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Task #12929 (closed)

Opened 9 years ago

Closed 9 years ago

Last modified 8 years ago

BUG: Import As freezes

Reported by: pwalczysko Owned by: dlindner
Priority: critical Milestone: OMERO-5.2.1
Component: Insight Version: 5.1.2
Keywords: Import As Cc: ux@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Observed on tadpole. Import as ome-trainer-1. Importing 2 dvs with lot of metadata. The import normally takes around 1 minute.

Workflow:

  • logged in as an admin, in read-annotate group
  • import as the members of the group (ome-user-1, 2, 3 etc.)
  • import into the same group , the same data
  • the data are on trout, user-4, read-only-1, project OMERO.figure
  • do not wait until the import finishes for each user, instead
  • continue immediately with import for another user
  • for each user create a Project at import stage and import the whole Dataset (containing the 2 dv images and 4 log files) into it
  • after some time, (possibly at the second import), the import of the second image does not go through, being stuck on "Reading metadata" stage
  • if you continue with the imports, you will finally see "Connection destroyed..." dialog and will have to close insight

This bug is perfectly repeatable on tadpole.
It is alos repeatable on trout (login as root and try to import into Read-annotate-1 for each user, using the OMERO.figure dv folder)

Change History (24)

comment:1 Changed 9 years ago by pwalczysko

The data are also under team/pwalczysko/OMERO.figure. Take the whole "Original File download" subfolder and import it as a folder each time.

comment:2 Changed 9 years ago by jamoore

A jstack is always appreciated when a client freezes.

comment:3 Changed 9 years ago by pwalczysko

@jamoore : Here is the jstack after the dialog "Connection destroyed" is displayed.

jstack 31684
2015-06-16 13:16:42
Full thread dump Java HotSpot(TM) 64-Bit Server VM (25.45-b02 mixed mode):

"Attach Listener" #1933 daemon prio=9 os_prio=31 tid=0x00007fcf57f46800 nid=0xdbf3 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Thread-1673" #1911 prio=6 os_prio=31 tid=0x00007fcf4ac3e000 nid=0x16827 in Object.wait() [0x00000001b8a7f000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:257)
	- locked <0x0000000120a00788> (a java.awt.Component$AWTTreeLock)
	at java.awt.Dialog.show(Dialog.java:1084)
	at java.awt.Component.show(Component.java:1654)
	at java.awt.Component.setVisible(Component.java:1606)
	at java.awt.Window.setVisible(Window.java:1014)
	at java.awt.Dialog.setVisible(Dialog.java:1005)
	at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:566)
	at org.openmicroscopy.shoola.env.data.DataServicesFactory.addListenerAndShow(DataServicesFactory.java:357)
	at org.openmicroscopy.shoola.env.data.DataServicesFactory.sessionExpiredExit(DataServicesFactory.java:463)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.handleConnectionException(OMEROGateway.java:877)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6737)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:236)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1338)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:79)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:104)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-30" #1767 prio=5 os_prio=31 tid=0x00007fcf4aa76000 nid=0x1097b runnable [0x00000001bd38d000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
	at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:198)
	at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:103)
	at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
	- locked <0x000000012106bc20> (a sun.nio.ch.Util$2)
	- locked <0x000000012106bc30> (a java.util.Collections$UnmodifiableSet)
	- locked <0x000000012106bbd0> (a sun.nio.ch.KQueueSelectorImpl)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
	at IceInternal.Selector.select(Selector.java:263)
	at IceInternal.ThreadPool.run(ThreadPool.java:338)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-0" #1269 prio=5 os_prio=31 tid=0x00007fcf53259000 nid=0xf7b3 runnable [0x00000001bc831000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
	at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:198)
	at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:103)
	at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
	- locked <0x000000012830b960> (a sun.nio.ch.Util$2)
	- locked <0x000000012830c090> (a java.util.Collections$UnmodifiableSet)
	- locked <0x000000012830b670> (a sun.nio.ch.KQueueSelectorImpl)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
	at IceInternal.Selector.select(Selector.java:263)
	at IceInternal.ThreadPool.run(ThreadPool.java:338)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.HostResolver" #1268 prio=6 os_prio=31 tid=0x00007fcf53258800 nid=0x140ef in Object.wait() [0x00000001bc72e000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:167)
	- locked <0x0000000128322ec8> (a IceInternal.EndpointHostResolver)
	at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:290)

"Ice.Timer" #1267 prio=6 os_prio=31 tid=0x00007fcf530e4000 nid=0x12ac7 in Object.wait() [0x00000001bb797000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.Timer.run(Timer.java:185)
	- locked <0x000000012830c5f8> (a IceInternal.Timer)

"Ice.ThreadPool.Client-0" #1265 prio=5 os_prio=31 tid=0x00007fcf4b07c000 nid=0x1180b runnable [0x00000001bb591000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
	at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:198)
	at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:103)
	at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
	- locked <0x00000001282ebc88> (a sun.nio.ch.Util$2)
	- locked <0x00000001282ec3c8> (a java.util.Collections$UnmodifiableSet)
	- locked <0x00000001282eb998> (a sun.nio.ch.KQueueSelectorImpl)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
	at IceInternal.Selector.select(Selector.java:263)
	at IceInternal.ThreadPool.run(ThreadPool.java:338)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.HostResolver" #1264 prio=6 os_prio=31 tid=0x00007fcf4b07b800 nid=0x1060b in Object.wait() [0x00000001b897d000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:167)
	- locked <0x00000001282feb48> (a IceInternal.EndpointHostResolver)
	at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:290)

"Ice.Timer" #1263 prio=6 os_prio=31 tid=0x00007fcf4bb1b000 nid=0x115cf in Object.wait() [0x00000001b887a000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.Timer.run(Timer.java:185)
	- locked <0x00000001282f27b0> (a IceInternal.Timer)

"Ice.ThreadPool.Client-26" #1139 prio=5 os_prio=31 tid=0x00007fcf5795f800 nid=0x1459f runnable [0x00000001b38cd000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
	at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:198)
	at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:103)
	at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
	- locked <0x0000000120eab400> (a sun.nio.ch.Util$2)
	- locked <0x0000000120eab8e0> (a java.util.Collections$UnmodifiableSet)
	- locked <0x0000000120eab098> (a sun.nio.ch.KQueueSelectorImpl)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
	at IceInternal.Selector.select(Selector.java:263)
	at IceInternal.ThreadPool.run(ThreadPool.java:338)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"pool-1-thread-1" #38 prio=5 os_prio=31 tid=0x00007fcf4c08e800 nid=0x10723 waiting on condition [0x00000001b124e000]
   java.lang.Thread.State: TIMED_WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00000001210592a0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
	at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
	at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

"Ice.HostResolver" #35 prio=5 os_prio=31 tid=0x00007fcf4a475000 nid=0xb507 in Object.wait() [0x00000001b0f45000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:167)
	- locked <0x0000000120ed4fb8> (a IceInternal.EndpointHostResolver)
	at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:290)

"Ice.Timer" #34 prio=5 os_prio=31 tid=0x00007fcf4d066800 nid=0x10407 in Object.wait() [0x00000001b0e42000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.Timer.run(Timer.java:185)
	- locked <0x0000000120eabe98> (a IceInternal.Timer)

"Ice.HostResolver" #31 prio=5 os_prio=31 tid=0x00007fcf4c462000 nid=0x25e3 in Object.wait() [0x00000001b052c000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:167)
	- locked <0x00000001210930d8> (a IceInternal.EndpointHostResolver)
	at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:290)

"Ice.Timer" #30 prio=5 os_prio=31 tid=0x00007fcf4c0f3800 nid=0xb627 in Object.wait() [0x00000001ad57d000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.Timer.run(Timer.java:185)
	- locked <0x0000000121093230> (a IceInternal.Timer)

"net.sf.ehcache.CacheManager@59b84511" #21 daemon prio=5 os_prio=31 tid=0x00007fcf4c270800 nid=0xf22f in Object.wait() [0x00000001afcac000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.util.TimerThread.mainLoop(Timer.java:552)
	- locked <0x0000000120a36ca0> (a java.util.TaskQueue)
	at java.util.TimerThread.run(Timer.java:505)

"TimerQueue" #20 daemon prio=5 os_prio=31 tid=0x00007fcf4b826800 nid=0xee37 waiting on condition [0x00000001acd7d000]
   java.lang.Thread.State: TIMED_WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x0000000120a36cf0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
	at java.util.concurrent.DelayQueue.take(DelayQueue.java:223)
	at javax.swing.TimerQueue.run(TimerQueue.java:171)
	at java.lang.Thread.run(Thread.java:745)

"AWT-EventQueue-0" #19 prio=6 os_prio=31 tid=0x00007fcf4c152800 nid=0xce03 waiting on condition [0x00000001ab9a6000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x0000000120a35120> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
	at java.awt.EventQueue.getNextEvent(EventQueue.java:554)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:170)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:229)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:227)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:227)
	at java.awt.Dialog.show(Dialog.java:1084)
	at java.awt.Component.show(Component.java:1654)
	at java.awt.Component.setVisible(Component.java:1606)
	at java.awt.Window.setVisible(Window.java:1014)
	at java.awt.Dialog.setVisible(Dialog.java:1005)
	at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:566)
	at org.openmicroscopy.shoola.agents.fsimporter.chooser.LocationDialog.centerLocation(LocationDialog.java:908)
	at org.openmicroscopy.shoola.agents.fsimporter.chooser.ImportDialog.showLocationDialog(ImportDialog.java:391)
	at org.openmicroscopy.shoola.agents.fsimporter.chooser.ImportDialog.propertyChange(ImportDialog.java:1635)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:303)
	at java.awt.Component.firePropertyChange(Component.java:8442)
	at javax.swing.JComponent.firePropertyChange(JComponent.java:4500)
	at org.openmicroscopy.shoola.agents.fsimporter.chooser.FileSelectionTable.actionPerformed(FileSelectionTable.java:701)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
	at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
	at java.awt.Component.processMouseEvent(Component.java:6525)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
	at java.awt.Component.processEvent(Component.java:6290)
	at java.awt.Container.processEvent(Container.java:2234)
	at java.awt.Component.dispatchEventImpl(Component.java:4881)
	at java.awt.Container.dispatchEventImpl(Container.java:2292)
	at java.awt.Component.dispatchEvent(Component.java:4703)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
	at java.awt.Container.dispatchEventImpl(Container.java:2278)
	at java.awt.Window.dispatchEventImpl(Window.java:2750)
	at java.awt.Component.dispatchEvent(Component.java:4703)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

"Timer-0" #17 daemon prio=5 os_prio=31 tid=0x00007fcf4aa01000 nid=0xca03 in Object.wait() [0x00000001ab392000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at java.util.TimerThread.mainLoop(Timer.java:526)
	- locked <0x0000000120a36e88> (a java.util.TaskQueue)
	at java.util.TimerThread.run(Timer.java:505)

"Java2D Disposer" #16 daemon prio=10 os_prio=31 tid=0x00007fcf4a219000 nid=0xc603 in Object.wait() [0x00000001ab057000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
	- locked <0x0000000120a1ff00> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
	at sun.java2d.Disposer.run(Disposer.java:148)
	at java.lang.Thread.run(Thread.java:745)

"Java2D Queue Flusher" #15 daemon prio=10 os_prio=31 tid=0x00007fcf4a24f800 nid=0xb707 in Object.wait() [0x00000001a9fb7000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:203)
	- locked <0x0000000120a15d18> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)

"AWT-Shutdown" #13 prio=5 os_prio=31 tid=0x00007fcf4b801800 nid=0x8b03 in Object.wait() [0x00000001a781a000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295)
	- locked <0x0000000120a371e0> (a java.lang.Object)
	at java.lang.Thread.run(Thread.java:745)

"AppKit Thread" #12 daemon prio=5 os_prio=31 tid=0x00007fcf4c12a000 nid=0xc07 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"DestroyJavaVM" #11 prio=5 os_prio=31 tid=0x00007fcf4c133000 nid=0x3e07 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Service Thread" #9 daemon prio=9 os_prio=31 tid=0x00007fcf4a089000 nid=0x7403 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C1 CompilerThread3" #8 daemon prio=9 os_prio=31 tid=0x00007fcf4b005000 nid=0x7203 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread2" #7 daemon prio=9 os_prio=31 tid=0x00007fcf4a079800 nid=0x7003 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" #6 daemon prio=9 os_prio=31 tid=0x00007fcf4c017800 nid=0x6e03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" #5 daemon prio=9 os_prio=31 tid=0x00007fcf4c016000 nid=0x6c03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" #4 daemon prio=9 os_prio=31 tid=0x00007fcf4a03a000 nid=0x6a03 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" #3 daemon prio=8 os_prio=31 tid=0x00007fcf4b004000 nid=0x6603 in Object.wait() [0x00000001a6120000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
	- locked <0x0000000120a5fad8> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"Reference Handler" #2 daemon prio=10 os_prio=31 tid=0x00007fcf4a060800 nid=0x6403 in Object.wait() [0x00000001a601d000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)
	- locked <0x0000000120a53378> (a java.lang.ref.Reference$Lock)

"VM Thread" os_prio=31 tid=0x00007fcf4a05e000 nid=0x6203 runnable 

"GC task thread#0 (ParallelGC)" os_prio=31 tid=0x00007fcf4901a000 nid=0x5203 runnable 

"GC task thread#1 (ParallelGC)" os_prio=31 tid=0x00007fcf4c014800 nid=0x5403 runnable 

"GC task thread#2 (ParallelGC)" os_prio=31 tid=0x00007fcf4a003000 nid=0x5603 runnable 

"GC task thread#3 (ParallelGC)" os_prio=31 tid=0x00007fcf4901b000 nid=0x5803 runnable 

"GC task thread#4 (ParallelGC)" os_prio=31 tid=0x00007fcf4c015000 nid=0x5a03 runnable 

"GC task thread#5 (ParallelGC)" os_prio=31 tid=0x00007fcf4a003800 nid=0x5c03 runnable 

"GC task thread#6 (ParallelGC)" os_prio=31 tid=0x00007fcf4901b800 nid=0x5e03 runnable 

"GC task thread#7 (ParallelGC)" os_prio=31 tid=0x00007fcf4901c000 nid=0x6003 runnable 

"VM Periodic Task Thread" os_prio=31 tid=0x00007fcf4c020000 nid=0x7603 waiting on condition 

JNI global references: 23690

comment:4 Changed 9 years ago by jamoore

Thanks, Petr. This is interesting; Doesn't look like any of the regular Ice.Communicator issues we've seen. This is more a pure Java hang.

comment:5 Changed 9 years ago by jamoore

  • Owner changed from jburel to mtbcarroll

Talking to Mark, it looks like the code which is causing the hang:

	at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:566)
	at org.openmicroscopy.shoola.env.data.DataServicesFactory.addListenerAndShow(DataServicesFactory.java:357)
	at org.openmicroscopy.shoola.env.data.DataServicesFactory.sessionExpiredExit(DataServicesFactory.java:463)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.handleConnectionException(OMEROGateway.java:877)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6737)

(outside the AWT thread) has been in place for some time. Likely what's happening is that a new exception is being thrown and triggering the hang without informing us of the root cause.

comment:6 Changed 9 years ago by pwalczysko

As just confirmed by Mark, the creation of new Projects on import stage is crucial for the bug reproduction

comment:7 Changed 9 years ago by mtbcarroll

Using the described workflow, including with user and group switching and project creation, I managed to get the outer try of OMEROGateway.importImageFile to catch a CommunicatorDestroyedException.

comment:8 Changed 9 years ago by mtbcarroll

(I didn't get the actual hang, though, I'm curious about that.)

comment:9 Changed 9 years ago by mtbcarroll

With Josh's help I extracted the stack trace from the exception:

Ice.CommunicatorDestroyedException
	at IceInternal.Outgoing.invoke(Outgoing.java:158)
	at omero.api._RawFileStoreDelM.write(_RawFileStoreDelM.java:379)
	at omero.api.RawFileStorePrxHelper.write(RawFileStorePrxHelper.java:1409)
	at omero.api.RawFileStorePrxHelper.write(RawFileStorePrxHelper.java:1381)
	at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:79)
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:430)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6708)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1202)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:80)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$0(ImagesImporter.java:74)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:104)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:745)

comment:10 Changed 9 years ago by jamoore

Hmmm..... slightly similar to one I saw while searching for this: ​https://trac.openmicroscopy.org/ome/ticket/12026

comment:11 Changed 9 years ago by mtbcarroll

So at the moment I triggered the exception this time, the Import Location dialog was open, and the currently uploading file now has "File Not Valid Upload" just to the right of the upload progress bar.

comment:12 Changed 9 years ago by mtbcarroll

Aha, that "File Not Valid" appears to arise from ImportLibrary.uploadFile notifying observers of ErrorHandler.FILE_EXCEPTION and StatusLabel updating accordingly.

comment:13 Changed 9 years ago by mtbcarroll

  • Owner changed from mtbcarroll to jmarie

Guessing that JM will take a look next week.

comment:14 Changed 9 years ago by mtbcarroll

  • Owner changed from jmarie to jburel

comment:15 Changed 9 years ago by jburel

  • Owner changed from jburel to dlindner

Passing it to Dominik who is currently investigating timeout issue see ​https://github.com/openmicroscopy/openmicroscopy/pull/4052

comment:16 Changed 9 years ago by dlindner

Tried to reproduce, noticed that the important part is to start another import while a previous "import as" is running. There's no error if multiple "import as" are queued and then launched at once.

comment:17 Changed 9 years ago by dlindner

  • Resolution set to fixed
  • Status changed from new to closed

Fixed by: ​https://github.com/openmicroscopy/openmicroscopy/pull/4075

comment:18 Changed 9 years ago by dlindner

  • Resolution fixed deleted
  • Status changed from closed to reopened

comment:19 Changed 9 years ago by jamoore

  • Milestone changed from 5.1.4 to OMERO-5.1.4

Splitting 5.1.4 due to milestone decoupling

comment:20 Changed 9 years ago by dlindner

  • Milestone changed from OMERO-5.1.4 to OMERO-5.2.0
  • Priority changed from blocker to critical

comment:21 Changed 9 years ago by dlindner

  • Milestone changed from OMERO-5.2.0 to OMERO-5.2.1

comment:22 Changed 9 years ago by dlindner

  • Resolution set to fixed
  • Status changed from reopened to closed

Fixed by: ​https://github.com/openmicroscopy/openmicroscopy/pull/4316

comment:23 Changed 8 years ago by jburel

  • Milestone changed from OMERO-5.2.1 to OMERO-5.2.2

Milestone OMERO-5.2.1 deleted

comment:24 Changed 8 years ago by jburel

  • Milestone changed from OMERO-5.2.2 to OMERO-5.2.1

Milestone OMERO-5.2.2 deleted

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