Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Napari doesn't quit when wrapping a local install #307

Closed
hinerm opened this issue Nov 8, 2024 · 6 comments · Fixed by #318
Closed

Napari doesn't quit when wrapping a local install #307

hinerm opened this issue Nov 8, 2024 · 6 comments · Fixed by #318
Labels
bug Something isn't working

Comments

@hinerm
Copy link
Member

hinerm commented Nov 8, 2024

Using napari-imagej from main. When I configure napari-imagej to wrap a local Fiji installation, after closing napari the terminal hangs:

image

Thread dump follows:


2024-11-08 16:00:33
Full thread dump OpenJDK 64-Bit Server VM (22.0.1+8 mixed mode, sharing):

Threads class SMR info:
_java_thread_list=0x0000017bc0e67210, length=25, elements={
0x0000017b558ffe80, 0x0000017b55904d40, 0x0000017b559074a0, 0x0000017b55904020,
0x0000017b55901230, 0x0000017b559025e0, 0x0000017b55902c70, 0x0000017b53aa1480,
0x0000017b53aa1b50, 0x0000017b559053d0, 0x0000017b55901f50, 0x0000017b55900510,
0x0000017b5590dda0, 0x0000017b5590bcd0, 0x0000017b55909570, 0x0000017b55909c00,
0x0000017b5590eac0, 0x0000017b55908ee0, 0x0000017b5590a290, 0x0000017b559046b0,
0x0000017b5590c9f0, 0x0000017bc6419ae0, 0x0000017bc641e310, 0x0000017bc641d5f0,
0x0000017bc4e8c220
}

"main" #1 [13104] prio=5 os_prio=0 cpu=859.38ms elapsed=319.90s tid=0x0000017b558ffe80 nid=13104 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
        - None

"Reference Handler" #9 [31860] daemon prio=10 os_prio=2 cpu=0.00ms elapsed=319.88s tid=0x0000017b55904d40 nid=31860 waiting on condition  [0x0000005279eaf000]
   java.lang.Thread.State: RUNNABLE
        at java.lang.ref.Reference.waitForReferencePendingList(java.base@22.0.1/Native Method)
        at java.lang.ref.Reference.processPendingReferences(java.base@22.0.1/Reference.java:246)
        at java.lang.ref.Reference$ReferenceHandler.run(java.base@22.0.1/Reference.java:208)

   Locked ownable synchronizers:
        - None

"Finalizer" #10 [9968] daemon prio=8 os_prio=1 cpu=0.00ms elapsed=319.88s tid=0x0000017b559074a0 nid=9968 in Object.wait()  [0x000000527a09e000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait0(java.base@22.0.1/Native Method)
        - waiting on <0x0000000682ca58e0> (a java.lang.ref.NativeReferenceQueue$Lock)
        at java.lang.Object.wait(java.base@22.0.1/Object.java:375)
        at java.lang.Object.wait(java.base@22.0.1/Object.java:348)
        at java.lang.ref.NativeReferenceQueue.await(java.base@22.0.1/NativeReferenceQueue.java:48)
        at java.lang.ref.ReferenceQueue.remove0(java.base@22.0.1/ReferenceQueue.java:158)
        at java.lang.ref.NativeReferenceQueue.remove(java.base@22.0.1/NativeReferenceQueue.java:89)
        - locked <0x0000000682ca58e0> (a java.lang.ref.NativeReferenceQueue$Lock)
        at java.lang.ref.Finalizer$FinalizerThread.run(java.base@22.0.1/Finalizer.java:173)

   Locked ownable synchronizers:
        - None

"Signal Dispatcher" #11 [14532] daemon prio=9 os_prio=2 cpu=0.00ms elapsed=319.88s tid=0x0000017b55904020 nid=14532 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
        - None

"Attach Listener" #12 [8364] daemon prio=5 os_prio=2 cpu=203.12ms elapsed=319.88s tid=0x0000017b55901230 nid=8364 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
        - None

"Service Thread" #13 [16568] daemon prio=9 os_prio=0 cpu=0.00ms elapsed=319.88s tid=0x0000017b559025e0 nid=16568 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
        - None

"Monitor Deflation Thread" #14 [2480] daemon prio=9 os_prio=0 cpu=0.00ms elapsed=319.88s tid=0x0000017b55902c70 nid=2480 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
        - None

"C2 CompilerThread0" #15 [1768] daemon prio=9 os_prio=2 cpu=890.62ms elapsed=319.88s tid=0x0000017b53aa1480 nid=1768 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   No compile task

   Locked ownable synchronizers:
        - None

"C1 CompilerThread0" #18 [32612] daemon prio=9 os_prio=2 cpu=250.00ms elapsed=319.88s tid=0x0000017b53aa1b50 nid=32612 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   No compile task

   Locked ownable synchronizers:
        - None

"Common-Cleaner" #19 [3292] daemon prio=8 os_prio=1 cpu=0.00ms elapsed=319.67s tid=0x0000017b559053d0 nid=3292 waiting on condition  [0x000000527ae2e000]
   java.lang.Thread.State: TIMED_WAITING (parking)
        at jdk.internal.misc.Unsafe.park(java.base@22.0.1/Native Method)
        - parking to wait for  <0x0000000682ca5d20> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
        at java.util.concurrent.locks.LockSupport.parkNanos(java.base@22.0.1/LockSupport.java:269)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@22.0.1/AbstractQueuedSynchronizer.java:1847)
        at java.lang.ref.ReferenceQueue.await(java.base@22.0.1/ReferenceQueue.java:71)
        at java.lang.ref.ReferenceQueue.remove0(java.base@22.0.1/ReferenceQueue.java:143)
        at java.lang.ref.ReferenceQueue.remove(java.base@22.0.1/ReferenceQueue.java:218)
        at jdk.internal.ref.CleanerImpl.run(java.base@22.0.1/CleanerImpl.java:140)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)
        at jdk.internal.misc.InnocuousThread.run(java.base@22.0.1/InnocuousThread.java:186)

   Locked ownable synchronizers:
        - None

"Notification Thread" #20 [19840] daemon prio=9 os_prio=0 cpu=0.00ms elapsed=319.67s tid=0x0000017b55901f50 nid=19840 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
        - None

"Python Reference Queue" #28 [21772] daemon prio=5 os_prio=0 cpu=1015.62ms elapsed=319.16s tid=0x0000017b55900510 nid=21772 waiting on condition  [0x000000527c37f000]
   java.lang.Thread.State: TIMED_WAITING (parking)
        at jdk.internal.misc.Unsafe.park(java.base@22.0.1/Native Method)
        - parking to wait for  <0x0000000698006728> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
        at java.util.concurrent.locks.LockSupport.parkNanos(java.base@22.0.1/LockSupport.java:269)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@22.0.1/AbstractQueuedSynchronizer.java:1847)
        at java.lang.ref.ReferenceQueue.await(java.base@22.0.1/ReferenceQueue.java:71)
        at java.lang.ref.ReferenceQueue.remove0(java.base@22.0.1/ReferenceQueue.java:143)
        at java.lang.ref.ReferenceQueue.remove(java.base@22.0.1/ReferenceQueue.java:218)
        at org.jpype.ref.JPypeReferenceQueue$Worker.run(Unknown Source)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - None

"Java2D Disposer" #32 [31296] daemon prio=10 os_prio=2 cpu=0.00ms elapsed=316.83s tid=0x0000017b5590dda0 nid=31296 waiting on condition  [0x000000527c94e000]
   java.lang.Thread.State: WAITING (parking)
        at jdk.internal.misc.Unsafe.park(java.base@22.0.1/Native Method)
        - parking to wait for  <0x0000000684ca06d0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
        at java.util.concurrent.locks.LockSupport.park(java.base@22.0.1/LockSupport.java:371)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@22.0.1/AbstractQueuedSynchronizer.java:519)
        at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@22.0.1/ForkJoinPool.java:4013)
        at java.util.concurrent.ForkJoinPool.managedBlock(java.base@22.0.1/ForkJoinPool.java:3961)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@22.0.1/AbstractQueuedSynchronizer.java:1707)
        at java.lang.ref.ReferenceQueue.await(java.base@22.0.1/ReferenceQueue.java:67)
        at java.lang.ref.ReferenceQueue.remove0(java.base@22.0.1/ReferenceQueue.java:158)
        at java.lang.ref.ReferenceQueue.remove(java.base@22.0.1/ReferenceQueue.java:234)
        at sun.java2d.Disposer.run(java.desktop@22.0.1/Disposer.java:145)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - None

"AWT-Windows" #34 [17308] daemon prio=6 os_prio=0 cpu=187.50ms elapsed=316.83s tid=0x0000017b5590bcd0 nid=17308 runnable  [0x000000527cd2f000]
   java.lang.Thread.State: RUNNABLE
        at sun.awt.windows.WToolkit.eventLoop(java.desktop@22.0.1/Native Method)
        at sun.awt.windows.WToolkit.run(java.desktop@22.0.1/WToolkit.java:297)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - None

"Thread-3" #43 [7688] daemon prio=5 os_prio=0 cpu=1921.88ms elapsed=315.54s tid=0x0000017b55909570 nid=7688 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
        - None

"TimerQueue" #44 [33260] daemon prio=5 os_prio=0 cpu=0.00ms elapsed=304.10s tid=0x0000017b55909c00 nid=33260 waiting on condition  [0x0000005278f2f000]
   java.lang.Thread.State: WAITING (parking)
        at jdk.internal.misc.Unsafe.park(java.base@22.0.1/Native Method)
        - parking to wait for  <0x0000000684ece7b8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
        at java.util.concurrent.locks.LockSupport.park(java.base@22.0.1/LockSupport.java:371)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@22.0.1/AbstractQueuedSynchronizer.java:519)
        at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@22.0.1/ForkJoinPool.java:4013)
        at java.util.concurrent.ForkJoinPool.managedBlock(java.base@22.0.1/ForkJoinPool.java:3961)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@22.0.1/AbstractQueuedSynchronizer.java:1707)
        at java.util.concurrent.DelayQueue.take(java.base@22.0.1/DelayQueue.java:242)
        at javax.swing.TimerQueue.run(java.desktop@22.0.1/TimerQueue.java:165)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - <0x0000000684ece7e0> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)

"D3D Screen Updater" #48 [35124] daemon prio=7 os_prio=1 cpu=0.00ms elapsed=303.23s tid=0x0000017b5590eac0 nid=35124 in Object.wait()  [0x000000527d4ef000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait0(java.base@22.0.1/Native Method)
        - waiting on <no object reference available>
        at java.lang.Object.wait(java.base@22.0.1/Object.java:375)
        at sun.java2d.d3d.D3DScreenUpdateManager.run(java.desktop@22.0.1/D3DScreenUpdateManager.java:425)
        - locked <0x0000000683b6b340> (a java.lang.Object)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - None

"JFR Recorder Thread" #49 [30576] daemon prio=5 os_prio=0 cpu=0.00ms elapsed=140.48s tid=0x0000017b55908ee0 nid=30576 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
        - None

"JFR Periodic Tasks" #50 [20968] daemon prio=5 os_prio=0 cpu=0.00ms elapsed=140.32s tid=0x0000017b5590a290 nid=20968 in Object.wait()  [0x0000005276e3e000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
        at java.lang.Object.wait0(java.base@22.0.1/Native Method)
        - waiting on <no object reference available>
        at java.lang.Object.wait(java.base@22.0.1/Object.java:375)
        at jdk.jfr.internal.PlatformRecorder.takeNap(jdk.jfr@22.0.1/PlatformRecorder.java:558)
        - locked <0x000000068ba2bfc0> (a jdk.jfr.internal.JVM$ChunkRotationMonitor)
        at jdk.jfr.internal.PlatformRecorder.periodicTask(jdk.jfr@22.0.1/PlatformRecorder.java:526)
        at jdk.jfr.internal.PlatformRecorder.lambda$startDiskMonitor$1(jdk.jfr@22.0.1/PlatformRecorder.java:446)
        at jdk.jfr.internal.PlatformRecorder$$Lambda/0x0000017b7b6784b0.run(jdk.jfr@22.0.1/Unknown Source)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - None

"RMI TCP Accept-0" #53 [29856] daemon prio=5 os_prio=0 cpu=0.00ms elapsed=4.83s tid=0x0000017b559046b0 nid=29856 runnable  [0x000000527740e000]
   java.lang.Thread.State: RUNNABLE
        at sun.nio.ch.Net.accept(java.base@22.0.1/Native Method)
        at sun.nio.ch.NioSocketImpl.accept(java.base@22.0.1/NioSocketImpl.java:748)
        at java.net.ServerSocket.implAccept(java.base@22.0.1/ServerSocket.java:695)
        at java.net.ServerSocket.platformImplAccept(java.base@22.0.1/ServerSocket.java:660)
        at java.net.ServerSocket.implAccept(java.base@22.0.1/ServerSocket.java:636)
        at java.net.ServerSocket.implAccept(java.base@22.0.1/ServerSocket.java:582)
        at java.net.ServerSocket.accept(java.base@22.0.1/ServerSocket.java:541)
        at sun.management.jmxremote.LocalRMIServerSocketFactory$1.accept(jdk.management.agent@22.0.1/LocalRMIServerSocketFactory.java:52)
        at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(java.rmi@22.0.1/TCPTransport.java:424)
        at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(java.rmi@22.0.1/TCPTransport.java:388)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - <0x000000068aafc540> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)

"RMI TCP Connection(1)-192.168.68.63" #54 [18940] daemon prio=5 os_prio=0 cpu=15.62ms elapsed=4.82s tid=0x0000017b5590c9f0 nid=18940 runnable  [0x00000052775fe000]
   java.lang.Thread.State: RUNNABLE
        at sun.nio.ch.Net.poll(java.base@22.0.1/Native Method)
        at sun.nio.ch.NioSocketImpl.park(java.base@22.0.1/NioSocketImpl.java:191)
        at sun.nio.ch.NioSocketImpl.timedRead(java.base@22.0.1/NioSocketImpl.java:280)
        at sun.nio.ch.NioSocketImpl.implRead(java.base@22.0.1/NioSocketImpl.java:304)
        at sun.nio.ch.NioSocketImpl.read(java.base@22.0.1/NioSocketImpl.java:346)
        at sun.nio.ch.NioSocketImpl$1.read(java.base@22.0.1/NioSocketImpl.java:796)
        at java.net.Socket$SocketInputStream.implRead(java.base@22.0.1/Socket.java:1108)
        at java.net.Socket$SocketInputStream.read(java.base@22.0.1/Socket.java:1095)
        at java.io.BufferedInputStream.fill(java.base@22.0.1/BufferedInputStream.java:291)
        at java.io.BufferedInputStream.implRead(java.base@22.0.1/BufferedInputStream.java:325)
        at java.io.BufferedInputStream.read(java.base@22.0.1/BufferedInputStream.java:312)
        at java.io.FilterInputStream.read(java.base@22.0.1/FilterInputStream.java:71)
        at sun.rmi.transport.tcp.TCPTransport.handleMessages(java.rmi@22.0.1/TCPTransport.java:580)
        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(java.rmi@22.0.1/TCPTransport.java:844)
        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(java.rmi@22.0.1/TCPTransport.java:721)
        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler$$Lambda/0x0000017b7b6fc748.run(java.rmi@22.0.1/Unknown Source)
        at java.security.AccessController.executePrivileged(java.base@22.0.1/AccessController.java:778)
        at java.security.AccessController.doPrivileged(java.base@22.0.1/AccessController.java:400)
        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(java.rmi@22.0.1/TCPTransport.java:720)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@22.0.1/ThreadPoolExecutor.java:1144)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@22.0.1/ThreadPoolExecutor.java:642)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - <0x000000068a429810> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
        - <0x000000068abe4a78> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
        - <0x000000068abe8430> (a java.util.concurrent.ThreadPoolExecutor$Worker)

"RMI Scheduler(0)" #55 [31880] daemon prio=5 os_prio=0 cpu=0.00ms elapsed=4.80s tid=0x0000017bc6419ae0 nid=31880 waiting on condition  [0x00000052777ee000]
   java.lang.Thread.State: TIMED_WAITING (parking)
        at jdk.internal.misc.Unsafe.park(java.base@22.0.1/Native Method)
        - parking to wait for  <0x000000068aaf6278> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
        at java.util.concurrent.locks.LockSupport.parkNanos(java.base@22.0.1/LockSupport.java:269)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(java.base@22.0.1/AbstractQueuedSynchronizer.java:1758)
        at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(java.base@22.0.1/ScheduledThreadPoolExecutor.java:1182)
        at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(java.base@22.0.1/ScheduledThreadPoolExecutor.java:899)
        at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@22.0.1/ThreadPoolExecutor.java:1070)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@22.0.1/ThreadPoolExecutor.java:1130)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@22.0.1/ThreadPoolExecutor.java:642)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - None

"JMX server connection timeout 56" #56 [24932] daemon prio=5 os_prio=0 cpu=0.00ms elapsed=4.79s tid=0x0000017bc641e310 nid=24932 in Object.wait()  [0x00000052779de000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
        at java.lang.Object.wait0(java.base@22.0.1/Native Method)
        - waiting on <no object reference available>
        at java.lang.Object.wait(java.base@22.0.1/Object.java:375)
        at com.sun.jmx.remote.internal.ServerCommunicatorAdmin$Timeout.run(java.management@22.0.1/ServerCommunicatorAdmin.java:171)
        - locked <0x000000068a468fe8> (a [I)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - None

"RMI TCP Connection(2)-192.168.68.63" #57 [11928] daemon prio=5 os_prio=0 cpu=15.62ms elapsed=3.70s tid=0x0000017bc641d5f0 nid=11928 runnable  [0x0000005277bce000]
   java.lang.Thread.State: RUNNABLE
        at sun.nio.ch.Net.poll(java.base@22.0.1/Native Method)
        at sun.nio.ch.NioSocketImpl.park(java.base@22.0.1/NioSocketImpl.java:191)
        at sun.nio.ch.NioSocketImpl.timedRead(java.base@22.0.1/NioSocketImpl.java:280)
        at sun.nio.ch.NioSocketImpl.implRead(java.base@22.0.1/NioSocketImpl.java:304)
        at sun.nio.ch.NioSocketImpl.read(java.base@22.0.1/NioSocketImpl.java:346)
        at sun.nio.ch.NioSocketImpl$1.read(java.base@22.0.1/NioSocketImpl.java:796)
        at java.net.Socket$SocketInputStream.implRead(java.base@22.0.1/Socket.java:1108)
        at java.net.Socket$SocketInputStream.read(java.base@22.0.1/Socket.java:1095)
        at java.io.BufferedInputStream.fill(java.base@22.0.1/BufferedInputStream.java:291)
        at java.io.BufferedInputStream.implRead(java.base@22.0.1/BufferedInputStream.java:325)
        at java.io.BufferedInputStream.read(java.base@22.0.1/BufferedInputStream.java:312)
        at java.io.FilterInputStream.read(java.base@22.0.1/FilterInputStream.java:71)
        at sun.rmi.transport.tcp.TCPTransport.handleMessages(java.rmi@22.0.1/TCPTransport.java:580)
        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(java.rmi@22.0.1/TCPTransport.java:844)
        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(java.rmi@22.0.1/TCPTransport.java:721)
        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler$$Lambda/0x0000017b7b6fc748.run(java.rmi@22.0.1/Unknown Source)
        at java.security.AccessController.executePrivileged(java.base@22.0.1/AccessController.java:778)
        at java.security.AccessController.doPrivileged(java.base@22.0.1/AccessController.java:400)
        at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(java.rmi@22.0.1/TCPTransport.java:720)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@22.0.1/ThreadPoolExecutor.java:1144)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@22.0.1/ThreadPoolExecutor.java:642)
        at java.lang.Thread.runWith(java.base@22.0.1/Thread.java:1583)
        at java.lang.Thread.run(java.base@22.0.1/Thread.java:1570)

   Locked ownable synchronizers:
        - <0x000000068a7dba00> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
        - <0x000000068abe86e0> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
        - <0x000000068abebd00> (a java.util.concurrent.ThreadPoolExecutor$Worker)

"C2 CompilerThread1" #16 [21876] daemon prio=9 os_prio=2 cpu=0.00ms elapsed=0.67s tid=0x0000017bc4e8c220 nid=21876 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   No compile task

   Locked ownable synchronizers:
        - None

"VM Thread" os_prio=2 cpu=15.62ms elapsed=319.89s tid=0x0000017b53649280 nid=25176 runnable  

"GC Thread#0" os_prio=2 cpu=46.88ms elapsed=319.90s tid=0x0000017b53648ed0 nid=16200 runnable  

"GC Thread#1" os_prio=2 cpu=46.88ms elapsed=319.51s tid=0x0000017b53647500 nid=18976 runnable  

"GC Thread#2" os_prio=2 cpu=15.62ms elapsed=319.51s tid=0x0000017b53644160 nid=8004 runnable  

"GC Thread#3" os_prio=2 cpu=15.62ms elapsed=319.51s tid=0x0000017b5364bec0 nid=1508 runnable  

"GC Thread#4" os_prio=2 cpu=15.62ms elapsed=319.51s tid=0x0000017b5364c270 nid=31040 runnable  

"GC Thread#5" os_prio=2 cpu=31.25ms elapsed=319.51s tid=0x0000017b53646640 nid=21544 runnable  

"GC Thread#6" os_prio=2 cpu=15.62ms elapsed=319.51s tid=0x0000017b5364b000 nid=8864 runnable  

"GC Thread#7" os_prio=2 cpu=0.00ms elapsed=319.51s tid=0x0000017b536453d0 nid=32108 runnable  

"G1 Main Marker" os_prio=2 cpu=0.00ms elapsed=319.90s tid=0x0000017b55af4500 nid=10120 runnable  

"G1 Conc#0" os_prio=2 cpu=0.00ms elapsed=319.90s tid=0x0000017b536448c0 nid=21832 runnable  

"G1 Conc#1" os_prio=2 cpu=0.00ms elapsed=317.71s tid=0x0000017b53649630 nid=32560 runnable  

"G1 Refine#0" os_prio=2 cpu=15.62ms elapsed=319.90s tid=0x0000017b53063fa0 nid=30752 runnable  

"G1 Service" os_prio=2 cpu=0.00ms elapsed=319.90s tid=0x0000017b55a3cd70 nid=12212 runnable  

"VM Periodic Task Thread" os_prio=2 cpu=15.62ms elapsed=319.89s tid=0x0000017b53279f10 nid=28592 waiting on condition  

JNI global refs: 6114, weak refs: 44
@hinerm hinerm added the bug Something isn't working label Nov 8, 2024
@hinerm
Copy link
Member Author

hinerm commented Nov 8, 2024

Note that this started happening even when using other initialization strings (e.g. sc.fiji:fiji:2.13.0) and even when falling back to napari 0.1.0. 😠

@gselzer gselzer mentioned this issue Nov 8, 2024
Open
@gselzer
Copy link
Collaborator

gselzer commented Nov 8, 2024

@hinerm does this still happen for you with d9fc267? If so, can you provide a MCVE? I have not found napari hanging with a local install when experimenting on that commit...

@ctrueden
Copy link
Member

ctrueden commented Nov 8, 2024

Napari doesn't quit

Time to make new T-shirts! 👕

@hinerm
Copy link
Member Author

hinerm commented Dec 3, 2024 •
edited
Loading

@gselzer

does this still happen for you with d9fc267?

Yes

If so, can you provide a MCVE?

I was unable to reproduce with any layer below napari-imagej.

  1. I create an environment with mamba create -n napari-imagej napari-imagej and activate that env
  2. I pip install -e . on napari-imagej main
  3. pip install jpype1==1.5.0 to work around napari-imagej breaks with Jpype 1.5.1 #316
  4. In the napari-imagej configuration, endpoint is set to sc.fiji:fiji:2.16.0 and base directory to .
  5. I'm launching napari from my home directory
  6. After starting napari I start the napari-imagej plugin. After it loads, I close the main napari app.

Whether or not the shutdown completes or hangs depends on the version of Java used, controlled by setting JAVA_HOME. Here's a summary of results:

Java version Hangs at shutdown?
23.0.1* yes
zulu21.38.21-ca-fx-jdk21.0.5-win_x64 yes
zulu17.54.21-ca-fx-jdk17.0.13-win_x64 no
zulu11.76.21-ca-fx-jdk11.0.25-win_x64 no
zulu8.80.0.17-ca-fx-jdk8.0.422-win_x64 no

*From the local \miniconda3\envs\napari-imagej\Library\lib\jvm, 2024-10-15 by Azul.

Note that the testing with sc.fiji:fiji:2.16.0 is for convenience. I can also reproduce when wrapping a local up-to-date Fiji (2.14.0) installation (which has been modified with a scijava-common >= 2.95.0), as well as an upgraded Fiji future.

Note that the only non-daemon thread running in the thread dump is:

"main" #1 [13104] prio=5 os_prio=0 cpu=859.38ms elapsed=319.90s tid=0x0000017b558ffe80 nid=13104 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

But it doesn't seem to be doing.. anything?

@hinerm hinerm mentioned this issue Dec 3, 2024
Open
1 task
@gselzer
Copy link
Collaborator

gselzer commented Dec 3, 2024

does this still happen for you with d9fc267?

Yes

☹️

If so, can you provide a MCVE?

I was unable to reproduce with any layer below napari-imagej.

Thank you for the detailed and thorough writeup. I'll take a look next week when I have more time.

@imagesc-bot
Copy link

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-friends-weekly-dev-update-thread/103718/29

@gselzer gselzer mentioned this issue Dec 9, 2024
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Detach initialization QThread after ImageJ initialized imagej/napari-imagej
4 participants
@ctrueden @hinerm @gselzer @imagesc-bot