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

Lee Kamentsky leek at broadinstitute.org
Wed Oct 16 14:46:45 CDT 2013 

Are you editing one of the POMs to pick up the 2.2.1-SNAPSHOT version of
scijava-common?


On Wed, Oct 16, 2013 at 3:45 PM, Barry DeZonia <bdezonia at gmail.com> wrote:

> 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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