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 09:35:15
Full thread dump Java HotSpot(TM) 64-Bit Server VM (16.0-b13 mixed mode):
"Attach Listener" daemon prio=10 tid=0x00007f921c001800 nid=0x28b2 waiting on
condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Thread-19" prio=10 tid=0x00007f91dc003000 nid=0x4514 waiting for monitor entry
[0x00007f91c2eea000]
java.lang.Thread.State: BLOCKED (on object monitor)
at java.lang.ClassLoader.checkCerts(ClassLoader.java:783)
- waiting to lock <0x00007f924da5e0e0> (a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.preDefineClass(ClassLoader.java:488)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:626)
at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
at
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:326)
- locked <0x00007f925c051608> (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:307)
- locked <0x00007f924dbd0bf0> (a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
at
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:326)
- locked <0x00007f925c0102a0> (a java.lang.Object)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
- locked <0x00007f924dbd0bf0> (a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at
org.embl.ebi.escience.scuflworkers.ProcessorHelper.getTaskWorker(ProcessorHelper.java:157)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:354)
- locked <0x00007f925bc4baf8> (a
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:282)
at
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
"Thread-8" prio=10 tid=0x00007f91dc035800 nid=0x450e waiting for monitor entry
[0x00007f91c33f1000]
java.lang.Thread.State: BLOCKED (on object monitor)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:325)
- waiting to lock <0x00007f925c051608> (a java.lang.Object)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
- locked <0x00007f924da5e0e0> (a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:358)
- locked <0x00007f925bc4b258> (a
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:282)
at
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
"Thread-4" prio=10 tid=0x00007f91dc022000 nid=0x450c waiting for monitor entry
[0x00007f9244566000]
java.lang.Thread.State: BLOCKED (on object monitor)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:358)
- locked <0x00007f925bc1e878> (a
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:282)
at
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
"Thread-2" prio=10 tid=0x00007f91dc001000 nid=0x4505 in Object.wait()
[0x00007f9245f61000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00007f925bd5d748> (a java.util.LinkedList)
at java.lang.Object.wait(Object.java:485)
at
uk.ac.soton.itinnovation.freefluo.util.event.Queue$ConsumerThread.run(Queue.java:81)
- locked <0x00007f925bd5d748> (a java.util.LinkedList)
"WorkflowEventDispatcher NotifyThread" daemon prio=10 tid=0x00007f926041e000
nid=0x4503 in Object.wait() [0x00007f92202ae000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00007f925bc05a88> (a
org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread)
at
org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:255)
- locked <0x00007f925bc05a88> (a
org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread)
"Java2D Disposer" daemon prio=10 tid=0x00007f91d002b800 nid=0x441a in
Object.wait() [0x00007f9245686000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00007f924dbd0bb8> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
- locked <0x00007f924dbd0bb8> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
at sun.java2d.Disposer.run(Disposer.java:125)
at java.lang.Thread.run(Thread.java:619)
"Low Memory Detector" daemon prio=10 tid=0x00007f92600cc000 nid=0x4406 runnable
[0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread1" daemon prio=10 tid=0x00007f92600ca000 nid=0x4405 waiting on
condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread0" daemon prio=10 tid=0x00007f92600c7000 nid=0x4404 waiting on
condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" daemon prio=10 tid=0x00007f92600c5000 nid=0x4403 runnable
[0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" daemon prio=10 tid=0x00007f9260091800 nid=0x4402 in Object.wait()
[0x00007f924735d000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00007f924d40c6a0> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
- locked <0x00007f924d40c6a0> (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=0x00007f926008f800 nid=0x4401 in
Object.wait() [0x00007f924745e000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00007f924d40c6d8> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:485)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
- locked <0x00007f924d40c6d8> (a java.lang.ref.Reference$Lock)
"main" prio=10 tid=0x00007f9260008800 nid=0x43fb in Object.wait()
[0x00007f9267e32000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00007f925bdd6e68> (a java.lang.Object)
at java.lang.Object.wait(Object.java:485)
at
org.embl.ebi.escience.scufl.tools.WorkflowLauncher.execute(WorkflowLauncher.java:311)
- locked <0x00007f925bdd6e68> (a java.lang.Object)
at
org.embl.ebi.escience.scufl.tools.WorkflowLauncher.<init>(WorkflowLauncher.java:602)
at
org.embl.ebi.escience.scufl.tools.WorkflowLauncher.main(WorkflowLauncher.java:667)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at net.sf.taverna.tools.Bootstrap.invokeWorkbench(Bootstrap.java:188)
at net.sf.taverna.tools.Bootstrap.main(Bootstrap.java:75)
"VM Thread" prio=10 tid=0x00007f926008b000 nid=0x4400 runnable
"GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f926001b800 nid=0x43fc
runnable
"GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f926001d800 nid=0x43fd
runnable
"GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f926001f000 nid=0x43fe
runnable
"GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f9260021000 nid=0x43ff
runnable
"VM Periodic Task Thread" prio=10 tid=0x00007f92600cf000 nid=0x4407 waiting on
condition
JNI global references: 994
Found one Java-level deadlock:
=============================
"Thread-19":
waiting to lock monitor 0x00007f91e0001d08 (object 0x00007f924da5e0e0, a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader),
which is held by "Thread-8"
"Thread-8":
waiting to lock monitor 0x00007f91f4018400 (object 0x00007f925c051608, a
java.lang.Object),
which is held by "Thread-19"
Java stack information for the threads listed above:
===================================================
"Thread-19":
at java.lang.ClassLoader.checkCerts(ClassLoader.java:783)
- waiting to lock <0x00007f924da5e0e0> (a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.preDefineClass(ClassLoader.java:488)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:626)
at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
at
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:326)
- locked <0x00007f925c051608> (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:307)
- locked <0x00007f924dbd0bf0> (a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
at
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:326)
- locked <0x00007f925c0102a0> (a java.lang.Object)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
- locked <0x00007f924dbd0bf0> (a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at
org.embl.ebi.escience.scuflworkers.ProcessorHelper.getTaskWorker(ProcessorHelper.java:157)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:354)
- locked <0x00007f925bc4baf8> (a
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:282)
at
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
"Thread-8":
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:325)
- waiting to lock <0x00007f925c051608> (a java.lang.Object)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
- locked <0x00007f924da5e0e0> (a
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:358)
- locked <0x00007f925bc4b258> (a
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:282)
at
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
Found 1 deadlock.
------------------------------------------------------------------------------
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