<font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
<span>Hi Johannes,<br><br>Now I have taken the threaddump after pressing the button that gets stuck<br>
and I didn't find anything about a dead lock.<br><br>Anyway I post the threaddump here, maybe you can find something since I<br>
really don't what every line means.<br><br><b>2013-09-30 11:29:41<br>Full thread dump Java HotSpot(TM) Client VM (19.1-b02 mixed mode):<br>
<br>"AWT-EventQueue-0" prio=6 tid=0x066a4800 nid=0x15e0 in Object.wait() [0x6376f000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
at java.lang.Object.wait(Object.java:485)<br> at java.awt.EventQueue.getNextEvent(EventQueue.java:485)<br>
- locked <0x1258db18> (a java.awt.EventQueue)<br>
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:236)<br>
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br>
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br>
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br>
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br>
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br>
<br> Locked ownable synchronizers:<br> - None<br>
<br>"RMI TCP Connection(2)-10.84.201.117" daemon prio=6 tid=0x09c7c000 nid=0x123c runnable [0x63d6f000]<br>
java.lang.Thread.State: RUNNABLE<br> at java.net.SocketInputStream.socketRead0(Native Method)<br>
at java.net.SocketInputStream.read(SocketInputStream.java:129)<br>
at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)<br>
at java.io.BufferedInputStream.read(BufferedInputStream.java:237)<br>
- locked <0x12da32e8> (a java.io.BufferedInputStream)<br>
at java.io.FilterInputStream.read(FilterInputStream.java:66)<br>
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:517)<br>
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:790)<br>
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:649)<br>
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)<br>
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- <0x12da49b8> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)<br>
<br>"JMX server connection timeout 60" daemon prio=6 tid=0x082ae400 nid=0x120c in Object.wait() [0x63b6f000]<br>
java.lang.Thread.State: TIMED_WAITING (on object monitor)<br>
at java.lang.Object.wait(Native Method)<br> at com.sun.jmx.remote.internal.ServerCommunicatorAdmin$Timeout.run(ServerCommunicatorAdmin.java:150)<br>
- locked <0x136d62c0> (a [I)<br> at java.lang.Thread.run(Thread.java:662)<br>
<br> Locked ownable synchronizers:<br> - None<br>
<br>"RMI Scheduler(0)" daemon prio=6 tid=0x07f0b400 nid=0x5f8 waiting on condition [0x6396f000]<br>
java.lang.Thread.State: TIMED_WAITING (parking)<br> at sun.misc.Unsafe.park(Native Method)<br>
- parking to wait for <0x1259f038> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)<br>
at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:198)<br>
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2025)<br>
at java.util.concurrent.DelayQueue.take(DelayQueue.java:164)<br>
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:609)<br>
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:602)<br>
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)<br>
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"RMI TCP Accept-0" daemon prio=6 tid=0x09e1b400 nid=0x179c runnable [0x633ef000]<br>
java.lang.Thread.State: RUNNABLE<br> at java.net.PlainSocketImpl.socketAccept(Native Method)<br>
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:408)<br>
- locked <0x12905d18> (a java.net.SocksSocketImpl)<br>
at java.net.ServerSocket.implAccept(ServerSocket.java:462)<br>
at java.net.ServerSocket.accept(ServerSocket.java:430)<br>
at sun.management.jmxremote.LocalRMIServerSocketFactory$1.accept(LocalRMIServerSocketFactory.java:34)<br>
at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:369)<br>
at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:341)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"Display thread" prio=6 tid=0x09e6e400 nid=0xd84 waiting on condition [0x630ef000]<br>
java.lang.Thread.State: WAITING (parking)<br> at sun.misc.Unsafe.park(Native Method)<br>
- parking to wait for <0x133dd148> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)<br>
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)<br>
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)<br>
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)<br>
at org.micromanager.MMStudioMainFrame$9.run(MMStudioMainFrame.java:681)<br>
<br> Locked ownable synchronizers:<br> - None<br>
<br>"zSelector" prio=6 tid=0x09e1fc00 nid=0x1390 in Object.wait() [0x62eef000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
at java.lang.Object.wait(Object.java:485)<br> at ij.gui.StackWindow.run(StackWindow.java:205)<br>
- locked <0x1339f840> (a org.micromanager.acquisition.VirtualAcquisitionDisplay$DisplayWindow)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"Timer-2" prio=6 tid=0x0a0c1400 nid=0xeb8 in Object.wait() [0x62aef000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
at java.lang.Object.wait(Object.java:485)<br> at java.util.TimerThread.mainLoop(Timer.java:483)<br>
- locked <0x12a44bc0> (a java.util.TaskQueue)<br>
at java.util.TimerThread.run(Timer.java:462)<br><br>
Locked ownable synchronizers:<br> - None<br>
<br>"Timer-1" prio=6 tid=0x0a0c3c00 nid=0x1564 in Object.wait() [0x628ef000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
at java.lang.Object.wait(Object.java:485)<br> at java.util.TimerThread.mainLoop(Timer.java:483)<br>
- locked <0x12bed7b0> (a java.util.TaskQueue)<br>
at java.util.TimerThread.run(Timer.java:462)<br><br>
Locked ownable synchronizers:<br> - None<br>
<br>"Live mode timer" prio=6 tid=0x09e8e400 nid=0xfdc in Object.wait() [0x60b3f000]<br>
java.lang.Thread.State: TIMED_WAITING (on object monitor)<br>
at java.lang.Object.wait(Native Method)<br> at java.util.TimerThread.mainLoop(Timer.java:509)<br>
- locked <0x12bed990> (a java.util.TaskQueue)<br>
at java.util.TimerThread.run(Timer.java:462)<br><br>
Locked ownable synchronizers:<br> - None<br>
<br>"Timer-0" daemon prio=6 tid=0x09efd400 nid=0x1518 runnable [0x0e98f000]<br>
java.lang.Thread.State: RUNNABLE<br> at mmcorej.MMCoreJJNI.CMMCore_getYPosition(Native Method)<br>
at mmcorej.CMMCore.getYPosition(CMMCore.java:1055)<br>
at spim.setup.GenericXYStage$SubStage.getPosition(GenericXYStage.java:78)<br>
at spim.SPIMAcquisition.updateMotorPositions(SPIMAcquisition.java:1236)<br>
at spim.SPIMAcquisition.access$600(SPIMAcquisition.java:92)<br>
at spim.SPIMAcquisition$18.run(SPIMAcquisition.java:1014)<br>
at java.util.TimerThread.mainLoop(Timer.java:512)<br>
at java.util.TimerThread.run(Timer.java:462)<br><br>
Locked ownable synchronizers:<br> - None<br>
<br>"Beanshell interpreter" prio=6 tid=0x0a172400 nid=0x1174 in Object.wait() [0x0e78f000]<br>
java.lang.Thread.State: TIMED_WAITING (on object monitor)<br>
at java.lang.Object.wait(Native Method)<br> at java.io.PipedInputStream.read(PipedInputStream.java:310)<br>
- locked <0x12d90f30> (a java.io.PipedInputStream)<br>
at java.io.PipedInputStream.read(PipedInputStream.java:361)<br>
- locked <0x12d90f30> (a java.io.PipedInputStream)<br>
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:264)<br>
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:306)<br>
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:158)<br>
- locked <0x12d8ada8> (a java.io.InputStreamReader)<br>
at java.io.InputStreamReader.read(InputStreamReader.java:167)<br>
at bsh.JavaCharStream.FillBuff(Unknown Source)<br> at bsh.JavaCharStream.ReadByte(Unknown Source)<br>
at bsh.JavaCharStream.readChar(Unknown Source)<br> at bsh.JavaCharStream.BeginToken(Unknown Source)<br>
at bsh.ParserTokenManager.getNextToken(Unknown Source)<br>
at bsh.Parser.jj_ntk(Unknown Source)<br> at bsh.Parser.Line(Unknown Source)<br>
at bsh.Interpreter.Line(Unknown Source)<br> at bsh.Interpreter.run(Unknown Source)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"Thread-6" prio=6 tid=0x09fdb800 nid=0xd88 in Object.wait() [0x0b0df000]<br>
java.lang.Thread.State: TIMED_WAITING (on object monitor)<br>
at java.lang.Object.wait(Native Method)<br> at bsh.util.JConsole$BlockingPipedInputStream.read(Unknown Source)<br>
- locked <0x12cea9a8> (a bsh.util.JConsole$BlockingPipedInputStream)<br>
at java.io.PipedInputStream.read(PipedInputStream.java:361)<br>
- locked <0x12cea9a8> (a bsh.util.JConsole$BlockingPipedInputStream)<br>
at java.io.InputStream.read(InputStream.java:85)<br>
at bsh.util.JConsole.inPipeWatcher(Unknown Source)<br>
at bsh.util.JConsole.run(Unknown Source)<br> at java.lang.Thread.run(Thread.java:662)<br>
<br> Locked ownable synchronizers:<br> - None<br>
<br>"Swing-Shell" daemon prio=6 tid=0x09e8fc00 nid=0x10a8 waiting on condition [0x0b2df000]<br>
java.lang.Thread.State: WAITING (parking)<br> at sun.misc.Unsafe.park(Native Method)<br>
- parking to wait for <0x12ceab50> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)<br>
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)<br>
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)<br>
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)<br>
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)<br>
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)<br>
at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Win32ShellFolderManager2.java:492)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"TimerQueue" daemon prio=6 tid=0x09c7d000 nid=0x1684 in Object.wait() [0x0aedf000]<br>
java.lang.Thread.State: TIMED_WAITING (on object monitor)<br>
at java.lang.Object.wait(Native Method)<br> at javax.swing.TimerQueue.run(TimerQueue.java:232)<br>
- locked <0x120b0820> (a javax.swing.TimerQueue)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"DestroyJavaVM" prio=6 tid=0x00a3ac00 nid=0xf14 waiting on condition [0x00000000]<br>
java.lang.Thread.State: RUNNABLE<br><br> Locked ownable synchronizers:<br>
- None<br><br>"GC Daemon" daemon prio=2 tid=0x07b79400 nid=0x177c in Object.wait() [0x0948f000]<br>
java.lang.Thread.State: TIMED_WAITING (on object monitor)<br>
at java.lang.Object.wait(Native Method)<br> - waiting on <0x12595b38> (a sun.misc.GC$LatencyLock)<br>
at sun.misc.GC$Daemon.run(GC.java:100)<br> - locked <0x12595b38> (a sun.misc.GC$LatencyLock)<br>
<br> Locked ownable synchronizers:<br> - None<br>
<br>"RMI Reaper" prio=6 tid=0x06689400 nid=0xdf4 in Object.wait() [0x0928f000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
- waiting on <0x12595b48> (a java.lang.ref.ReferenceQueue$Lock)<br>
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)<br>
- locked <0x12595b48> (a java.lang.ref.ReferenceQueue$Lock)<br>
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)<br>
at sun.rmi.transport.ObjectTable$Reaper.run(ObjectTable.java:333)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"RMI TCP Accept-0" daemon prio=6 tid=0x07bdf400 nid=0x16ac runnable [0x0908f000]<br>
java.lang.Thread.State: RUNNABLE<br> at java.net.PlainSocketImpl.socketAccept(Native Method)<br>
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:408)<br>
- locked <0x125308d0> (a java.net.SocksSocketImpl)<br>
at java.net.ServerSocket.implAccept(ServerSocket.java:462)<br>
at java.net.ServerSocket.accept(ServerSocket.java:430)<br>
at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:369)<br>
at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:341)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"AWT-Windows" daemon prio=6 tid=0x07af9400 nid=0x14d8 runnable [0x08dff000]<br>
java.lang.Thread.State: RUNNABLE<br> at sun.awt.windows.WToolkit.eventLoop(Native Method)<br>
at sun.awt.windows.WToolkit.run(WToolkit.java:293)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"AWT-Shutdown" prio=6 tid=0x07aa8400 nid=0x17d8 in Object.wait() [0x08bff000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
at java.lang.Object.wait(Object.java:485)<br> at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)<br>
- locked <0x125957c8> (a java.lang.Object)<br>
at java.lang.Thread.run(Thread.java:662)<br><br> Locked ownable synchronizers:<br>
- None<br><br>"Java2D Disposer" daemon prio=10 tid=0x06600400 nid=0xef0 in Object.wait() [0x089ff000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)<br>
- locked <0x1258f1f8> (a java.lang.ref.ReferenceQueue$Lock)<br>
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)<br>
at sun.java2d.Disposer.run(Disposer.java:127)<br> at java.lang.Thread.run(Thread.java:662)<br>
<br> Locked ownable synchronizers:<br> - None<br>
<br>"Low Memory Detector" daemon prio=6 tid=0x0656f800 nid=0x171c runnable [0x00000000]<br>
java.lang.Thread.State: RUNNABLE<br><br> Locked ownable synchronizers:<br>
- None<br><br>"CompilerThread0" daemon prio=10 tid=0x06569400 nid=0x778 waiting on condition [0x00000000]<br>
java.lang.Thread.State: RUNNABLE<br><br> Locked ownable synchronizers:<br>
- None<br><br>"Attach Listener" daemon prio=10 tid=0x06567c00 nid=0x14a4 waiting on condition [0x00000000]<br>
java.lang.Thread.State: RUNNABLE<br><br> Locked ownable synchronizers:<br>
- None<br><br>"Signal Dispatcher" daemon prio=10 tid=0x06566800 nid=0x16d8 runnable [0x00000000]<br>
java.lang.Thread.State: RUNNABLE<br><br> Locked ownable synchronizers:<br>
- None<br><br>"Surrogate Locker Thread (CMS)" daemon prio=6 tid=0x06565000 nid=0x4e4 waiting on condition [0x00000000]<br>
java.lang.Thread.State: RUNNABLE<br><br> Locked ownable synchronizers:<br>
- None<br><br>"Finalizer" daemon prio=8 tid=0x06553400 nid=0x1458 in Object.wait() [0x06e9f000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)<br>
- locked <0x12165290> (a java.lang.ref.ReferenceQueue$Lock)<br>
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)<br>
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)<br>
<br> Locked ownable synchronizers:<br> - None<br>
<br>"Reference Handler" daemon prio=10 tid=0x06552000 nid=0x16e4 in Object.wait() [0x06c9f000]<br>
java.lang.Thread.State: WAITING (on object monitor)<br> at java.lang.Object.wait(Native Method)<br>
at java.lang.Object.wait(Object.java:485)<br> at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)<br>
- locked <0x121652a0> (a java.lang.ref.Reference$Lock)<br>
<br> Locked ownable synchronizers:<br> - None<br>
<br>"VM Thread" prio=10 tid=0x0654e400 nid=0x16dc runnable <br><br>"Gang worker#0 (Parallel GC Threads)" prio=10 tid=0x009a7400 nid=0xc40 runnable <br>
<br>"Gang worker#1 (Parallel GC Threads)" prio=10 tid=0x009a9000 nid=0x1620 runnable <br>
<br>"Concurrent Mark-Sweep GC Thread" prio=10 tid=0x009afc00 nid=0xa58 runnable <br>
"VM Periodic Task Thread" prio=10 tid=0x0657a000 nid=0xacc waiting on condition <br>
<br>JNI global references: 4648<br><br><br></b>Kind regards, <br>Edgar<br>
<br><table border="0" cellpadding="0" cellspacing="0" width="457,5"><tbody>
<tr><td colspan="3"><font face="sans-serif" size="2">_________________________________________________________________________<br>
<br>Fraunhofer-Institut für Produktionstechnologie IPT <br>Edgar Escobar Nieto <br>
<br><br> <br> <br>Steinbachstraße 17 <br>52074 Aachen <br><br>edgar.escobar.nieto@ipt.fraunhofer.de </font>
<font color="blue" size="3"><u><br></u></font><a href="http://www.ipt.fraunhofer.de/">
<font color="blue" face="sans-serif" size="2"><u>http://www.ipt.fraunhofer.de</u>
</font></a><font face="sans-serif" size="2"><br>_________________________________________________________________________</font>
<br></td></tr><tr><td valign="top" width="225"><br></td><td width="7,5">
<br></td><td valign="top" width="225"><br></td></tr></tbody></table></span>
<br><br><font color="#990099">-----Johannes Schindelin <Johannes.Schindelin@gmx.de> schrieb: -----</font>
<div style="padding-left:5px;"><div style="padding-right:0px;padding-left:5px;border-left:solid black 2px;">
An: edgar.escobar.nieto@ipt.fraunhofer.de<br>Von: Johannes Schindelin <Johannes.Schindelin@gmx.de><br>
Datum: 27.09.2013 20:40<br>Kopie: openspim@openspim.org, Luke Stuyvenberg <stuyvenberg@wisc.edu><br>
Betreff: Re: [OpenSPIM] SPIMage plugin_Stack at this Z plus<br><br><div>
<font face="Courier New,Courier,monospace" size="2">Hi Edgar,<br><br>On Fri, 27 Sep 2013, edgar.escobar.nieto@ipt.fraunhofer.de wrote:<br>
<br>> Sorry for the late reply, it was a little bit hard to understand the<br>
> instructions about finding the "dead lock" since I am not a programming<br>
> guy :-/. It is the first time I do that.<br>> <br>> I already look through the lines of the threaddump and I didn't find<br>
> anything like "dead lock detected between thread 2 and 17" so, is there<br>
> something else I could do in order to find a solution to this?<br>
<br>Have you taken the thread dump after pressing that button that gets stuck?<br>
How about posting the thread dump here?<br><br>Ciao,<br>Johannes<br></font>
</div></div></div><div></div></font>