2013-01-16 10:39:54 Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.12-b01-434 mixed mode): "Attach Listener" daemon prio=9 tid=119498800 nid=0x10e9a2000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "Thread-26" prio=6 tid=11946b000 nid=0x1177c9000 waiting for monitor entry [1177c8000] java.lang.Thread.State: BLOCKED (on object monitor) at org.openmicroscopy.shoola.env.data.OMEROGateway.isSessionAlive(OMEROGateway.java:432) - waiting to lock <7bdb95258> (a org.openmicroscopy.shoola.env.data.OMEROGateway) at org.openmicroscopy.shoola.env.data.OMEROGateway.loadContainerHierarchy(OMEROGateway.java:2640) at org.openmicroscopy.shoola.env.data.OmeroDataServiceImpl.loadContainerHierarchy(OmeroDataServiceImpl.java:222) at org.openmicroscopy.shoola.env.data.views.calls.DMLoader$1.doCall(DMLoader.java:91) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) "Thread-25" prio=6 tid=119468800 nid=0x115222000 waiting for monitor entry [115221000] java.lang.Thread.State: BLOCKED (on object monitor) at org.openmicroscopy.shoola.env.data.OMEROGateway.isSessionAlive(OMEROGateway.java:432) - waiting to lock <7bdb95258> (a org.openmicroscopy.shoola.env.data.OMEROGateway) at org.openmicroscopy.shoola.env.data.OMEROGateway.loadAnnotations(OMEROGateway.java:2725) at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredAnnotations(OmeroMetadataServiceImpl.java:1022) at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredData(OmeroMetadataServiceImpl.java:707) at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredData(OmeroMetadataServiceImpl.java:811) at org.openmicroscopy.shoola.env.data.views.calls.StructuredAnnotationLoader$6.doCall(StructuredAnnotationLoader.java:211) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) "Ice.ThreadPool.Client-2" prio=5 tid=115c22800 nid=0x111101000 in Object.wait() [111100000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:485) at IceInternal.ThreadPool.run(ThreadPool.java:315) - locked <7be30ee80> (a IceInternal.ThreadPool) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) "pool-1-thread-1" prio=5 tid=1109de800 nid=0x1149c1000 runnable [1149c0000] java.lang.Thread.State: RUNNABLE at java.util.Arrays.sort(Arrays.java:1210) at java.util.Collections.sort(Collections.java:157) at IceInternal.RoutableReference.filterEndpoints(RoutableReference.java:747) at IceInternal.RoutableReference.createConnection(RoutableReference.java:831) at IceInternal.RoutableReference$1.setEndpoints(RoutableReference.java:484) at IceInternal.RouterInfo.getClientEndpoints(RouterInfo.java:92) at IceInternal.RoutableReference.getConnection(RoutableReference.java:476) at IceInternal.ConnectRequestHandler.connect(ConnectRequestHandler.java:41) at Ice._ObjectDelM.setup(_ObjectDelM.java:275) at Ice.ObjectPrxHelperBase.createDelegate(ObjectPrxHelperBase.java:1007) at Ice.ObjectPrxHelperBase.__getDelegate(ObjectPrxHelperBase.java:946) - locked <7be5c2930> (a omero.api.ServiceFactoryPrxHelper) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:1648) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:1622) at org.openmicroscopy.shoola.env.data.Connector.keepSessionAlive(Connector.java:708) at org.openmicroscopy.shoola.env.data.OMEROGateway.keepSessionAlive(OMEROGateway.java:5542) at org.openmicroscopy.shoola.env.data.KeepClientAlive.run(KeepClientAlive.java:63) - locked <7bdb95258> (a org.openmicroscopy.shoola.env.data.OMEROGateway) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439) at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:317) at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:150) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$101(ScheduledThreadPoolExecutor.java:98) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.runPeriodic(ScheduledThreadPoolExecutor.java:180) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:204) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:680) "Ice.ThreadPool.Client-1" prio=5 tid=110a91000 nid=0x1148be000 runnable [1148bd000] java.lang.Thread.State: RUNNABLE at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method) at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:136) at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:69) at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69) - locked <7be5c39f8> (a sun.nio.ch.Util$2) - locked <7be5c3a10> (a java.util.Collections$UnmodifiableSet) - locked <7be4f80d8> (a sun.nio.ch.KQueueSelectorImpl) at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80) at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:84) at IceInternal.Selector.select(Selector.java:139) at IceInternal.ThreadPool.run(ThreadPool.java:335) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) "Ice.Timer" prio=5 tid=104a65000 nid=0x1147bb000 in Object.wait() [1147ba000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <7be49f938> (a IceInternal.Timer) at java.lang.Object.wait(Object.java:485) at IceInternal.Timer.run(Timer.java:177) - locked <7be49f938> (a IceInternal.Timer) "Ice.SelectorThread" prio=5 tid=104a64800 nid=0x1146b8000 runnable [1146b7000] java.lang.Thread.State: RUNNABLE at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method) at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:136) at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:69) at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69) - locked <7be5c3ab8> (a sun.nio.ch.Util$2) - locked <7be5c3aa0> (a java.util.Collections$UnmodifiableSet) - locked <7be4f8120> (a sun.nio.ch.KQueueSelectorImpl) at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80) at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:84) at IceInternal.Selector.select(Selector.java:139) at IceInternal.SelectorThread.run(SelectorThread.java:120) at IceInternal.SelectorThread$HelperThread.run(SelectorThread.java:273) "Ice.ThreadPool.Client-0" prio=5 tid=104c04000 nid=0x1145b5000 in Object.wait() [1145b4000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:485) at IceInternal.ThreadPool.run(ThreadPool.java:710) - locked <7be30ee80> (a IceInternal.ThreadPool) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) "Ice.EndpointHostResolverThread" prio=5 tid=104a0f000 nid=0x1144b2000 in Object.wait() [1144b1000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <7be59c3c0> (a IceInternal.EndpointHostResolver) at java.lang.Object.wait(Object.java:485) at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:77) - locked <7be59c3c0> (a IceInternal.EndpointHostResolver) at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:146) "Ice.ThreadPool.Client-1" prio=5 tid=110a8a800 nid=0x1143af000 runnable [1143ae000] java.lang.Thread.State: RUNNABLE at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method) at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:136) at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:69) at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69) - locked <7be2e97d0> (a sun.nio.ch.Util$2) - locked <7be2e97b8> (a java.util.Collections$UnmodifiableSet) - locked <7be2ec0a8> (a sun.nio.ch.KQueueSelectorImpl) at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80) at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:84) at IceInternal.Selector.select(Selector.java:139) at IceInternal.ThreadPool.run(ThreadPool.java:335) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) "Ice.Timer" prio=5 tid=11098a000 nid=0x1142ac000 in Object.wait() [1142ab000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <7be49fbe0> (a IceInternal.Timer) at java.lang.Object.wait(Object.java:485) at IceInternal.Timer.run(Timer.java:177) - locked <7be49fbe0> (a IceInternal.Timer) "Ice.SelectorThread" prio=5 tid=1109fd000 nid=0x1141a9000 runnable [1141a8000] java.lang.Thread.State: RUNNABLE at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method) at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:136) at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:69) at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69) - locked <7be2e9470> (a sun.nio.ch.Util$2) - locked <7be2e9458> (a java.util.Collections$UnmodifiableSet) - locked <7be2ec138> (a sun.nio.ch.KQueueSelectorImpl) at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80) at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:84) at IceInternal.Selector.select(Selector.java:139) at IceInternal.SelectorThread.run(SelectorThread.java:120) at IceInternal.SelectorThread$HelperThread.run(SelectorThread.java:273) "Ice.ThreadPool.Client-0" prio=5 tid=110892800 nid=0x1140a6000 in Object.wait() [1140a5000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:485) at IceInternal.ThreadPool.run(ThreadPool.java:710) - locked <7be326bd0> (a IceInternal.ThreadPool) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) "Ice.EndpointHostResolverThread" prio=5 tid=104985800 nid=0x113fa3000 in Object.wait() [113fa2000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <7be4975e8> (a IceInternal.EndpointHostResolver) at java.lang.Object.wait(Object.java:485) at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:77) - locked <7be4975e8> (a IceInternal.EndpointHostResolver) at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:146) "Poller SunPKCS11-Darwin" daemon prio=1 tid=104905800 nid=0x111cd9000 waiting on condition [111cd8000] java.lang.Thread.State: TIMED_WAITING (sleeping) at java.lang.Thread.sleep(Native Method) at sun.security.pkcs11.SunPKCS11$TokenPoller.run(SunPKCS11.java:692) at java.lang.Thread.run(Thread.java:680) "TimerQueue" daemon prio=5 tid=11093b000 nid=0x111bd6000 in Object.wait() [111bd5000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at javax.swing.TimerQueue.postExpiredTimers(TimerQueue.java:214) - locked <7bd913838> (a javax.swing.TimerQueue) at javax.swing.TimerQueue.run(TimerQueue.java:230) - locked <7bd913838> (a javax.swing.TimerQueue) at java.lang.Thread.run(Thread.java:680) "AWT-EventQueue-0" prio=6 tid=104a86800 nid=0x1106d2000 runnable [1106cf000] java.lang.Thread.State: RUNNABLE at java.lang.Throwable.fillInStackTrace(Native Method) - locked <7bbe999e8> (a IceInternal.LocalExceptionWrapper) at java.lang.Throwable.(Throwable.java:181) at java.lang.Exception.(Exception.java:29) at IceInternal.LocalExceptionWrapper.(LocalExceptionWrapper.java:16) at Ice.ConnectionI.sendRequest(ConnectionI.java:346) - locked <7be5e48d0> (a Ice.ConnectionI) at IceInternal.ConnectionRequestHandler.sendRequest(ConnectionRequestHandler.java:36) at IceInternal.Outgoing.invoke(Outgoing.java:66) at omero.api._ThumbnailStoreDelM.close(_ThumbnailStoreDelM.java:63) at omero.api.ThumbnailStorePrxHelper.close(ThumbnailStorePrxHelper.java:117) at omero.api.ThumbnailStorePrxHelper.close(ThumbnailStorePrxHelper.java:89) at org.openmicroscopy.shoola.env.data.Connector.close(Connector.java:724) at org.openmicroscopy.shoola.env.data.Connector.shutDownServices(Connector.java:678) at org.openmicroscopy.shoola.env.data.OMEROGateway.shutDownServices(OMEROGateway.java:4066) at org.openmicroscopy.shoola.env.data.OMEROGateway.logout(OMEROGateway.java:2599) at org.openmicroscopy.shoola.env.data.DataServicesFactory.shutdown(DataServicesFactory.java:696) at org.openmicroscopy.shoola.env.data.DataServicesFactory.exitApplication(DataServicesFactory.java:760) at org.openmicroscopy.shoola.env.ui.TaskBarManager.exitApplication(TaskBarManager.java:622) at org.openmicroscopy.shoola.env.ui.TaskBarManager.doExit(TaskBarManager.java:554) at org.openmicroscopy.shoola.env.ui.TaskBarManager.eventFired(TaskBarManager.java:983) at org.openmicroscopy.shoola.env.event.EventBusImpl.dispatch(EventBusImpl.java:91) at org.openmicroscopy.shoola.env.event.EventBusImpl.post(EventBusImpl.java:222) at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerComponent.closeWindow(TreeViewerComponent.java:1023) at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerControl$2.windowClosing(TreeViewerControl.java:624) at java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:332) at java.awt.Window.processWindowEvent(Window.java:1871) at javax.swing.JFrame.processWindowEvent(JFrame.java:274) at java.awt.Window.processEvent(Window.java:1829) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2141) at java.awt.Window.dispatchEventImpl(Window.java:2489) at java.awt.Component.dispatchEvent(Component.java:4572) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:704) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:663) at java.awt.EventQueue$2.run(EventQueue.java:661) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$3.run(EventQueue.java:677) at java.awt.EventQueue$3.run(EventQueue.java:675) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:674) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) "AWT-Shutdown" prio=5 tid=110944800 nid=0x10e81d000 in Object.wait() [10e81c000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:485) at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265) - locked <7bd913880> (a java.lang.Object) at java.lang.Thread.run(Thread.java:680) "Timer-0" daemon prio=5 tid=104149000 nid=0x1105cf000 in Object.wait() [1105ce000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:485) at java.util.TimerThread.mainLoop(Timer.java:483) - locked <7bd913898> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:462) "Java2D Disposer" daemon prio=10 tid=104a8d800 nid=0x10dc06000 in Object.wait() [10dc05000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118) - locked <7bd9138b0> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134) at sun.java2d.Disposer.run(Disposer.java:127) at java.lang.Thread.run(Thread.java:680) "AWT-AppKit" daemon prio=5 tid=104179800 nid=0x7fff7e903960 runnable [00000000] java.lang.Thread.State: RUNNABLE "DestroyJavaVM" prio=5 tid=104000800 nid=0x103201000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "Low Memory Detector" daemon prio=5 tid=10402f800 nid=0x10cdc9000 runnable [00000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread1" daemon prio=9 tid=10402e800 nid=0x10ccc6000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread0" daemon prio=9 tid=10402e000 nid=0x10cbc3000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "Signal Dispatcher" daemon prio=9 tid=10402d000 nid=0x10cac0000 runnable [00000000] java.lang.Thread.State: RUNNABLE "Surrogate Locker Thread (Concurrent GC)" daemon prio=5 tid=104894800 nid=0x10c9bd000 waiting on condition [00000000] java.lang.Thread.State: RUNNABLE "Finalizer" daemon prio=8 tid=104019800 nid=0x10c8ba000 in Object.wait() [10c8b9000] 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 <7bd790310> (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=104002000 nid=0x10c7b7000 in Object.wait() [10c7b6000] 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$ReferenceHandler.run(Reference.java:116) - locked <7bd80bd78> (a java.lang.ref.Reference$Lock) "VM Thread" prio=9 tid=10488f800 nid=0x10c6b4000 runnable "Gang worker#0 (Parallel GC Threads)" prio=9 tid=104800800 nid=0x108102000 runnable "Gang worker#1 (Parallel GC Threads)" prio=9 tid=104801000 nid=0x108205000 runnable "Concurrent Mark-Sweep GC Thread" prio=9 tid=10484c000 nid=0x10c3c0000 runnable "VM Periodic Task Thread" prio=10 tid=104041000 nid=0x10cecc000 waiting on condition "Exception Catcher Thread" prio=10 tid=104001800 nid=0x103f01000 runnable JNI global references: 68840