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  1. Jalview
  2. JAL-3917

Deadlock on J11 OSX launch via eclipse when clicking on menu bar whilst example file windows are opening

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2
    • Fix Version/s: None
    • Component/s: None
    • Labels:
    • Environment:
      Java version: 11.0.13
      Java Home: /Library/Java/JavaVirtualMachines/temurin-11.jdk/Contents/Home
      x86_64 Mac OS X 11.6

      Description

      Start jalview and immediatly try to open dropdown menus when the Jalvie desktop menubar appears. Reproducibly deadlocks - particularly when exampleFile_2_7.jvp is opened.

      Thread dump from jvisualvm suggests due to multiple threads operating on LaF & gui at same time..
      "Attach Listener" #41 daemon prio=9 os_prio=31 cpu=120.11ms elapsed=7.29s tid=0x00007f8a97a9f800 nid=0x11a0b waiting on condition [0x0000000000000000]
         java.lang.Thread.State: RUNNABLE

         Locked ownable synchronizers:
              - None

      "RMI TCP Accept-0" #42 daemon prio=9 os_prio=31 cpu=1.89ms elapsed=6.21s tid=0x00007f8a9fa98800 nid=0x1f40b runnable [0x0000700004ae9000]
         java.lang.Thread.State: RUNNABLE
              at java.net.PlainSocketImpl.socketAccept(java.base@11.0.13/Native Method)
              at java.net.AbstractPlainSocketImpl.accept(java.base@11.0.13/AbstractPlainSocketImpl.java:458)
              at java.net.ServerSocket.implAccept(java.base@11.0.13/ServerSocket.java:565)
              at java.net.ServerSocket.accept(java.base@11.0.13/ServerSocket.java:533)
              at sun.management.jmxremote.LocalRMIServerSocketFactory$1.accept(jdk.management.agent@11.0.13/LocalRMIServerSocketFactory.java:52)
              at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(java.rmi@11.0.13/TCPTransport.java:394)
              at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(java.rmi@11.0.13/TCPTransport.java:366)
              at java.lang.Thread.run(java.base@11.0.13/Thread.java:829)

         Locked ownable synchronizers:
              - None

      "RMI TCP Connection(1)-192.168.1.108" #43 daemon prio=9 os_prio=31 cpu=116.50ms elapsed=6.15s tid=0x00007f8a9fa5a000 nid=0xce0f runnable [0x0000700005917000]
         java.lang.Thread.State: RUNNABLE
              at java.net.SocketInputStream.socketRead0(java.base@11.0.13/Native Method)
              at java.net.SocketInputStream.socketRead(java.base@11.0.13/SocketInputStream.java:115)
              at java.net.SocketInputStream.read(java.base@11.0.13/SocketInputStream.java:168)
              at java.net.SocketInputStream.read(java.base@11.0.13/SocketInputStream.java:140)
              at java.io.BufferedInputStream.fill(java.base@11.0.13/BufferedInputStream.java:252)
              at java.io.BufferedInputStream.read(java.base@11.0.13/BufferedInputStream.java:271)
              - locked <0x00000007114db8c8> (a java.io.BufferedInputStream)
              at java.io.FilterInputStream.read(java.base@11.0.13/FilterInputStream.java:83)
              at sun.rmi.transport.tcp.TCPTransport.handleMessages(java.rmi@11.0.13/TCPTransport.java:544)
              at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(java.rmi@11.0.13/TCPTransport.java:796)
              at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(java.rmi@11.0.13/TCPTransport.java:677)
              at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler$$Lambda$404/0x00000008005e3c40.run(java.rmi@11.0.13/Unknown Source)
              at java.security.AccessController.doPrivileged(java.base@11.0.13/Native Method)
              at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(java.rmi@11.0.13/TCPTransport.java:676)
              at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@11.0.13/ThreadPoolExecutor.java:1128)
              at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@11.0.13/ThreadPoolExecutor.java:628)
              at java.lang.Thread.run(java.base@11.0.13/Thread.java:829)

         Locked ownable synchronizers:
              - <0x0000000711401890> (a java.util.concurrent.ThreadPoolExecutor$Worker)

      "RMI Scheduler(0)" #44 daemon prio=9 os_prio=31 cpu=0.27ms elapsed=6.12s tid=0x00007f8a9f9a2800 nid=0x7f07 waiting on condition [0x0000700005c22000]
         java.lang.Thread.State: TIMED_WAITING (parking)
              at jdk.internal.misc.Unsafe.park(java.base@11.0.13/Native Method)
              - parking to wait for <0x00000007115f6498> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
              at java.util.concurrent.locks.LockSupport.parkNanos(java.base@11.0.13/LockSupport.java:234)
              at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(java.base@11.0.13/AbstractQueuedSynchronizer.java:2123)
              at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(java.base@11.0.13/ScheduledThreadPoolExecutor.java:1182)
              at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(java.base@11.0.13/ScheduledThreadPoolExecutor.java:899)
              at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@11.0.13/ThreadPoolExecutor.java:1054)
              at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@11.0.13/ThreadPoolExecutor.java:1114)
              at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@11.0.13/ThreadPoolExecutor.java:628)
              at java.lang.Thread.run(java.base@11.0.13/Thread.java:829)

         Locked ownable synchronizers:
              - None

      "JMX server connection timeout 45" #45 daemon prio=9 os_prio=31 cpu=4.50ms elapsed=6.11s tid=0x00007f8a97a98000 nid=0x8207 in Object.wait() [0x000070000643a000]
         java.lang.Thread.State: TIMED_WAITING (on object monitor)
              at java.lang.Object.wait(java.base@11.0.13/Native Method)
              - waiting on <no object reference available>
              at com.sun.jmx.remote.internal.ServerCommunicatorAdmin$Timeout.run(java.management@11.0.13/ServerCommunicatorAdmin.java:171)
              - waiting to re-lock in wait() <0x00000007113297e8> (a [I)
              at java.lang.Thread.run(java.base@11.0.13/Thread.java:829)

         Locked ownable synchronizers:
              - None

      "VM Thread" os_prio=31 cpu=116.44ms elapsed=122.23s tid=0x00007f8a958e4800 nid=0x3303 runnable

      "GC Thread#0" os_prio=31 cpu=29.06ms elapsed=122.25s tid=0x00007f8a95010800 nid=0x5003 runnable

      "GC Thread#1" os_prio=31 cpu=29.42ms elapsed=121.51s tid=0x00007f8a9737d000 nid=0xd703 runnable

      "GC Thread#2" os_prio=31 cpu=27.24ms elapsed=121.51s tid=0x00007f8a9a0a8800 nid=0x12f03 runnable

      "GC Thread#3" os_prio=31 cpu=30.31ms elapsed=121.51s tid=0x00007f8a9737d800 nid=0xd903 runnable

      "GC Thread#4" os_prio=31 cpu=28.26ms elapsed=121.51s tid=0x00007f8a988da800 nid=0xdb03 runnable

      "GC Thread#5" os_prio=31 cpu=29.36ms elapsed=121.51s tid=0x00007f8a99881800 nid=0xdc03 runnable

      "GC Thread#6" os_prio=31 cpu=18.43ms elapsed=120.10s tid=0x00007f8a97627000 nid=0x15813 runnable

      "GC Thread#7" os_prio=31 cpu=19.25ms elapsed=120.10s tid=0x00007f8a95e0f800 nid=0x1fd03 runnable

      "G1 Main Marker" os_prio=31 cpu=0.76ms elapsed=122.25s tid=0x00007f8a9883d800 nid=0x4f03 runnable

      "G1 Conc#0" os_prio=31 cpu=27.02ms elapsed=122.25s tid=0x00007f8a95011800 nid=0x4e03 runnable

      "G1 Conc#1" os_prio=31 cpu=27.04ms elapsed=121.27s tid=0x00007f8a973b3000 nid=0x1341f runnable

      "G1 Refine#0" os_prio=31 cpu=7.24ms elapsed=122.25s tid=0x00007f8a958bb000 nid=0x4c03 runnable

      "G1 Refine#1" os_prio=31 cpu=4.20ms elapsed=121.51s tid=0x00007f8a9a0b4800 nid=0x1290b runnable

      "G1 Refine#2" os_prio=31 cpu=1.65ms elapsed=120.09s tid=0x00007f8a9762b000 nid=0x15707 runnable

      "G1 Refine#3" os_prio=31 cpu=0.82ms elapsed=120.09s tid=0x00007f8a99895000 nid=0x1fa07 runnable

      "G1 Young RemSet Sampling" os_prio=31 cpu=21.74ms elapsed=122.25s tid=0x00007f8a958bb800 nid=0x4a03 runnable
      "VM Periodic Task Thread" os_prio=31 cpu=63.60ms elapsed=122.18s tid=0x00007f8a9502f000 nid=0x5c03 waiting on condition

      JNI global refs: 158, weak refs: 177

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: