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

Wed Oct 16 14:54:21 CDT 2013

In imagej/pom.xml I added:

 <scijava-common.version>2.2.1-SNAPSHOT</scijava-common.version>

in the <properties> section

On Wed, Oct 16, 2013 at 2:46 PM, Lee Kamentsky <leek at broadinstitute.org>wrote:

> 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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