Hi,
I was using taverna workbench (1.7.2) for executing another workflow
this afternoon. It has entered into a frozen state last two hours that
I'm not able to do anything with the interface except resizing the main
window. I have attached its jstack output for your information, it
doesn't report a deadlock. If you want to see the workflow Xose can
provide it.
Regards,
Mahmut
On Wed, 2010-02-17 at 09:55 +0000, Mahmut Uludag wrote:
> Hi,
>
> I'm using taverna-1.7.2 to execute a workflow Achille wrote. In my
> latest two tests, the workflow returned successfully when running using
> the taverna workbench but ended up with a deadlock when using the
> executeworkflow script. I have attached the jstack output for your
> information. If you need to see the workflow and its inputs I'm sure
> Achille can provide them. I should note that my previous attempt using
> the same executescript command line returned successfully.
>
> Regards,
> Mahmut
>
2010-02-17 15:25:27
Full thread dump Java HotSpot(TM) 64-Bit Server VM (16.0-b13 mixed mode):
"Attach Listener" daemon prio=10 tid=0x00007f78dc001000 nid=0x2835 waiting on
condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Thread-115" prio=10 tid=0x00007f7890019000 nid=0xebd in Object.wait()
[0x00007f7904341000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at
uk.ac.soton.itinnovation.freefluo.util.event.Queue$ConsumerThread.run(Queue.java:81)
- locked <0x00007f794584a230> (a java.util.LinkedList)
"Enactor invocation status thread" prio=10 tid=0x00007f78b4129800 nid=0xebb
waiting for monitor entry [0x00007f78e13bf000]
java.lang.Thread.State: BLOCKED (on object monitor)
at
org.embl.ebi.escience.scuflui.graph.RowLayout.layout(RowLayout.java:52)
- waiting to lock <0x00007f79459dce00> (a
org.embl.ebi.escience.scuflui.graph.RowLayout)
at
org.embl.ebi.escience.scuflui.graph.WorkflowEditor$1$1.graphChanged(WorkflowEditor.java:335)
at
org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel.fireGraphChangedEvent(ScuflGraphModel.java:716)
at
org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel.edit(ScuflGraphModel.java:635)
at
org.embl.ebi.escience.scuflui.graph.WorkflowEditor.updateStatus(WorkflowEditor.java:693)
at
org.embl.ebi.escience.scuflui.EnactorInvocation$EnactorInvocationStatusThread.run(EnactorInvocation.java:707)
"Reconcile ScuflModel" prio=10 tid=0x00007f789000c000 nid=0xeba in
Object.wait() [0x00007f78e1bc7000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at
org.embl.ebi.escience.scuflui.graph.model.ScuflModelReconciler$1.run(ScuflModelReconciler.java:41)
- locked <0x00007f7945b522b8> (a
org.embl.ebi.escience.scuflui.graph.model.ScuflModelReconciler$1)
"ScuflModelNotifyThread:TLDA_up" daemon prio=10 tid=0x00007f7890040800
nid=0xeb9 in Object.wait() [0x00007f78e14c0000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at org.embl.ebi.escience.scufl.NotifyThread.run(ScuflModel.java:761)
- locked <0x00007f7945b52528> (a
org.embl.ebi.escience.scufl.NotifyThread)
"Timer-37" daemon prio=10 tid=0x00007f78b4021800 nid=0xe71 in Object.wait()
[0x00007f7904c4a000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at java.util.TimerThread.mainLoop(Timer.java:483)
- locked <0x00007f7945b52a98> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)
"RunnableQueue-14" daemon prio=10 tid=0x00007f78b4146800 nid=0xe70 in
Object.wait() [0x00007f78e19c5000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at org.apache.batik.util.RunnableQueue.run(Unknown Source)
- locked <0x00007f7945b53008> (a org.apache.batik.util.DoublyLinkedList)
at java.lang.Thread.run(Thread.java:619)
"ScuflModelNotifyThread:TLDA_up" daemon prio=10 tid=0x00007f78b4026800
nid=0xe64 in Object.wait() [0x00007f79062f2000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at org.embl.ebi.escience.scufl.NotifyThread.run(ScuflModel.java:761)
- locked <0x00007f79458496b8> (a
org.embl.ebi.escience.scufl.NotifyThread)
"ScuflModelNotifyThread:Untitled workflow #11" daemon prio=10
tid=0x00007f78b4064800 nid=0xe2f in Object.wait() [0x00007f7904240000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at org.embl.ebi.escience.scufl.NotifyThread.run(ScuflModel.java:761)
- locked <0x00007f79457b6f60> (a
org.embl.ebi.escience.scufl.NotifyThread)
"Timer-29" prio=10 tid=0x00007f78b4156000 nid=0xe26 in Object.wait()
[0x00007f78e17c3000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.util.TimerThread.mainLoop(Timer.java:509)
- locked <0x00007f79461133e0> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)
"Timer-3" daemon prio=10 tid=0x00007f78b4013000 nid=0xb31 in Object.wait()
[0x00007f7904d4b000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.util.TimerThread.mainLoop(Timer.java:509)
- locked <0x00007f79138ba0c8> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:462)
"Thread-3" daemon prio=10 tid=0x00007f789c009000 nid=0xa1a in Object.wait()
[0x00007f7904b49000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00007f790f5dd340> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
- locked <0x00007f790f5dd340> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
at org.apache.batik.util.CleanerThread.run(Unknown Source)
"DestroyJavaVM" prio=10 tid=0x00007f7a24008000 nid=0x9ef waiting on condition
[0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"WorkflowEventDispatcher NotifyThread" daemon prio=10 tid=0x00007f7a25025000
nid=0xa0c in Object.wait() [0x00007f7905890000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at
org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:255)
- locked <0x00007f790f6877e0> (a
org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread)
"TimerQueue" daemon prio=10 tid=0x00007f7a24ffa000 nid=0xa0a in Object.wait()
[0x00007f790578f000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at javax.swing.TimerQueue.run(TimerQueue.java:232)
- locked <0x00007f790f2ccff0> (a javax.swing.TimerQueue)
at java.lang.Thread.run(Thread.java:619)
"AWT-EventQueue-0" prio=10 tid=0x00007f7a24231800 nid=0xa00 runnable
[0x00007f79060ef000]
java.lang.Thread.State: RUNNABLE
at
org.embl.ebi.escience.scuflui.graph.PositionLayout.getPort(PositionLayout.java:771)
at
org.embl.ebi.escience.scuflui.graph.PositionLayout.getPort(PositionLayout.java:763)
at
org.embl.ebi.escience.scuflui.graph.PositionLayout.getSlack(PositionLayout.java:745)
at
org.embl.ebi.escience.scuflui.graph.GraphSpanningTree$2.compare(GraphSpanningTree.java:523)
at java.util.Arrays.mergeSort(Arrays.java:1293)
at java.util.Arrays.sort(Arrays.java:1210)
at java.util.Collections.sort(Collections.java:159)
at
org.embl.ebi.escience.scuflui.graph.GraphSpanningTree.optimiseTree(GraphSpanningTree.java:513)
at
org.embl.ebi.escience.scuflui.graph.RowLayout.layout(RowLayout.java:123)
- locked <0x00007f79459dce00> (a
org.embl.ebi.escience.scuflui.graph.RowLayout)
at
org.embl.ebi.escience.scuflui.graph.WorkflowEditor$1$1.graphChanged(WorkflowEditor.java:335)
at
org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel.fireGraphChangedEvent(ScuflGraphModel.java:716)
at
org.embl.ebi.escience.scuflui.graph.model.ScuflGraphModel.graphChanged(ScuflGraphModel.java:813)
at
org.embl.ebi.escience.scuflui.graph.model.ScuflModelReconciler$1$1.run(ScuflModelReconciler.java:78)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
"AWT-Shutdown" prio=10 tid=0x00007f7a240f6000 nid=0x9ff in Object.wait()
[0x00007f79061f1000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)
- locked <0x00007f790e085a98> (a java.lang.Object)
at java.lang.Thread.run(Thread.java:619)
"AWT-XAWT" daemon prio=10 tid=0x00007f7a241f1000 nid=0x9fd runnable
[0x00007f79063f3000]
java.lang.Thread.State: RUNNABLE
at sun.awt.X11.XToolkit.waitForEvents(Native Method)
at sun.awt.X11.XToolkit.run(XToolkit.java:541)
at sun.awt.X11.XToolkit.run(XToolkit.java:505)
at java.lang.Thread.run(Thread.java:619)
"Java2D Disposer" daemon prio=10 tid=0x00007f7a2419a000 nid=0x9fc in
Object.wait() [0x00007f79065fc000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
- locked <0x00007f790e08eb80> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
at sun.java2d.Disposer.run(Disposer.java:125)
at java.lang.Thread.run(Thread.java:619)
"Low Memory Detector" daemon prio=10 tid=0x00007f7a240cc000 nid=0x9fa runnable
[0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread1" daemon prio=10 tid=0x00007f7a240c9800 nid=0x9f9 waiting on
condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread0" daemon prio=10 tid=0x00007f7a240c6800 nid=0x9f8 waiting on
condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" daemon prio=10 tid=0x00007f7a240c4800 nid=0x9f7 runnable
[0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" daemon prio=10 tid=0x00007f7a24091000 nid=0x9f6 in Object.wait()
[0x00007f79073e2000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
- locked <0x00007f790e0a0460> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
"Reference Handler" daemon prio=10 tid=0x00007f7a2408f000 nid=0x9f5 in
Object.wait() [0x00007f79074e3000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
- locked <0x00007f790e0a0498> (a java.lang.ref.Reference$Lock)
"VM Thread" prio=10 tid=0x00007f7a2408b000 nid=0x9f4 runnable
"GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f7a2401b000 nid=0x9f0
runnable
"GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f7a2401d000 nid=0x9f1
runnable
"GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f7a2401e800 nid=0x9f2
runnable
"GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f7a24020800 nid=0x9f3
runnable
"VM Periodic Task Thread" prio=10 tid=0x00007f7a240ce800 nid=0x9fb waiting on
condition
JNI global references: 2020
------------------------------------------------------------------------------
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