Reporter:

Stian Soiland-Reyes

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Dates

Created:

2007-05-16 09:51

Updated:

2009-05-28 12:44

Resolved:

2009-05-28 12:43

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