2016-11-16 12:35:26 Full thread dump Java HotSpot(TM) 64-Bit Server VM (25.111-b14 mixed mode): "JMX server connection timeout 205" #205 daemon prio=9 os_prio=31 tid=0x00007fd6cd106000 nid=0x65d7 in Object.wait() [0x00000001ad812000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at com.sun.jmx.remote.internal.ServerCommunicatorAdmin$Timeout.run(ServerCommunicatorAdmin.java:168) - locked <0x00000007ab5e9678> (a [I) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "RMI Scheduler(0)" #204 daemon prio=9 os_prio=31 tid=0x00007fd6c52f1000 nid=0x12497 waiting on condition [0x00000001ad70f000] java.lang.Thread.State: TIMED_WAITING (parking) at sun.misc.Unsafe.park(Native Method) - parking to wait for <0x00000007ab430550> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject) at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215) at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078) at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093) at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809) at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "RMI TCP Connection(1)-10.128.71.194" #203 daemon prio=9 os_prio=31 tid=0x00007fd6c5eea000 nid=0xe86f runnable [0x00000001ad60b000] java.lang.Thread.State: RUNNABLE at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at java.io.BufferedInputStream.fill(BufferedInputStream.java:246) at java.io.BufferedInputStream.read(BufferedInputStream.java:265) - locked <0x00000007ab5b7e18> (a java.io.BufferedInputStream) at java.io.FilterInputStream.read(FilterInputStream.java:83) at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:550) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler$$Lambda$30/680287831.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - <0x00000007ab4838d8> (a java.util.concurrent.ThreadPoolExecutor$Worker) "RMI TCP Accept-0" #202 daemon prio=9 os_prio=31 tid=0x00007fd6c5b87800 nid=0x30ef runnable [0x00000001ac356000] java.lang.Thread.State: RUNNABLE at java.net.PlainSocketImpl.socketAccept(Native Method) at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:409) at java.net.ServerSocket.implAccept(ServerSocket.java:545) at java.net.ServerSocket.accept(ServerSocket.java:513) at sun.management.jmxremote.LocalRMIServerSocketFactory$1.accept(LocalRMIServerSocketFactory.java:52) at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:400) at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:372) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "Attach Listener" #201 daemon prio=9 os_prio=31 tid=0x00007fd6cc180800 nid=0x1221f waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE Locked ownable synchronizers: - None "HoverWatcher" #200 prio=1 os_prio=31 tid=0x00007fd6c4a1b800 nid=0xecff waiting on condition [0x00000001ab1ca000] java.lang.Thread.State: TIMED_WAITING (sleeping) at java.lang.Thread.sleep(Native Method) at org.jmol.thread.JmolThread.runSleep(JmolThread.java:154) at org.jmol.thread.HoverWatcherThread.run1(HoverWatcherThread.java:69) at org.jmol.thread.JmolThread.run(JmolThread.java:105) Locked ownable synchronizers: - None "QueueThread0" #199 prio=6 os_prio=31 tid=0x00007fd6c507d000 nid=0x977b waiting for monitor entry [0x000000019e104000] java.lang.Thread.State: BLOCKED (on object monitor) at java.awt.Container.remove(Container.java:1261) - waiting to lock <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at jalview.gui.ProgressBar.removeRow(ProgressBar.java:188) - locked <0x0000000782ca8d38> (a javax.swing.JPanel) at jalview.gui.ProgressBar.setProgressBar(ProgressBar.java:141) at jalview.gui.StructureChooser.setProgressBar(StructureChooser.java:1161) at jalview.structure.StructureSelectionManager.setProgressBar(StructureSelectionManager.java:1350) at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:573) - locked <0x000000078116e1b8> (a jalview.structure.StructureSelectionManager) at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:327) - locked <0x000000078116e1b8> (a jalview.structure.StructureSelectionManager) at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded(JalviewJmolBinding.java:1181) at jalview.ext.jmol.JalviewJmolBinding.notifyCallback(JalviewJmolBinding.java:991) at org.jmol.viewer.StatusManager.setFileLoadStatus(StatusManager.java:407) - locked <0x0000000782c0e858> (a org.jmol.viewer.StatusManager) at org.jmol.viewer.Viewer.setFileLoadStatus(Viewer.java:4694) at org.jmol.viewer.Viewer.createModelSetAndReturnError(Viewer.java:2249) at org.jmol.viewer.Viewer.loadModelFromFile(Viewer.java:1737) at org.jmol.script.ScriptEval.cmdLoad(ScriptEval.java:4671) at org.jmol.script.ScriptEval.processCommand(ScriptEval.java:2380) at org.jmol.script.ScriptEval.commandLoop(ScriptEval.java:2248) at org.jmol.script.ScriptEval.dispatchCommands(ScriptEval.java:2111) at org.jmol.script.ScriptEval.executeCommands(ScriptEval.java:417) at org.jmol.script.ScriptEval.evaluateCompiledScript(ScriptEval.java:403) at org.jmol.script.ScriptManager.evalStringWaitStatusQueued(ScriptManager.java:356) at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Viewer.java:3835) - locked <0x0000000782bcd020> (a org.jmol.viewer.Viewer) at org.jmol.script.ScriptQueueThread.runNextScript(ScriptQueueThread.java:111) at org.jmol.script.ScriptQueueThread.run1(ScriptQueueThread.java:78) at org.jmol.thread.JmolThread.run(JmolThread.java:105) Locked ownable synchronizers: - None "TimerQueue" #69 daemon prio=5 os_prio=31 tid=0x00007fd6c49cb000 nid=0x12517 waiting on condition [0x00000001b998a000] java.lang.Thread.State: WAITING (parking) at sun.misc.Unsafe.park(Native Method) - parking to wait for <0x0000000780fdb4f0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject) at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175) at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039) at java.util.concurrent.DelayQueue.take(DelayQueue.java:211) at javax.swing.TimerQueue.run(TimerQueue.java:174) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - <0x0000000780fdb518> (a java.util.concurrent.locks.ReentrantLock$NonfairSync) "pool-3-thread-1" #66 prio=5 os_prio=31 tid=0x00007fd6c4b11000 nid=0x12807 waiting on condition [0x00000001b9887000] java.lang.Thread.State: WAITING (parking) at sun.misc.Unsafe.park(Native Method) - parking to wait for <0x0000000780fd6bf8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject) at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175) at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039) at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442) at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "Thread-18" #55 daemon prio=5 os_prio=31 tid=0x00007fd6c5ddb000 nid=0x11a03 in Object.wait() [0x000000019e002000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at jalview.gui.Console.run(Console.java:488) - locked <0x0000000780fcfbd0> (a jalview.gui.Console) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "Thread-17" #54 daemon prio=5 os_prio=31 tid=0x00007fd6c48fb800 nid=0x11803 in Object.wait() [0x000000019c245000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at jalview.gui.Console.run(Console.java:422) - locked <0x0000000780fcfbd0> (a jalview.gui.Console) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "Thread-16" #53 daemon prio=5 os_prio=31 tid=0x00007fd6c4ec2000 nid=0x10d13 in Object.wait() [0x000000019c142000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at jalview.gui.Console.run(Console.java:392) - locked <0x0000000780fcfbd0> (a jalview.gui.Console) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "AWT-EventQueue-2" #50 prio=6 os_prio=31 tid=0x00007fd6c5934000 nid=0xb107 waiting for monitor entry [0x00000001296b2000] java.lang.Thread.State: BLOCKED (on object monitor) at org.jmol.viewer.StatusManager.setStatusResized(StatusManager.java:321) - waiting to lock <0x0000000782c0e858> (a org.jmol.viewer.StatusManager) at org.jmol.viewer.Viewer.setStatusResized(Viewer.java:4859) at org.jmol.viewer.Viewer.resizeImage(Viewer.java:3465) at org.jmol.viewer.Viewer.setScreenDimension(Viewer.java:3412) at org.jmol.viewer.Viewer.updateWindow(Viewer.java:3588) at org.jmol.viewer.Viewer.renderScreenImageStereo(Viewer.java:3515) at org.jmol.viewer.Viewer.renderScreenImage(Viewer.java:3598) at jalview.gui.AppJmol$RenderPanel.paintComponent(AppJmol.java:1065) at javax.swing.JComponent.paint(JComponent.java:1056) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Locked ownable synchronizers: - None "TimerQueue" #43 daemon prio=5 os_prio=31 tid=0x00007fd6c5c72000 nid=0x10c27 waiting on condition [0x000000019a2e2000] java.lang.Thread.State: WAITING (parking) at sun.misc.Unsafe.park(Native Method) - parking to wait for <0x000000078072b550> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject) at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175) at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039) at java.util.concurrent.DelayQueue.take(DelayQueue.java:211) at javax.swing.TimerQueue.run(TimerQueue.java:174) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - <0x000000078072b7f0> (a java.util.concurrent.locks.ReentrantLock$NonfairSync) "CacheCleanUpThread" #24 daemon prio=5 os_prio=31 tid=0x00007fd6c4927800 nid=0xe103 in Object.wait() [0x000000012b186000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at com.sun.deploy.cache.CleanupThread.run(Unknown Source) - locked <0x00000007802daac0> (a com.sun.deploy.cache.CleanupThread) Locked ownable synchronizers: - None "CacheMemoryCleanUpThread" #21 daemon prio=5 os_prio=31 tid=0x00007fd6c5a93000 nid=0xdf03 in Object.wait() [0x000000012b083000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143) - locked <0x000000078018dcb8> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164) at com.sun.deploy.cache.MemoryCache$LoadedResourceCleanupThread.run(Unknown Source) Locked ownable synchronizers: - None "MemoryCache-DelayedCleanup" #22 daemon prio=5 os_prio=31 tid=0x00007fd6c5a6c800 nid=0xdd03 in Object.wait() [0x000000012af80000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at java.util.TimerThread.mainLoop(Timer.java:526) - locked <0x00000007802bdeb0> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:505) Locked ownable synchronizers: - None "ConsoleTraceListener" #20 daemon prio=5 os_prio=31 tid=0x00007fd6c491d000 nid=0xdc1f in Object.wait() [0x000000012ae7d000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at com.sun.deploy.uitoolkit.ui.ConsoleTraceListener$ConsoleWriterThread.run(Unknown Source) - locked <0x00000007802daec0> (a com.sun.deploy.uitoolkit.ui.ConsoleTraceListener$BoundedStringBuffer) Locked ownable synchronizers: - None "Java2D Disposer" #19 daemon prio=10 os_prio=31 tid=0x00007fd6c4161000 nid=0xd907 in Object.wait() [0x000000012ab71000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143) - locked <0x00000007801a6ca0> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164) at sun.java2d.Disposer.run(Disposer.java:148) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "Java2D Queue Flusher" #18 daemon prio=10 os_prio=31 tid=0x00007fd6c515e800 nid=0xb907 in Object.wait() [0x00000001298bb000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:203) - locked <0x00000007801b7e88> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher) Locked ownable synchronizers: - None "AWT-EventQueue-1" #17 prio=6 os_prio=31 tid=0x00007fd6c40d3000 nid=0xb303 waiting for monitor entry [0x00000001297b6000] java.lang.Thread.State: BLOCKED (on object monitor) at java.awt.Container.findComponentAt(Container.java:2662) - waiting to lock <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at java.awt.Container$1.findComponentAt(Container.java:266) at sun.lwawt.LWCursorManager.findComponent(LWCursorManager.java:109) at sun.lwawt.LWCursorManager.updateCursorImpl(LWCursorManager.java:81) at sun.lwawt.LWCursorManager.updateCursor(LWCursorManager.java:57) at sun.lwawt.LWComponentPeer.updateCursorImmediately(LWComponentPeer.java:896) at java.awt.Component.updateCursorImmediately(Component.java:3145) at java.awt.Container.validate(Container.java:1642) at javax.swing.RepaintManager$3.run(RepaintManager.java:711) at javax.swing.RepaintManager$3.run(RepaintManager.java:709) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Locked ownable synchronizers: - None "DestroyJavaVM" #16 prio=5 os_prio=31 tid=0x00007fd6c5a2c800 nid=0x1303 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE Locked ownable synchronizers: - None "Javaws Secure Thread" #14 daemon prio=5 os_prio=31 tid=0x00007fd6c5148000 nid=0xaf03 in Object.wait() [0x00000001295b2000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at com.sun.javaws.ui.JavawsSysRun$SecureThread.run(Unknown Source) - locked <0x00000007802a4a50> (a java.lang.Object) Locked ownable synchronizers: - None "AWT-EventQueue-0" #13 prio=6 os_prio=31 tid=0x00007fd6c48cc000 nid=0xad0f waiting on condition [0x00000001294af000] java.lang.Thread.State: WAITING (parking) at sun.misc.Unsafe.park(Native Method) - parking to wait for <0x00000007801fadc0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject) at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175) at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039) at java.awt.EventQueue.getNextEvent(EventQueue.java:554) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:170) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Locked ownable synchronizers: - None "AWT-Shutdown" #12 prio=5 os_prio=31 tid=0x00007fd6c48db000 nid=0xac0f in Object.wait() [0x000000012908e000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295) - locked <0x00000007802b0ef8> (a java.lang.Object) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "traceMsgQueueThread" #10 daemon prio=5 os_prio=31 tid=0x00007fd6c58a6000 nid=0x770f in Object.wait() [0x0000000126d09000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at com.sun.deploy.trace.Trace$TraceMsgQueueChecker.run(Unknown Source) - locked <0x00000007801de878> (a java.util.ArrayList) at java.lang.Thread.run(Thread.java:745) Locked ownable synchronizers: - None "AppKit Thread" #9 daemon prio=5 os_prio=31 tid=0x00007fd6c4051000 nid=0x513 runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE Locked ownable synchronizers: - None "Service Thread" #8 daemon prio=9 os_prio=31 tid=0x00007fd6c500f000 nid=0x4703 runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE Locked ownable synchronizers: - None "C1 CompilerThread2" #7 daemon prio=9 os_prio=31 tid=0x00007fd6c4051800 nid=0x4503 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE Locked ownable synchronizers: - None "C2 CompilerThread1" #6 daemon prio=9 os_prio=31 tid=0x00007fd6c4045000 nid=0x4303 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE Locked ownable synchronizers: - None "C2 CompilerThread0" #5 daemon prio=9 os_prio=31 tid=0x00007fd6c5800000 nid=0x4103 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE Locked ownable synchronizers: - None "Signal Dispatcher" #4 daemon prio=9 os_prio=31 tid=0x00007fd6c482c800 nid=0x3117 runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE Locked ownable synchronizers: - None "Finalizer" #3 daemon prio=8 os_prio=31 tid=0x00007fd6c4845800 nid=0x2d03 in Object.wait() [0x0000000121fc1000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143) - locked <0x000000078029dd20> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164) at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209) Locked ownable synchronizers: - None "Reference Handler" #2 daemon prio=10 os_prio=31 tid=0x00007fd6c4808000 nid=0x2b03 in Object.wait() [0x0000000121ebe000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at java.lang.ref.Reference.tryHandlePending(Reference.java:191) - locked <0x000000078019c9b0> (a java.lang.ref.Reference$Lock) at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:153) Locked ownable synchronizers: - None "VM Thread" os_prio=31 tid=0x00007fd6c402f800 nid=0x2903 runnable "GC task thread#0 (ParallelGC)" os_prio=31 tid=0x00007fd6c4815800 nid=0x2103 runnable "GC task thread#1 (ParallelGC)" os_prio=31 tid=0x00007fd6c4816000 nid=0x2303 runnable "GC task thread#2 (ParallelGC)" os_prio=31 tid=0x00007fd6c5801800 nid=0x2503 runnable "GC task thread#3 (ParallelGC)" os_prio=31 tid=0x00007fd6c400b000 nid=0x2703 runnable "VM Periodic Task Thread" os_prio=31 tid=0x00007fd6c4827000 nid=0x4903 waiting on condition JNI global references: 2107 Found one Java-level deadlock: ============================= "QueueThread0": waiting to lock monitor 0x00007fd6c4194bf8 (object 0x00000007801dc7b0, a java.awt.Component$AWTTreeLock), which is held by "AWT-EventQueue-2" "AWT-EventQueue-2": waiting to lock monitor 0x00007fd6c5803298 (object 0x0000000782c0e858, a org.jmol.viewer.StatusManager), which is held by "QueueThread0" Java stack information for the threads listed above: =================================================== "QueueThread0": at java.awt.Container.remove(Container.java:1261) - waiting to lock <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at jalview.gui.ProgressBar.removeRow(ProgressBar.java:188) - locked <0x0000000782ca8d38> (a javax.swing.JPanel) at jalview.gui.ProgressBar.setProgressBar(ProgressBar.java:141) at jalview.gui.StructureChooser.setProgressBar(StructureChooser.java:1161) at jalview.structure.StructureSelectionManager.setProgressBar(StructureSelectionManager.java:1350) at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:573) - locked <0x000000078116e1b8> (a jalview.structure.StructureSelectionManager) at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:327) - locked <0x000000078116e1b8> (a jalview.structure.StructureSelectionManager) at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded(JalviewJmolBinding.java:1181) at jalview.ext.jmol.JalviewJmolBinding.notifyCallback(JalviewJmolBinding.java:991) at org.jmol.viewer.StatusManager.setFileLoadStatus(StatusManager.java:407) - locked <0x0000000782c0e858> (a org.jmol.viewer.StatusManager) at org.jmol.viewer.Viewer.setFileLoadStatus(Viewer.java:4694) at org.jmol.viewer.Viewer.createModelSetAndReturnError(Viewer.java:2249) at org.jmol.viewer.Viewer.loadModelFromFile(Viewer.java:1737) at org.jmol.script.ScriptEval.cmdLoad(ScriptEval.java:4671) at org.jmol.script.ScriptEval.processCommand(ScriptEval.java:2380) at org.jmol.script.ScriptEval.commandLoop(ScriptEval.java:2248) at org.jmol.script.ScriptEval.dispatchCommands(ScriptEval.java:2111) at org.jmol.script.ScriptEval.executeCommands(ScriptEval.java:417) at org.jmol.script.ScriptEval.evaluateCompiledScript(ScriptEval.java:403) at org.jmol.script.ScriptManager.evalStringWaitStatusQueued(ScriptManager.java:356) at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Viewer.java:3835) - locked <0x0000000782bcd020> (a org.jmol.viewer.Viewer) at org.jmol.script.ScriptQueueThread.runNextScript(ScriptQueueThread.java:111) at org.jmol.script.ScriptQueueThread.run1(ScriptQueueThread.java:78) at org.jmol.thread.JmolThread.run(JmolThread.java:105) "AWT-EventQueue-2": at org.jmol.viewer.StatusManager.setStatusResized(StatusManager.java:321) - waiting to lock <0x0000000782c0e858> (a org.jmol.viewer.StatusManager) at org.jmol.viewer.Viewer.setStatusResized(Viewer.java:4859) at org.jmol.viewer.Viewer.resizeImage(Viewer.java:3465) at org.jmol.viewer.Viewer.setScreenDimension(Viewer.java:3412) at org.jmol.viewer.Viewer.updateWindow(Viewer.java:3588) at org.jmol.viewer.Viewer.renderScreenImageStereo(Viewer.java:3515) at org.jmol.viewer.Viewer.renderScreenImage(Viewer.java:3598) at jalview.gui.AppJmol$RenderPanel.paintComponent(AppJmol.java:1065) at javax.swing.JComponent.paint(JComponent.java:1056) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) - locked <0x00000007801dc7b0> (a java.awt.Component$AWTTreeLock) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Found 1 deadlock.