[OpenSPIM] SPIMage plugin_Stack at this Z plus

edgar.escobar.nieto at ipt.fraunhofer.de edgar.escobar.nieto at ipt.fraunhofer.de
Tue Oct 8 12:38:09 CDT 2013 

Hi Luke,

I attach a corelog that was just made. In the OpenSPIM.app folder also appears a .log file named hs_err_pid5456, maybe
could be helpful as well. I have to point out that I am not controlling the laser using the plugin (the laser I am using
is not supported by MicroManager) so as happen with Aurelia a message is shown saying that my setup appears to be invalid
before executing the acquire SPIM image plugin.

Kind regards,
Edgar

 _________________________________________________________________________

Fraunhofer-Institut für Produktionstechnologie IPT 
Edgar Escobar Nieto  
 

 
 
Steinbachstraße 17 
52074 Aachen 

edgar.escobar.nieto at ipt.fraunhofer.de 
http://www.ipt.fraunhofer.de
_________________________________________________________________________
 
 
 


-----Luke Stuyvenberg <stuyvenberg at wisc.edu> schrieb: -----
An: edgar.escobar.nieto at ipt.fraunhofer.de, Johannes Schindelin <Johannes.Schindelin at gmx.de>
Von: Luke Stuyvenberg <stuyvenberg at wisc.edu>
Datum: 07.10.2013 22:35
Kopie: openspim at openspim.org
Betreff: Re: [OpenSPIM] SPIMage plugin_Stack at this Z plus

Hi Edgar,

Nothing in this thread dump seems to me to indicate a dead lock of any kind -- however, I suspect the issue with 'insert stack at this Z plus' is being caused by an exception being thrown and not being presented to the user interface. Would you kindly attach a core log of a session with this issue? There may be useful information there.


Thanks,
Luke

On 09/30/13, edgar.escobar.nieto at ipt.fraunhofer.de wrote:
> Hi Johannes,
> 
> Now I have taken the threaddump after pressing the button that gets stuck
> and I didn't find anything about a dead lock.
> 
> Anyway I post the threaddump here, maybe you can find something since I
> really don't what every line means.
> 
> 2013-09-30 11:29:41
> Full thread dump Java HotSpot(TM) Client VM (19.1-b02 mixed mode):
> 
> "AWT-EventQueue-0" prio=6 tid=0x066a4800 nid=0x15e0 in Object.wait() [0x6376f000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.lang.Object.wait(Object.java:485)
> at java.awt.EventQueue.getNextEvent(EventQueue.java:485)
> - locked <0x1258db18> (a java.awt.EventQueue)
> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:236)
> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> 
> Locked ownable synchronizers:
> - None
> 
> "RMI TCP Connection(2)-10.84.201.117" daemon prio=6 tid=0x09c7c000 nid=0x123c runnable [0x63d6f000]
> java.lang.Thread.State: RUNNABLE
> at java.net.SocketInputStream.socketRead0(Native Method)
> at java.net.SocketInputStream.read(SocketInputStream.java:129)
> at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
> at java.io.BufferedInputStream.read(BufferedInputStream.java:237)
> - locked <0x12da32e8> (a java.io.BufferedInputStream)
> at java.io.FilterInputStream.read(FilterInputStream.java:66)
> at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:517)
> at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:790)
> at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:649)
> at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - <0x12da49b8> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
> 
> "JMX server connection timeout 60" daemon prio=6 tid=0x082ae400 nid=0x120c in Object.wait() [0x63b6f000]
> java.lang.Thread.State: TIMED_WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at com.sun.jmx.remote.internal.ServerCommunicatorAdmin$Timeout.run(ServerCommunicatorAdmin.java:150)
> - locked <0x136d62c0> (a [I)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "RMI Scheduler(0)" daemon prio=6 tid=0x07f0b400 nid=0x5f8 waiting on condition [0x6396f000]
> java.lang.Thread.State: TIMED_WAITING (parking)
> at sun.misc.Unsafe.park(Native Method)
> - parking to wait for <0x1259f038> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
> at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:198)
> at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2025)
> at java.util.concurrent.DelayQueue.take(DelayQueue.java:164)
> at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:609)
> at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:602)
> at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "RMI TCP Accept-0" daemon prio=6 tid=0x09e1b400 nid=0x179c runnable [0x633ef000]
> java.lang.Thread.State: RUNNABLE
> at java.net.PlainSocketImpl.socketAccept(Native Method)
> at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:408)
> - locked <0x12905d18> (a java.net.SocksSocketImpl)
> at java.net.ServerSocket.implAccept(ServerSocket.java:462)
> at java.net.ServerSocket.accept(ServerSocket.java:430)
> at sun.management.jmxremote.LocalRMIServerSocketFactory$1.accept(LocalRMIServerSocketFactory.java:34)
> at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:369)
> at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:341)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "Display thread" prio=6 tid=0x09e6e400 nid=0xd84 waiting on condition [0x630ef000]
> java.lang.Thread.State: WAITING (parking)
> at sun.misc.Unsafe.park(Native Method)
> - parking to wait for <0x133dd148> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
> at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
> at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
> at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
> at org.micromanager.MMStudioMainFrame$9.run(MMStudioMainFrame.java:681)
> 
> Locked ownable synchronizers:
> - None
> 
> "zSelector" prio=6 tid=0x09e1fc00 nid=0x1390 in Object.wait() [0x62eef000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.lang.Object.wait(Object.java:485)
> at ij.gui.StackWindow.run(StackWindow.java:205)
> - locked <0x1339f840> (a org.micromanager.acquisition.VirtualAcquisitionDisplay$DisplayWindow)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "Timer-2" prio=6 tid=0x0a0c1400 nid=0xeb8 in Object.wait() [0x62aef000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.lang.Object.wait(Object.java:485)
> at java.util.TimerThread.mainLoop(Timer.java:483)
> - locked <0x12a44bc0> (a java.util.TaskQueue)
> at java.util.TimerThread.run(Timer.java:462)
> 
> Locked ownable synchronizers:
> - None
> 
> "Timer-1" prio=6 tid=0x0a0c3c00 nid=0x1564 in Object.wait() [0x628ef000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.lang.Object.wait(Object.java:485)
> at java.util.TimerThread.mainLoop(Timer.java:483)
> - locked <0x12bed7b0> (a java.util.TaskQueue)
> at java.util.TimerThread.run(Timer.java:462)
> 
> Locked ownable synchronizers:
> - None
> 
> "Live mode timer" prio=6 tid=0x09e8e400 nid=0xfdc in Object.wait() [0x60b3f000]
> java.lang.Thread.State: TIMED_WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.util.TimerThread.mainLoop(Timer.java:509)
> - locked <0x12bed990> (a java.util.TaskQueue)
> at java.util.TimerThread.run(Timer.java:462)
> 
> Locked ownable synchronizers:
> - None
> 
> "Timer-0" daemon prio=6 tid=0x09efd400 nid=0x1518 runnable [0x0e98f000]
> java.lang.Thread.State: RUNNABLE
> at mmcorej.MMCoreJJNI.CMMCore_getYPosition(Native Method)
> at mmcorej.CMMCore.getYPosition(CMMCore.java:1055)
> at spim.setup.GenericXYStage$SubStage.getPosition(GenericXYStage.java:78)
> at spim.SPIMAcquisition.updateMotorPositions(SPIMAcquisition.java:1236)
> at spim.SPIMAcquisition.access$600(SPIMAcquisition.java:92)
> at spim.SPIMAcquisition$18.run(SPIMAcquisition.java:1014)
> at java.util.TimerThread.mainLoop(Timer.java:512)
> at java.util.TimerThread.run(Timer.java:462)
> 
> Locked ownable synchronizers:
> - None
> 
> "Beanshell interpreter" prio=6 tid=0x0a172400 nid=0x1174 in Object.wait() [0x0e78f000]
> java.lang.Thread.State: TIMED_WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.io.PipedInputStream.read(PipedInputStream.java:310)
> - locked <0x12d90f30> (a java.io.PipedInputStream)
> at java.io.PipedInputStream.read(PipedInputStream.java:361)
> - locked <0x12d90f30> (a java.io.PipedInputStream)
> at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:264)
> at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:306)
> at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:158)
> - locked <0x12d8ada8> (a java.io.InputStreamReader)
> at java.io.InputStreamReader.read(InputStreamReader.java:167)
> at bsh.JavaCharStream.FillBuff(Unknown Source)
> at bsh.JavaCharStream.ReadByte(Unknown Source)
> at bsh.JavaCharStream.readChar(Unknown Source)
> at bsh.JavaCharStream.BeginToken(Unknown Source)
> at bsh.ParserTokenManager.getNextToken(Unknown Source)
> at bsh.Parser.jj_ntk(Unknown Source)
> at bsh.Parser.Line(Unknown Source)
> at bsh.Interpreter.Line(Unknown Source)
> at bsh.Interpreter.run(Unknown Source)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "Thread-6" prio=6 tid=0x09fdb800 nid=0xd88 in Object.wait() [0x0b0df000]
> java.lang.Thread.State: TIMED_WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at bsh.util.JConsole$BlockingPipedInputStream.read(Unknown Source)
> - locked <0x12cea9a8> (a bsh.util.JConsole$BlockingPipedInputStream)
> at java.io.PipedInputStream.read(PipedInputStream.java:361)
> - locked <0x12cea9a8> (a bsh.util.JConsole$BlockingPipedInputStream)
> at java.io.InputStream.read(InputStream.java:85)
> at bsh.util.JConsole.inPipeWatcher(Unknown Source)
> at bsh.util.JConsole.run(Unknown Source)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "Swing-Shell" daemon prio=6 tid=0x09e8fc00 nid=0x10a8 waiting on condition [0x0b2df000]
> java.lang.Thread.State: WAITING (parking)
> at sun.misc.Unsafe.park(Native Method)
> - parking to wait for <0x12ceab50> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
> at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
> at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
> at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
> at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
> at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Win32ShellFolderManager2.java:492)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "TimerQueue" daemon prio=6 tid=0x09c7d000 nid=0x1684 in Object.wait() [0x0aedf000]
> java.lang.Thread.State: TIMED_WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at javax.swing.TimerQueue.run(TimerQueue.java:232)
> - locked <0x120b0820> (a javax.swing.TimerQueue)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "DestroyJavaVM" prio=6 tid=0x00a3ac00 nid=0xf14 waiting on condition [0x00000000]
> java.lang.Thread.State: RUNNABLE
> 
> Locked ownable synchronizers:
> - None
> 
> "GC Daemon" daemon prio=2 tid=0x07b79400 nid=0x177c in Object.wait() [0x0948f000]
> java.lang.Thread.State: TIMED_WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> - waiting on <0x12595b38> (a sun.misc.GC$LatencyLock)
> at sun.misc.GC$Daemon.run(GC.java:100)
> - locked <0x12595b38> (a sun.misc.GC$LatencyLock)
> 
> Locked ownable synchronizers:
> - None
> 
> "RMI Reaper" prio=6 tid=0x06689400 nid=0xdf4 in Object.wait() [0x0928f000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> - waiting on <0x12595b48> (a java.lang.ref.ReferenceQueue$Lock)
> at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
> - locked <0x12595b48> (a java.lang.ref.ReferenceQueue$Lock)
> at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
> at sun.rmi.transport.ObjectTable$Reaper.run(ObjectTable.java:333)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "RMI TCP Accept-0" daemon prio=6 tid=0x07bdf400 nid=0x16ac runnable [0x0908f000]
> java.lang.Thread.State: RUNNABLE
> at java.net.PlainSocketImpl.socketAccept(Native Method)
> at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:408)
> - locked <0x125308d0> (a java.net.SocksSocketImpl)
> at java.net.ServerSocket.implAccept(ServerSocket.java:462)
> at java.net.ServerSocket.accept(ServerSocket.java:430)
> at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:369)
> at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:341)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "AWT-Windows" daemon prio=6 tid=0x07af9400 nid=0x14d8 runnable [0x08dff000]
> java.lang.Thread.State: RUNNABLE
> at sun.awt.windows.WToolkit.eventLoop(Native Method)
> at sun.awt.windows.WToolkit.run(WToolkit.java:293)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "AWT-Shutdown" prio=6 tid=0x07aa8400 nid=0x17d8 in Object.wait() [0x08bff000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.lang.Object.wait(Object.java:485)
> at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)
> - locked <0x125957c8> (a java.lang.Object)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "Java2D Disposer" daemon prio=10 tid=0x06600400 nid=0xef0 in Object.wait() [0x089ff000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
> - locked <0x1258f1f8> (a java.lang.ref.ReferenceQueue$Lock)
> at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
> at sun.java2d.Disposer.run(Disposer.java:127)
> at java.lang.Thread.run(Thread.java:662)
> 
> Locked ownable synchronizers:
> - None
> 
> "Low Memory Detector" daemon prio=6 tid=0x0656f800 nid=0x171c runnable [0x00000000]
> java.lang.Thread.State: RUNNABLE
> 
> Locked ownable synchronizers:
> - None
> 
> "CompilerThread0" daemon prio=10 tid=0x06569400 nid=0x778 waiting on condition [0x00000000]
> java.lang.Thread.State: RUNNABLE
> 
> Locked ownable synchronizers:
> - None
> 
> "Attach Listener" daemon prio=10 tid=0x06567c00 nid=0x14a4 waiting on condition [0x00000000]
> java.lang.Thread.State: RUNNABLE
> 
> Locked ownable synchronizers:
> - None
> 
> "Signal Dispatcher" daemon prio=10 tid=0x06566800 nid=0x16d8 runnable [0x00000000]
> java.lang.Thread.State: RUNNABLE
> 
> Locked ownable synchronizers:
> - None
> 
> "Surrogate Locker Thread (CMS)" daemon prio=6 tid=0x06565000 nid=0x4e4 waiting on condition [0x00000000]
> java.lang.Thread.State: RUNNABLE
> 
> Locked ownable synchronizers:
> - None
> 
> "Finalizer" daemon prio=8 tid=0x06553400 nid=0x1458 in Object.wait() [0x06e9f000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
> - locked <0x12165290> (a java.lang.ref.ReferenceQueue$Lock)
> at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
> at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
> 
> Locked ownable synchronizers:
> - None
> 
> "Reference Handler" daemon prio=10 tid=0x06552000 nid=0x16e4 in Object.wait() [0x06c9f000]
> java.lang.Thread.State: WAITING (on object monitor)
> at java.lang.Object.wait(Native Method)
> at java.lang.Object.wait(Object.java:485)
> at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
> - locked <0x121652a0> (a java.lang.ref.Reference$Lock)
> 
> Locked ownable synchronizers:
> - None
> 
> "VM Thread" prio=10 tid=0x0654e400 nid=0x16dc runnable 
> 
> "Gang worker#0 (Parallel GC Threads)" prio=10 tid=0x009a7400 nid=0xc40 runnable 
> 
> "Gang worker#1 (Parallel GC Threads)" prio=10 tid=0x009a9000 nid=0x1620 runnable 
> 
> "Concurrent Mark-Sweep GC Thread" prio=10 tid=0x009afc00 nid=0xa58 runnable 
> "VM Periodic Task Thread" prio=10 tid=0x0657a000 nid=0xacc waiting on condition 
> 
> JNI global references: 4648
> 
> 
> Kind regards, 
> Edgar
> 
> 
> 
> _________________________________________________________________________
> 
> Fraunhofer-Institut fr Produktionstechnologie IPT 
> Edgar Escobar Nieto 
> 
> 
> 
> 
> Steinbachstraáe 17 
> 52074 Aachen 
> 
> edgar.escobar.nieto at ipt.fraunhofer.de 
> http://www.ipt.fraunhofer.deÿ
> _________________________________________________________________________ 
> 
> 
> 
> 
> 
> 
> -----Johannes Schindelin <Johannes.Schindelin at gmx.de> schrieb: ----- An: edgar.escobar.nieto at ipt.fraunhofer.de
> Von: Johannes Schindelin <Johannes.Schindelin at gmx.de>
> Datum: 27.09.2013 20:40
> Kopie: openspim at openspim.org, Luke Stuyvenberg <stuyvenberg at wisc.edu>
> Betreff: Re: [OpenSPIM] SPIMage plugin_Stack at this Z plus
> 
> Hi Edgar,
> 
> On Fri, 27 Sep 2013, edgar.escobar.nieto at ipt.fraunhofer.de wrote:
> 
> > Sorry for the late reply, it was a little bit hard to understand the
> > instructions about finding the "dead lock" since I am not a programming
> > guy :-/. It is the first time I do that.
> > 
> > I already look through the lines of the threaddump and I didn't find
> > anything like "dead lock detected between thread 2 and 17" so, is there
> > something else I could do in order to find a solution to this?
> 
> Have you taken the thread dump after pressing that button that gets stuck?
> How about posting the thread dump here?
> 
> Ciao,
> Johannes
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