[ImageJ-devel] Deadlock: DefaultStatusService.showStatus calls EventService.publish / AbstractColorTool.drawIcon gets active dataset view

Barry DeZonia bdezonia at gmail.com
Wed Oct 16 14:45:02 CDT 2013 

I'm not having any problems building scijava-common master against IJ2
master.


On Wed, Oct 16, 2013 at 2:25 PM, Lee Kamentsky <leek at broadinstitute.org>wrote:

> I have a very simple fix in scijava-common, but it seems that the head of
> the scijava-common master branch is not going to build with the head of the
> imagej master branch. How should I proceed? I could branch off off
> scijava-common-2.2.0 I suppose.
>
>
> On Wed, Oct 16, 2013 at 2:44 PM, Barry DeZonia <bdezonia at gmail.com> wrote:
>
>> Thanks. I also updated the ticket a bit a few minutes ago. In my second
>> example problem (closing app with sample image open) it looks like the
>> original open samples legacy command was not finishing its run. Not sure if
>> this is related to your event processing changes.
>>
>>
>> On Wed, Oct 16, 2013 at 1:19 PM, Lee Kamentsky <leek at broadinstitute.org>wrote:
>>
>>> Sorry, I missed it. I'll see if I can take a look at it,
>>>
>>>
>>> On Wed, Oct 16, 2013 at 2:15 PM, Barry DeZonia <bdezonia at gmail.com>wrote:
>>>
>>>> Lee did you see I reopened ticket #1992 (
>>>> http://trac.imagej.net/ticket/1992) that was related to this code
>>>> change?
>>>>
>>>>
>>>> On Mon, Oct 7, 2013 at 10:15 AM, Barry DeZonia <bdezonia at gmail.com>wrote:
>>>>
>>>>> Merged
>>>>>
>>>>>
>>>>> On Mon, Sep 30, 2013 at 2:34 PM, Lee Kamentsky <
>>>>> leek at broadinstitute.org> wrote:
>>>>>
>>>>>> I submitted a patch to scijava-common with the changes.
>>>>>>
>>>>>> https://github.com/scijava/scijava-common/pull/13
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Sep 30, 2013 at 3:32 PM, Barry DeZonia <bdezonia at gmail.com>wrote:
>>>>>>
>>>>>>> A proposed fix would be good Lee. I'd like to test the async status
>>>>>>> update code for responsiveness (i.e. when opening a large image let's say).
>>>>>>> Let me know when your fix is in place. Thanks.
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Sep 27, 2013 at 6:54 AM, Lee Kamentsky <
>>>>>>> leek at broadinstitute.org> wrote:
>>>>>>>
>>>>>>>> Thanks Barry, the email was a little rushed - finished it while
>>>>>>>> going out the door. What do you think about sending the status messages
>>>>>>>> asynchronously? It looks to me like the AWT event processing will display
>>>>>>>> them in the order received, so that makes sure that a "Finished" message
>>>>>>>> will be seen after a "% complete" message. Status reporting is such a
>>>>>>>> common thing - it'd be a shame for all the worker threads to stall because
>>>>>>>> a user was using ImageJ to watch a movie of a cat falling off a TV while
>>>>>>>> their batch job was running.
>>>>>>>>
>>>>>>>> I think I'll submit a patch to DefaultStatusService for asynch
>>>>>>>> reporting and maybe Curtis or you could look it over and accept it. If you
>>>>>>>> reject, NP.
>>>>>>>>
>>>>>>>> --Lee
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Sep 26, 2013 at 7:53 PM, Barry DeZonia <bdezonia at gmail.com>wrote:
>>>>>>>>
>>>>>>>>> Hi Lee,
>>>>>>>>>
>>>>>>>>> I added the synchronized keyword yesterday to fix a bug. We can
>>>>>>>>> undo that change. I can work around the problem in another fashion if
>>>>>>>>> necessary.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Sep 26, 2013 at 3:57 PM, Lee Kamentsky <
>>>>>>>>> leek at broadinstitute.org> wrote:
>>>>>>>>>
>>>>>>>>>> Hi all, I'm getting a deadly embrace that happens when the AWT
>>>>>>>>>> event queue thread tries to get a lock within DefaultDatasetView.getColor
>>>>>>>>>> and when DefaultStatusService.showStatus on a worker thread tries to
>>>>>>>>>> publish a synchronous request for status display after taking the
>>>>>>>>>> DefaultDatasetView's lock in DefaultDatasetView.rebuild. It happens
>>>>>>>>>> periodically, but it's timing-dependent, so not so reproducible.
>>>>>>>>>>
>>>>>>>>>> The bug is somewhat debatable. Possible candidates: It's a little
>>>>>>>>>> drastic for DefaultDatasetView.getColor to synchronize on the view itself.
>>>>>>>>>> Maybe some proxy for the color system could have a synchronizing object.
>>>>>>>>>> The other candidate is DefaultEventService.showStatus which could use
>>>>>>>>>> EventService.publishLater - I don't think there's much need for status
>>>>>>>>>> publishers to wait around for the status to show on the screen.
>>>>>>>>>>
>>>>>>>>>> The two stack traces:
>>>>>>>>>> Thread [AWT-EventQueue-0] (Suspended)
>>>>>>>>>> DefaultDatasetView.getColor(ChannelCollection) line: 261 Synchronized
>>>>>>>>>> method on DefaultDatasetView
>>>>>>>>>>  FgColorTool(AbstractColorTool).drawIcon() line: 175
>>>>>>>>>> FgColorTool(AbstractColorTool).onEvent(DisplayActivatedEvent)
>>>>>>>>>> line: 184
>>>>>>>>>>  NativeMethodAccessorImpl.invoke0(Method, Object, Object[])
>>>>>>>>>> line: not available [native method]
>>>>>>>>>> NativeMethodAccessorImpl.invoke(Object, Object[]) line: 39
>>>>>>>>>>  DelegatingMethodAccessorImpl.invoke(Object, Object[]) line: 25
>>>>>>>>>> Method.invoke(Object, Object...) line: 597
>>>>>>>>>>  DefaultEventService$ProxySubscriber<E>.onEvent(E) line: 282
>>>>>>>>>> DefaultEventService$ProxySubscriber<E>.onEvent(Object) line: 1
>>>>>>>>>>  DefaultEventBus(ThreadSafeEventService).publish(Object, String,
>>>>>>>>>> Object, List, List, StackTraceElement[]) line: 971
>>>>>>>>>>  DefaultEventBus.access$1(DefaultEventBus, Object, String,
>>>>>>>>>> Object, List, List, StackTraceElement[]) line: 1
>>>>>>>>>> DefaultEventBus$1.run() line: 201
>>>>>>>>>>  DefaultThreadService.invoke(Runnable) line: 91
>>>>>>>>>> DefaultEventBus.publishNow(Object, String, Object, List, List,
>>>>>>>>>> StackTraceElement[]) line: 195
>>>>>>>>>>  DefaultEventBus.publishNow(Object) line: 86
>>>>>>>>>> DefaultEventService.publish(E) line: 95
>>>>>>>>>>  DefaultDisplayService.setActiveDisplay(Display<?>) line: 129
>>>>>>>>>> DefaultDisplayService.onEvent(WinActivatedEvent) line: 247
>>>>>>>>>>  NativeMethodAccessorImpl.invoke0(Method, Object, Object[])
>>>>>>>>>> line: not available [native method]
>>>>>>>>>> NativeMethodAccessorImpl.invoke(Object, Object[]) line: 39
>>>>>>>>>>  DelegatingMethodAccessorImpl.invoke(Object, Object[]) line: 25
>>>>>>>>>> Method.invoke(Object, Object...) line: 597
>>>>>>>>>>  DefaultEventService$ProxySubscriber<E>.onEvent(E) line: 282
>>>>>>>>>> DefaultEventService$ProxySubscriber<E>.onEvent(Object) line: 1
>>>>>>>>>>  DefaultEventBus(ThreadSafeEventService).publish(Object, String,
>>>>>>>>>> Object, List, List, StackTraceElement[]) line: 971
>>>>>>>>>>  DefaultEventBus.access$1(DefaultEventBus, Object, String,
>>>>>>>>>> Object, List, List, StackTraceElement[]) line: 1
>>>>>>>>>> DefaultEventBus$1.run() line: 201
>>>>>>>>>>  DefaultThreadService.invoke(Runnable) line: 91
>>>>>>>>>> DefaultEventBus.publishNow(Object, String, Object, List, List,
>>>>>>>>>> StackTraceElement[]) line: 195
>>>>>>>>>>  DefaultEventBus.publishNow(Object) line: 86
>>>>>>>>>> DefaultEventService.publish(E) line: 95
>>>>>>>>>>  AWTWindowEventDispatcher.windowActivated(WindowEvent) line: 94
>>>>>>>>>> SwingDisplayWindow(Window).processWindowEvent(WindowEvent) line:
>>>>>>>>>> 1877
>>>>>>>>>>  SwingDisplayWindow(JFrame).processWindowEvent(WindowEvent)
>>>>>>>>>> line: 274
>>>>>>>>>> SwingDisplayWindow(Window).processEvent(AWTEvent) line: 1823
>>>>>>>>>>  SwingDisplayWindow(Component).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>> 4630
>>>>>>>>>> SwingDisplayWindow(Container).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>> 2099
>>>>>>>>>>  SwingDisplayWindow(Window).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>> 2478
>>>>>>>>>> SwingDisplayWindow(Component).dispatchEvent(AWTEvent) line: 4460
>>>>>>>>>>  DefaultKeyboardFocusManager(KeyboardFocusManager).redispatchEvent(Component,
>>>>>>>>>> AWTEvent) line: 1850
>>>>>>>>>> DefaultKeyboardFocusManager.typeAheadAssertions(Component,
>>>>>>>>>> AWTEvent) line: 910
>>>>>>>>>>  DefaultKeyboardFocusManager.dispatchEvent(AWTEvent) line: 409
>>>>>>>>>> SwingDisplayWindow(Component).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>> 4502
>>>>>>>>>>  SwingDisplayWindow(Container).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>> 2099
>>>>>>>>>> SwingDisplayWindow(Window).dispatchEventImpl(AWTEvent) line: 2478
>>>>>>>>>>  SwingDisplayWindow(Component).dispatchEvent(AWTEvent) line: 4460
>>>>>>>>>> EventQueue.dispatchEvent(AWTEvent) line: 599
>>>>>>>>>>  DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent(SentEvent).dispatch()
>>>>>>>>>> line: 55
>>>>>>>>>> DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent.dispatch()
>>>>>>>>>> line: 183
>>>>>>>>>>  DefaultKeyboardFocusManager.sendMessage(Component, AWTEvent)
>>>>>>>>>> line: 210
>>>>>>>>>> DefaultKeyboardFocusManager.dispatchEvent(AWTEvent) line: 286
>>>>>>>>>>  SwingDisplayWindow(Component).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>> 4502
>>>>>>>>>> SwingDisplayWindow(Container).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>> 2099
>>>>>>>>>>  SwingDisplayWindow(Window).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>> 2478
>>>>>>>>>> SwingDisplayWindow(Component).dispatchEvent(AWTEvent) line: 4460
>>>>>>>>>>  EventQueue.dispatchEvent(AWTEvent) line: 599
>>>>>>>>>> SequencedEvent.dispatch() line: 101
>>>>>>>>>>  EventQueue.dispatchEvent(AWTEvent) line: 597
>>>>>>>>>> EventDispatchThread.pumpOneEventForFilters(int) line: 269
>>>>>>>>>>  EventDispatchThread.pumpEventsForFilter(int, Conditional,
>>>>>>>>>> EventFilter) line: 184
>>>>>>>>>> EventDispatchThread.pumpEventsForHierarchy(int, Conditional,
>>>>>>>>>> Component) line: 174
>>>>>>>>>>  EventDispatchThread.pumpEvents(int, Conditional) line: 169
>>>>>>>>>> EventDispatchThread.pumpEvents(Conditional) line: 161
>>>>>>>>>>  EventDispatchThread.run() line: 122
>>>>>>>>>>
>>>>>>>>>> Thread [SciJava-4b2922f6-Thread-27] (Suspended)
>>>>>>>>>>  Object.wait(long) line: not available [native method]
>>>>>>>>>> EventQueue$1AWTInvocationLock(Object).wait() line: 485 Waiting
>>>>>>>>>> for AWT event thread to read invocation request.
>>>>>>>>>>  EventQueue.invokeAndWait(Runnable) line: 993
>>>>>>>>>> DefaultThreadService.invoke(Runnable) line: 95
>>>>>>>>>>  DefaultEventBus.publishNow(Object, String, Object, List, List,
>>>>>>>>>> StackTraceElement[]) line: 195
>>>>>>>>>> DefaultEventBus.publishNow(Object) line: 86
>>>>>>>>>>  DefaultEventService.publish(E) line: 95
>>>>>>>>>> DefaultStatusService.showStatus(int, int, String) line: 77
>>>>>>>>>>  DefaultMinMaxMethod<T>.report() line: 296
>>>>>>>>>> DefaultMinMaxMethod<T>.process() line: 155
>>>>>>>>>>  DefaultAutoscaleMethod<T>.getRange(IterableInterval<T>) line: 70
>>>>>>>>>> DefaultAutoscaleService.getDefaultIntervalRange(IterableInterval<RealType<?>>)
>>>>>>>>>> line: 97
>>>>>>>>>>  DefaultAutoscaleService.getDefaultRandomAccessRange(RandomAccessibleInterval<RealType<?>>)
>>>>>>>>>> line: 105
>>>>>>>>>>  DefaultDatasetView.autoscale(int) line: 176
>>>>>>>>>> DefaultDatasetView.initializeView(boolean) line: 499
>>>>>>>>>>  DefaultDatasetView.rebuild() line: 383 Takes the
>>>>>>>>>> DefaultDatasetView lock.
>>>>>>>>>> DefaultImageDisplay.rebuild() line: 140
>>>>>>>>>>  DefaultImageDisplay.display(Object) line: 273
>>>>>>>>>> DefaultOverlayService.addOverlays(ImageDisplay, List<Overlay>)
>>>>>>>>>> line: 148
>>>>>>>>>>  TurboRegRegister.run() line: 144
>>>>>>>>>> CommandModule.run() line: 196
>>>>>>>>>>  ModuleRunner.run() line: 168
>>>>>>>>>> ModuleRunner.call() line: 129
>>>>>>>>>>  ModuleRunner.call() line: 1
>>>>>>>>>> FutureTask$Sync.innerRun() line: 303
>>>>>>>>>>  FutureTask<V>.run() line: 138
>>>>>>>>>> ThreadPoolExecutor$Worker.runTask(Runnable) line: 886
>>>>>>>>>>  ThreadPoolExecutor$Worker.run() line: 908
>>>>>>>>>> Thread.run() line: 662
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> ImageJ-devel mailing list
>>>>>>>>>> ImageJ-devel at imagej.net
>>>>>>>>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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