{"action":"created","issue":{"url":"https://api.github.com/repos/micro-manager/micro-manager/issues/480","repository_url":"https://api.github.com/repos/micro-manager/micro-manager","labels_url":"https://api.github.com/repos/micro-manager/micro-manager/issues/480/labels{/name}","comments_url":"https://api.github.com/repos/micro-manager/micro-manager/issues/480/comments","events_url":"https://api.github.com/repos/micro-manager/micro-manager/issues/480/events","html_url":"https://github.com/micro-manager/micro-manager/issues/480","id":187252420,"number":480,"title":"Deadlock while starting an acquisition","user":{"login":"nicost","id":2153771,"avatar_url":"https://avatars.githubusercontent.com/u/2153771?v=3","gravatar_id":"","url":"https://api.github.com/users/nicost","html_url":"https://github.com/nicost","followers_url":"https://api.github.com/users/nicost/followers","following_url":"https://api.github.com/users/nicost/following{/other_user}","gists_url":"https://api.github.com/users/nicost/gists{/gist_id}","starred_url":"https://api.github.com/users/nicost/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nicost/subscriptions","organizations_url":"https://api.github.com/users/nicost/orgs","repos_url":"https://api.github.com/users/nicost/repos","events_url":"https://api.github.com/users/nicost/events{/privacy}","received_events_url":"https://api.github.com/users/nicost/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-11-04T04:39:18Z","updated_at":"2016-11-04T17:36:19Z","closed_at":null,"body":"I have a potential fix, needs testing:\r\n\r\n\r\ndebug:\r\n2016-11-03T17:23:11.738566 tid5020 [IFO,LogManager] Enabled logging to stderr\r\nAsked to load file at path C:\\Program Files\\Micro-Manager-2.0beta\\GlobalUserProfile.txt which doesn't exist; instead providing a default empty PropertyMap.\r\n2016-11-03T17:23:11.832167 tid5020 [IFO,LogManager] Enabled primary log file C:\\Program Files\\Micro-Manager-2.0beta\\CoreLogs\\CoreLog20161103T172311_pid4248.txt\r\n2016-11-03T17:23:11.832167 tid5020 [IFO,App] User: Vale Lab\r\n2016-11-03T17:23:11.832167 tid5020 [IFO,App] Host: Uberscope\r\n2016-11-03T17:23:11.832167 tid5020 [IFO,App] MM Studio version: 2.0.x dev\r\n---- snip ---\r\n2016-11-03T17:24:25.703410 tid2396 [IFO,App] EDTHangLogger: Missed heartbeat; waiting to see if we are stuck on a single event\r\n2016-11-03T17:24:26.704467 tid2396 [IFO,App] EDTHangLogger: Event handling has exceeded at least 1000 ms (currently 5500 ms since heartbeat timebase)\r\n                                   [       ] Stack traces follow (note: thread states queried later than stack traces)\r\n                                   [       ] Thread 2 [Reference Handler] WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.lang.Object.wait(Object.java:485)\r\n                                   [       ]   at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)\r\n                                   [       ] Thread 3 [Finalizer] WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)\r\n                                   [       ]   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)\r\n                                   [       ]   at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:171)\r\n                                   [       ] Thread 4 [Signal Dispatcher] RUNNABLE\r\n                                   [       ] Thread 5 [Attach Listener] RUNNABLE\r\n                                   [       ] Thread 13 [Java2D Disposer] WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)\r\n                                   [       ]   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)\r\n                                   [       ]   at sun.java2d.Disposer.run(Disposer.java:127)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 14 [AWT-Shutdown] WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.lang.Object.wait(Object.java:485)\r\n                                   [       ]   at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 15 [AWT-Windows] RUNNABLE\r\n                                   [       ]   at sun.awt.windows.WToolkit.eventLoop(Native Method)\r\n                                   [       ]   at sun.awt.windows.WToolkit.run(WToolkit.java:293)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 18 [AWT-EventQueue-0] BLOCKED\r\n                                   [       ]   at com.google.common.eventbus.SynchronizedEventSubscriber.handleEvent(SynchronizedEventSubscriber.java:47)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.dispatch(EventBus.java:322)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:304)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.post(EventBus.java:275)\r\n                                   [       ]   at org.micromanager.display.internal.DefaultDisplayWindow.setDisplaySettings(DefaultDisplayWindow.java:791)\r\n                                   [       ]   at org.micromanager.display.internal.DefaultDisplayWindow.setDisplaySettings(DefaultDisplayWindow.java:773)\r\n                                   [       ]   at org.micromanager.display.internal.LUTMaster.updateDisplayLUTForChannel(LUTMaster.java:319)\r\n                                   [       ]   at org.micromanager.display.internal.LUTMaster.updateDisplayLUTs(LUTMaster.java:289)\r\n                                   [       ]   at org.micromanager.display.internal.LUTMaster.initializeDisplay(LUTMaster.java:261)\r\n                                   [       ]   at org.micromanager.display.internal.CanvasUpdateQueue.showImage(CanvasUpdateQueue.java:333)\r\n                                   [       ]   at org.micromanager.display.internal.CanvasUpdateQueue.consumeImages(CanvasUpdateQueue.java:219)\r\n                                   [       ]   at org.micromanager.display.internal.CanvasUpdateQueue.access$000(CanvasUpdateQueue.java:71)\r\n                                   [       ]   at org.micromanager.display.internal.CanvasUpdateQueue$1.run(CanvasUpdateQueue.java:158)\r\n                                   [       ]   at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)\r\n                                   [       ]   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:672)\r\n                                   [       ]   at java.awt.EventQueue.access$400(EventQueue.java:81)\r\n                                   [       ]   at java.awt.EventQueue$2.run(EventQueue.java:633)\r\n                                   [       ]   at java.awt.EventQueue$2.run(EventQueue.java:631)\r\n                                   [       ]   at java.security.AccessController.doPrivileged(Native Method)\r\n                                   [       ]   at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)\r\n                                   [       ]   at java.awt.EventQueue.dispatchEvent(EventQueue.java:642)\r\n                                   [       ]   at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)\r\n                                   [       ]   at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)\r\n                                   [       ]   at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)\r\n                                   [       ]   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)\r\n                                   [       ]   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)\r\n                                   [       ]   at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)\r\n                                   [       ] Thread 21 [org.netbeans.modules.debugger.jpda.visual AWT Access Loop] TIMED_WAITING\r\n                                   [       ]   at java.lang.Thread.sleep(Native Method)\r\n                                   [       ]   at org.netbeans.modules.debugger.jpda.visual.remote.RemoteAWTService$AWTAccessLoop.run(RemoteAWTService.java:236)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 22 [DestroyJavaVM] RUNNABLE\r\n                                   [       ] Thread 23 [User profile save thread] TIMED_WAITING\r\n                                   [       ]   at java.lang.Thread.sleep(Native Method)\r\n                                   [       ]   at org.micromanager.internal.utils.DefaultUserProfile.runSaveThread(DefaultUserProfile.java:191)\r\n                                   [       ]   at org.micromanager.internal.utils.DefaultUserProfile.access$000(DefaultUserProfile.java:22)\r\n                                   [       ]   at org.micromanager.internal.utils.DefaultUserProfile$1.run(DefaultUserProfile.java:168)\r\n                                   [       ] Thread 24 [EDTHangLogger timer] RUNNABLE\r\n                                   [       ]   at java.lang.Thread.dumpThreads(Native Method)\r\n                                   [       ]   at java.lang.Thread.getAllStackTraces(Thread.java:1530)\r\n                                   [       ]   at org.micromanager.internal.diagnostics.EDTHangLogger.checkForHang(EDTHangLogger.java:233)\r\n                                   [       ]   at org.micromanager.internal.diagnostics.EDTHangLogger.access$200(EDTHangLogger.java:34)\r\n                                   [       ]   at org.micromanager.internal.diagnostics.EDTHangLogger$4.run(EDTHangLogger.java:220)\r\n                                   [       ]   at java.util.TimerThread.mainLoop(Timer.java:512)\r\n                                   [       ]   at java.util.TimerThread.run(Timer.java:462)\r\n                                   [       ] Thread 27 [TimerQueue] TIMED_WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at javax.swing.TimerQueue.run(TimerQueue.java:232)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 28 [D3D Screen Updater] TIMED_WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at sun.java2d.d3d.D3DScreenUpdateManager.run(D3DScreenUpdateManager.java:419)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 48 [Thread-23] TIMED_WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at bsh.util.JConsole$BlockingPipedInputStream.read(JConsole.java:771)\r\n                                   [       ]   at java.io.PipedInputStream.read(PipedInputStream.java:361)\r\n                                   [       ]   at java.io.InputStream.read(InputStream.java:82)\r\n                                   [       ]   at bsh.util.JConsole.inPipeWatcher(JConsole.java:667)\r\n                                   [       ]   at bsh.util.JConsole.run(JConsole.java:677)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 49 [BeanShell interpreter] TIMED_WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.io.PipedInputStream.read(PipedInputStream.java:310)\r\n                                   [       ]   at java.io.PipedInputStream.read(PipedInputStream.java:361)\r\n                                   [       ]   at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:264)\r\n                                   [       ]   at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:306)\r\n                                   [       ]   at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:158)\r\n                                   [       ]   at java.io.InputStreamReader.read(InputStreamReader.java:167)\r\n                                   [       ]   at bsh.JavaCharStream.FillBuff(JavaCharStream.java:160)\r\n                                   [       ]   at bsh.JavaCharStream.ReadByte(JavaCharStream.java:188)\r\n                                   [       ]   at bsh.JavaCharStream.readChar(JavaCharStream.java:289)\r\n                                   [       ]   at bsh.JavaCharStream.BeginToken(JavaCharStream.java:209)\r\n                                   [       ]   at bsh.ParserTokenManager.getNextToken(ParserTokenManager.java:2072)\r\n                                   [       ]   at bsh.Parser.jj_ntk(Parser.java:6022)\r\n                                   [       ]   at bsh.Parser.Line(Parser.java:163)\r\n                                   [       ]   at bsh.Interpreter.Line(Interpreter.java:1011)\r\n                                   [       ]   at bsh.Interpreter.run(Interpreter.java:462)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 62 [Thread-33] TIMED_WAITING\r\n                                   [       ]   at java.lang.Thread.sleep(Native Method)\r\n                                   [       ]   at org.micromanager.display.internal.inspector.MetadataPanel.updateMetadata(MetadataPanel.java:262)\r\n                                   [       ]   at org.micromanager.display.internal.inspector.MetadataPanel.access$000(MetadataPanel.java:62)\r\n                                   [       ]   at org.micromanager.display.internal.inspector.MetadataPanel$1.run(MetadataPanel.java:107)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 63 [Thread-34] TIMED_WAITING\r\n                                   [       ]   at java.lang.Thread.sleep(Native Method)\r\n                                   [       ]   at org.micromanager.display.internal.inspector.CommentsPanel.updateComments(CommentsPanel.java:180)\r\n                                   [       ]   at org.micromanager.display.internal.inspector.CommentsPanel.access$000(CommentsPanel.java:46)\r\n                                   [       ]   at org.micromanager.display.internal.inspector.CommentsPanel$1.run(CommentsPanel.java:67)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 74 [Scrollbar panel update thread] TIMED_WAITING\r\n                                   [       ]   at java.lang.Thread.sleep(Native Method)\r\n                                   [       ]   at org.micromanager.display.internal.ScrollerPanel.runUpdateThread(ScrollerPanel.java:422)\r\n                                   [       ]   at org.micromanager.display.internal.ScrollerPanel.access$100(ScrollerPanel.java:68)\r\n                                   [       ]   at org.micromanager.display.internal.ScrollerPanel$1.run(ScrollerPanel.java:192)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 75 [zSelector] WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.lang.Object.wait(Object.java:485)\r\n                                   [       ]   at ij.gui.StackWindow.run(StackWindow.java:226)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 86 [FPS display blank] WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.lang.Object.wait(Object.java:485)\r\n                                   [       ]   at java.util.TimerThread.mainLoop(Timer.java:483)\r\n                                   [       ]   at java.util.TimerThread.run(Timer.java:462)\r\n                                   [       ] Thread 99 [TaggedImage sink thread] BLOCKED\r\n                                   [       ]   at org.micromanager.display.internal.CanvasUpdateQueue.enqueue(CanvasUpdateQueue.java:145)\r\n                                   [       ]   at org.micromanager.display.internal.CanvasUpdateQueue.redraw(CanvasUpdateQueue.java:544)\r\n                                   [       ]   at org.micromanager.display.internal.CanvasUpdateQueue.reapplyLUTs(CanvasUpdateQueue.java:535)\r\n                                   [       ]   at org.micromanager.display.internal.CanvasUpdateQueue.onNewDisplaySettings(CanvasUpdateQueue.java:576)\r\n                                   [       ]   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r\n                                   [       ]   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r\n                                   [       ]   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r\n                                   [       ]   at java.lang.reflect.Method.invoke(Method.java:597)\r\n                                   [       ]   at com.google.common.eventbus.EventSubscriber.handleEvent(EventSubscriber.java:74)\r\n                                   [       ]   at com.google.common.eventbus.SynchronizedEventSubscriber.handleEvent(SynchronizedEventSubscriber.java:47)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.dispatch(EventBus.java:322)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:304)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.post(EventBus.java:275)\r\n                                   [       ]   at org.micromanager.display.internal.DefaultDisplayWindow.setDisplaySettings(DefaultDisplayWindow.java:791)\r\n                                   [       ]   at org.micromanager.display.internal.DefaultDisplayWindow.setDisplaySettings(DefaultDisplayWindow.java:773)\r\n                                   [       ]   at org.micromanager.display.internal.DefaultDisplayWindow.receiveNewImage(DefaultDisplayWindow.java:1094)\r\n                                   [       ]   at org.micromanager.display.internal.DefaultDisplayWindow.onNewImage(DefaultDisplayWindow.java:1062)\r\n                                   [       ]   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r\n                                   [       ]   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r\n                                   [       ]   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r\n                                   [       ]   at java.lang.reflect.Method.invoke(Method.java:597)\r\n                                   [       ]   at com.google.common.eventbus.EventSubscriber.handleEvent(EventSubscriber.java:74)\r\n                                   [       ]   at com.google.common.eventbus.SynchronizedEventSubscriber.handleEvent(SynchronizedEventSubscriber.java:47)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.dispatch(EventBus.java:322)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:304)\r\n                                   [       ]   at com.google.common.eventbus.EventBus.post(EventBus.java:275)\r\n                                   [       ]   at org.micromanager.internal.utils.PrioritizedEventBus.post(PrioritizedEventBus.java:63)\r\n                                   [       ]   at org.micromanager.data.internal.DefaultDatastore.putImage(DefaultDatastore.java:202)\r\n                                   [       ]   at org.micromanager.data.internal.pipeline.DefaultPipeline.insertImage(DefaultPipeline.java:111)\r\n                                   [       ]   at org.micromanager.acquisition.internal.DefaultTaggedImageSink$1.run(DefaultTaggedImageSink.java:70)\r\n                                   [       ] Thread 103 [Scrollbar panel update thread] TIMED_WAITING\r\n                                   [       ]   at java.lang.Thread.sleep(Native Method)\r\n                                   [       ]   at org.micromanager.display.internal.ScrollerPanel.runUpdateThread(ScrollerPanel.java:422)\r\n                                   [       ]   at org.micromanager.display.internal.ScrollerPanel.access$100(ScrollerPanel.java:68)\r\n                                   [       ]   at org.micromanager.display.internal.ScrollerPanel$1.run(ScrollerPanel.java:192)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 104 [zSelector] WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.lang.Object.wait(Object.java:485)\r\n                                   [       ]   at ij.gui.StackWindow.run(StackWindow.java:226)\r\n                                   [       ]   at java.lang.Thread.run(Thread.java:662)\r\n                                   [       ] Thread 106 [FPS display blank] WAITING\r\n                                   [       ]   at java.lang.Object.wait(Native Method)\r\n                                   [       ]   at java.lang.Object.wait(Object.java:485)\r\n                                   [       ]   at java.util.TimerThread.mainLoop(Timer.java:483)\r\n                                   [       ]   at java.util.TimerThread.run(Timer.java:462)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/micro-manager/micro-manager/issues/comments/258498176","html_url":"https://github.com/micro-manager/micro-manager/issues/480#issuecomment-258498176","issue_url":"https://api.github.com/repos/micro-manager/micro-manager/issues/480","id":258498176,"user":{"login":"kthorn","id":484758,"avatar_url":"https://avatars.githubusercontent.com/u/484758?v=3","gravatar_id":"","url":"https://api.github.com/users/kthorn","html_url":"https://github.com/kthorn","followers_url":"https://api.github.com/users/kthorn/followers","following_url":"https://api.github.com/users/kthorn/following{/other_user}","gists_url":"https://api.github.com/users/kthorn/gists{/gist_id}","starred_url":"https://api.github.com/users/kthorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kthorn/subscriptions","organizations_url":"https://api.github.com/users/kthorn/orgs","repos_url":"https://api.github.com/users/kthorn/repos","events_url":"https://api.github.com/users/kthorn/events{/privacy}","received_events_url":"https://api.github.com/users/kthorn/received_events","type":"User","site_admin":false},"created_at":"2016-11-04T17:36:19Z","updated_at":"2016-11-04T17:36:19Z","body":"I see what looks like the same hang in the latest nightly build. I was able to acquire a few images before it occurred, so it appears to be sporadic."}}
{"actor":{"display_login":"kthorn"}}