[OpenSPIM] SPIMage plugin_Stack at this Z plus

Mon Sep 30 04:43:20 CDT 2013

 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)
ÿÿÿ at java.lang.Object.wait(Object.java:485)
ÿÿÿ at ij.gui.StackWindow.run(StackWindow.java:205)
ÿÿÿ - locked <0x1339f840> (a org.micromanager.acquisition.VirtualAcquisitionDisplay$DisplayWindow)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Timer-2" prio=6 tid=0x0a0c1400 nid=0xeb8 in Object.wait() [0x62aef000]
ÿÿ java.lang.Thread.State: WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at java.lang.Object.wait(Object.java:485)
ÿÿÿ at java.util.TimerThread.mainLoop(Timer.java:483)
ÿÿÿ - locked <0x12a44bc0> (a java.util.TaskQueue)
ÿÿÿ at java.util.TimerThread.run(Timer.java:462)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Timer-1" prio=6 tid=0x0a0c3c00 nid=0x1564 in Object.wait() [0x628ef000]
ÿÿ java.lang.Thread.State: WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at java.lang.Object.wait(Object.java:485)
ÿÿÿ at java.util.TimerThread.mainLoop(Timer.java:483)
ÿÿÿ - locked <0x12bed7b0> (a java.util.TaskQueue)
ÿÿÿ at java.util.TimerThread.run(Timer.java:462)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Live mode timer" prio=6 tid=0x09e8e400 nid=0xfdc in Object.wait() [0x60b3f000]
ÿÿ java.lang.Thread.State: TIMED_WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at java.util.TimerThread.mainLoop(Timer.java:509)
ÿÿÿ - locked <0x12bed990> (a java.util.TaskQueue)
ÿÿÿ at java.util.TimerThread.run(Timer.java:462)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Timer-0" daemon prio=6 tid=0x09efd400 nid=0x1518 runnable [0x0e98f000]
ÿÿ java.lang.Thread.State: RUNNABLE
ÿÿÿ at mmcorej.MMCoreJJNI.CMMCore_getYPosition(Native Method)
ÿÿÿ at mmcorej.CMMCore.getYPosition(CMMCore.java:1055)
ÿÿÿ at spim.setup.GenericXYStage$SubStage.getPosition(GenericXYStage.java:78)
ÿÿÿ at spim.SPIMAcquisition.updateMotorPositions(SPIMAcquisition.java:1236)
ÿÿÿ at spim.SPIMAcquisition.access$600(SPIMAcquisition.java:92)
ÿÿÿ at spim.SPIMAcquisition$18.run(SPIMAcquisition.java:1014)
ÿÿÿ at java.util.TimerThread.mainLoop(Timer.java:512)
ÿÿÿ at java.util.TimerThread.run(Timer.java:462)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Beanshell interpreter" prio=6 tid=0x0a172400 nid=0x1174 in Object.wait() [0x0e78f000]
ÿÿ java.lang.Thread.State: TIMED_WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at java.io.PipedInputStream.read(PipedInputStream.java:310)
ÿÿÿ - locked <0x12d90f30> (a java.io.PipedInputStream)
ÿÿÿ at java.io.PipedInputStream.read(PipedInputStream.java:361)
ÿÿÿ - locked <0x12d90f30> (a java.io.PipedInputStream)
ÿÿÿ at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:264)
ÿÿÿ at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:306)
ÿÿÿ at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:158)
ÿÿÿ - locked <0x12d8ada8> (a java.io.InputStreamReader)
ÿÿÿ at java.io.InputStreamReader.read(InputStreamReader.java:167)
ÿÿÿ at bsh.JavaCharStream.FillBuff(Unknown Source)
ÿÿÿ at bsh.JavaCharStream.ReadByte(Unknown Source)
ÿÿÿ at bsh.JavaCharStream.readChar(Unknown Source)
ÿÿÿ at bsh.JavaCharStream.BeginToken(Unknown Source)
ÿÿÿ at bsh.ParserTokenManager.getNextToken(Unknown Source)
ÿÿÿ at bsh.Parser.jj_ntk(Unknown Source)
ÿÿÿ at bsh.Parser.Line(Unknown Source)
ÿÿÿ at bsh.Interpreter.Line(Unknown Source)
ÿÿÿ at bsh.Interpreter.run(Unknown Source)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Thread-6" prio=6 tid=0x09fdb800 nid=0xd88 in Object.wait() [0x0b0df000]
ÿÿ java.lang.Thread.State: TIMED_WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at bsh.util.JConsole$BlockingPipedInputStream.read(Unknown Source)
ÿÿÿ - locked <0x12cea9a8> (a bsh.util.JConsole$BlockingPipedInputStream)
ÿÿÿ at java.io.PipedInputStream.read(PipedInputStream.java:361)
ÿÿÿ - locked <0x12cea9a8> (a bsh.util.JConsole$BlockingPipedInputStream)
ÿÿÿ at java.io.InputStream.read(InputStream.java:85)
ÿÿÿ at bsh.util.JConsole.inPipeWatcher(Unknown Source)
ÿÿÿ at bsh.util.JConsole.run(Unknown Source)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Swing-Shell" daemon prio=6 tid=0x09e8fc00 nid=0x10a8 waiting on condition [0x0b2df000]
ÿÿ java.lang.Thread.State: WAITING (parking)
ÿÿÿ at sun.misc.Unsafe.park(Native Method)
ÿÿÿ - parking to wait forÿ <0x12ceab50> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
ÿÿÿ at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
ÿÿÿ at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
ÿÿÿ at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
ÿÿÿ at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
ÿÿÿ at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
ÿÿÿ at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Win32ShellFolderManager2.java:492)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"TimerQueue" daemon prio=6 tid=0x09c7d000 nid=0x1684 in Object.wait() [0x0aedf000]
ÿÿ java.lang.Thread.State: TIMED_WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at javax.swing.TimerQueue.run(TimerQueue.java:232)
ÿÿÿ - locked <0x120b0820> (a javax.swing.TimerQueue)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"DestroyJavaVM" prio=6 tid=0x00a3ac00 nid=0xf14 waiting on condition [0x00000000]
ÿÿ java.lang.Thread.State: RUNNABLE

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"GC Daemon" daemon prio=2 tid=0x07b79400 nid=0x177c in Object.wait() [0x0948f000]
ÿÿ java.lang.Thread.State: TIMED_WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ - waiting on <0x12595b38> (a sun.misc.GC$LatencyLock)
ÿÿÿ at sun.misc.GC$Daemon.run(GC.java:100)
ÿÿÿ - locked <0x12595b38> (a sun.misc.GC$LatencyLock)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"RMI Reaper" prio=6 tid=0x06689400 nid=0xdf4 in Object.wait() [0x0928f000]
ÿÿ java.lang.Thread.State: WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ - waiting on <0x12595b48> (a java.lang.ref.ReferenceQueue$Lock)
ÿÿÿ at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
ÿÿÿ - locked <0x12595b48> (a java.lang.ref.ReferenceQueue$Lock)
ÿÿÿ at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
ÿÿÿ at sun.rmi.transport.ObjectTable$Reaper.run(ObjectTable.java:333)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"RMI TCP Accept-0" daemon prio=6 tid=0x07bdf400 nid=0x16ac runnable [0x0908f000]
ÿÿ java.lang.Thread.State: RUNNABLE
ÿÿÿ at java.net.PlainSocketImpl.socketAccept(Native Method)
ÿÿÿ at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:408)
ÿÿÿ - locked <0x125308d0> (a java.net.SocksSocketImpl)
ÿÿÿ at java.net.ServerSocket.implAccept(ServerSocket.java:462)
ÿÿÿ at java.net.ServerSocket.accept(ServerSocket.java:430)
ÿÿÿ at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:369)
ÿÿÿ at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:341)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"AWT-Windows" daemon prio=6 tid=0x07af9400 nid=0x14d8 runnable [0x08dff000]
ÿÿ java.lang.Thread.State: RUNNABLE
ÿÿÿ at sun.awt.windows.WToolkit.eventLoop(Native Method)
ÿÿÿ at sun.awt.windows.WToolkit.run(WToolkit.java:293)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"AWT-Shutdown" prio=6 tid=0x07aa8400 nid=0x17d8 in Object.wait() [0x08bff000]
ÿÿ java.lang.Thread.State: WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at java.lang.Object.wait(Object.java:485)
ÿÿÿ at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)
ÿÿÿ - locked <0x125957c8> (a java.lang.Object)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Java2D Disposer" daemon prio=10 tid=0x06600400 nid=0xef0 in Object.wait() [0x089ff000]
ÿÿ java.lang.Thread.State: WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
ÿÿÿ - locked <0x1258f1f8> (a java.lang.ref.ReferenceQueue$Lock)
ÿÿÿ at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
ÿÿÿ at sun.java2d.Disposer.run(Disposer.java:127)
ÿÿÿ at java.lang.Thread.run(Thread.java:662)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Low Memory Detector" daemon prio=6 tid=0x0656f800 nid=0x171c runnable [0x00000000]
ÿÿ java.lang.Thread.State: RUNNABLE

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"CompilerThread0" daemon prio=10 tid=0x06569400 nid=0x778 waiting on condition [0x00000000]
ÿÿ java.lang.Thread.State: RUNNABLE

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Attach Listener" daemon prio=10 tid=0x06567c00 nid=0x14a4 waiting on condition [0x00000000]
ÿÿ java.lang.Thread.State: RUNNABLE

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Signal Dispatcher" daemon prio=10 tid=0x06566800 nid=0x16d8 runnable [0x00000000]
ÿÿ java.lang.Thread.State: RUNNABLE

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Surrogate Locker Thread (CMS)" daemon prio=6 tid=0x06565000 nid=0x4e4 waiting on condition [0x00000000]
ÿÿ java.lang.Thread.State: RUNNABLE

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Finalizer" daemon prio=8 tid=0x06553400 nid=0x1458 in Object.wait() [0x06e9f000]
ÿÿ java.lang.Thread.State: WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
ÿÿÿ - locked <0x12165290> (a java.lang.ref.ReferenceQueue$Lock)
ÿÿÿ at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
ÿÿÿ at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - None

"Reference Handler" daemon prio=10 tid=0x06552000 nid=0x16e4 in Object.wait() [0x06c9f000]
ÿÿ java.lang.Thread.State: WAITING (on object monitor)
ÿÿÿ at java.lang.Object.wait(Native Method)
ÿÿÿ at java.lang.Object.wait(Object.java:485)
ÿÿÿ at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
ÿÿÿ - locked <0x121652a0> (a java.lang.ref.Reference$Lock)

ÿÿ Locked ownable synchronizers:
ÿÿÿ - 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 fr Produktionstechnologie IPT 
Edgar Escobar Nieto  

Steinbachstraáe 17 
52074 Aachen 

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

-----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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