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Ticket #600 (new defect)

Opened 20 months ago

Last modified 20 months ago

possible threading issue on OMERO.importer on Linux

Reported by: omero Owned by: callan
Priority: major Milestone: Unscheduled
Component: Import Version: 3.0-M1
Keywords: Cc:

Description (last modified by callan) (diff)

When running OMERO.importer on my Ubuntu Edgy system, attempting to add a server by clicking the wrench icon caused the program to lock up. The full stack trace generated with Ctrl+\ follows. The program behaves as expected on my Mac OS X installation. -Curtis 

curtis@monk:~/apps/OMERO_Import$ ./OMERO.importer.sh 
Starting OMEROFormats...
Java exec found in PATH. Verifying...
Suitable java version found [java = 1.5.0_06]
Configuring environment...
Loading OMEROFormats:
/usr/share/themes/Human/gtk-2.0/gtkrc:70: Engine "ubuntulooks" is unsupported, ignoring
/usr/share/themes/Human/gtk-2.0/gtkrc:240: Priority specification is unsupported, ignoring
/usr/share/themes/Human/gtk-2.0/gtkrc:70: Engine "ubuntulooks" is unsupported, ignoring
/usr/share/themes/Human/gtk-2.0/gtkrc:240: Priority specification is unsupported, ignoring
Full thread dump Java HotSpot(TM) Client VM (1.5.0_06-b05 mixed mode, sharing):

"TimerQueue" daemon prio=1 tid=0x08621030 nid=0x3fbb in Object.wait() [0xb0114000..0xb01150e0]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x7df6ca90> (a javax.swing.TimerQueue)
        at javax.swing.TimerQueue.run(TimerQueue.java:233)
        - locked <0x7df6ca90> (a javax.swing.TimerQueue)
        at java.lang.Thread.run(Thread.java:595)

"Timer-0" daemon prio=1 tid=0x085671b0 nid=0x3f81 in Object.wait() [0xb039d000..0xb039d1e0]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x7df0a7b8> (a java.util.TaskQueue)
        at java.util.TimerThread.mainLoop(Timer.java:509)
        - locked <0x7df0a7b8> (a java.util.TaskQueue)
        at java.util.TimerThread.run(Timer.java:462)

"AWT-EventQueue-0" prio=1 tid=0x08557d70 nid=0x3f80 in Object.wait() [0xb04d0000..0xb04d0e60]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x7de039c0> (a java.awt.EventQueue)
        at java.lang.Object.wait(Object.java:474)
        at java.awt.EventQueue.getNextEvent(EventQueue.java:345)
        - locked <0x7de039c0> (a java.awt.EventQueue)
        at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:189)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:153)
        at java.awt.Dialog$1.run(Dialog.java:515)
        at java.awt.Dialog.show(Dialog.java:536)
        at java.awt.Component.show(Component.java:1300)
        at java.awt.Component.setVisible(Component.java:1253)
        at ome.formats.importer.LoginDialog.actionPerformed(LoginDialog.java:351)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)
        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:234)
        at java.awt.Component.processMouseEvent(Component.java:5488)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
        at java.awt.Component.processEvent(Component.java:5253)
        at java.awt.Container.processEvent(Container.java:1966)
        at java.awt.Component.dispatchEventImpl(Component.java:3955)
        at java.awt.Container.dispatchEventImpl(Container.java:2024)
        at java.awt.Component.dispatchEvent(Component.java:3803)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
        at java.awt.Container.dispatchEventImpl(Container.java:2010)
        at java.awt.Window.dispatchEventImpl(Window.java:1774)
        at java.awt.Component.dispatchEvent(Component.java:3803)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
        at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:153)
        at java.awt.Dialog$1.run(Dialog.java:515)
        at java.awt.Dialog.show(Dialog.java:536)
        at java.awt.Component.show(Component.java:1300)
        at java.awt.Component.setVisible(Component.java:1253)
        at ome.formats.importer.LoginDialog.<init>(LoginDialog.java:251)
        at ome.formats.importer.LoginHandler.displayLoginDialog(LoginHandler.java:133)
        at ome.formats.importer.LoginHandler.tryLogin(LoginHandler.java:74)
        at ome.formats.importer.LoginHandler.<init>(LoginHandler.java:64)
        at ome.formats.importer.Main.<init>(Main.java:236)
        at ome.formats.importer.Main$3.run(Main.java:466)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:199)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
        at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

"AWT-Shutdown" prio=1 tid=0x08557340 nid=0x3f7f in Object.wait() [0xb0551000..0xb0551ee0]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x7ddf4338> (a java.lang.Object)
        at java.lang.Object.wait(Object.java:474)
        at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:259)
        - locked <0x7ddf4338> (a java.lang.Object)
        at java.lang.Thread.run(Thread.java:595)

"AWT-XAWT" daemon prio=1 tid=0x0851efc8 nid=0x3f7d runnable [0xb0653000..0xb0653fe0]
        at sun.awt.X11.XToolkit.waitForEvents(Native Method)
        at sun.awt.X11.XToolkit.run(XToolkit.java:463)
        at sun.awt.X11.XToolkit.run(XToolkit.java:438)
        at java.lang.Thread.run(Thread.java:595)

"Java2D Disposer" daemon prio=1 tid=0x08513378 nid=0x3f7c in Object.wait() [0xb06ef000..0xb06f0060]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x7de07a90> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:116)
        - locked <0x7de07a90> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:132)
        at sun.java2d.Disposer.run(Disposer.java:107)
        at java.lang.Thread.run(Thread.java:595)

"Low Memory Detector" daemon prio=1 tid=0x080a6740 nid=0x3f7a runnable [0x00000000..0x00000000]

"CompilerThread0" daemon prio=1 tid=0x080a5198 nid=0x3f79 waiting on condition [0x00000000..0xb2226bc8]

"Signal Dispatcher" daemon prio=1 tid=0x080a4238 nid=0x3f78 runnable [0x00000000..0x00000000]

"Finalizer" daemon prio=1 tid=0x0809c7e0 nid=0x3f77 in Object.wait() [0xb2362000..0xb2362ee0]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x7ddd48e0> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:116)
        - locked <0x7ddd48e0> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:132)
        at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=1 tid=0x0809ba88 nid=0x3f76 in Object.wait() [0xb23e3000..0xb23e3f60]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x7ddd4960> (a java.lang.ref.Reference$Lock)
        at java.lang.Object.wait(Object.java:474)
        at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
        - locked <0x7ddd4960> (a java.lang.ref.Reference$Lock)

"main" prio=1 tid=0x0805e740 nid=0x3f74 in Object.wait() [0xbf956000..0xbf957658]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x7dee6950> (a java.awt.EventQueue$1AWTInvocationLock)
        at java.lang.Object.wait(Object.java:474)
        at java.awt.EventQueue.invokeAndWait(EventQueue.java:846)
        - locked <0x7dee6950> (a java.awt.EventQueue$1AWTInvocationLock)
        at javax.swing.SwingUtilities.invokeAndWait(SwingUtilities.java:1257)
        at ome.formats.importer.Main.main(Main.java:464)
        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:585)
        at ome.formats.importer.SplashWindow.invokeMain(SplashWindow.java:211)
        at ome.formats.importer.Splasher.main(Splasher.java:54)

"VM Thread" prio=1 tid=0x08098ef0 nid=0x3f75 runnable 

"VM Periodic Task Thread" prio=1 tid=0x080a7c28 nid=0x3f7b waiting on condition

Change History

Changed 20 months ago by callan

  • description modified (diff)
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