(196/211) 4044 - NPE on exit, won't exit

Do you have any plugins installed when you see this? This looks like it probably has a fairly simple fix (check for null), but it would be good to be able to reproduce this issue first.

I don't see this NPE anymore, whether running jedit -noplugins or not, but it still does not exits and uses 100% cpu. Here's the thread dump when hanging on exit.

Full thread dump OpenJDK 64-Bit Server VM (25.131-b11 mixed mode):

"SwingWorker-pool-1-thread-10" #36 daemon prio=5 os_prio=0 tid=0x00007fa570d6f000 nid=0x372e waiting on condition [0x00007fa5742a7000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SwingWorker-pool-1-thread-9" #35 daemon prio=5 os_prio=0 tid=0x00007fa570d39000 nid=0x372a waiting on condition [0x00007fa5743a8000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SwingWorker-pool-1-thread-8" #34 daemon prio=5 os_prio=0 tid=0x00007fa570d4f800 nid=0x36f7 waiting on condition [0x00007fa5744a9000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SwingWorker-pool-1-thread-7" #33 daemon prio=5 os_prio=0 tid=0x00007fa570d3e800 nid=0x36f3 waiting on condition [0x00007fa5745aa000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SwingWorker-pool-1-thread-6" #32 daemon prio=5 os_prio=0 tid=0x00007fa570d22000 nid=0x36ed waiting on condition [0x00007fa5746ab000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SwingWorker-pool-1-thread-5" #31 daemon prio=5 os_prio=0 tid=0x00007fa570d24000 nid=0x36e4 waiting on condition [0x00007fa5747ac000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SwingWorker-pool-1-thread-4" #30 daemon prio=5 os_prio=0 tid=0x00007fa570d78800 nid=0x36dc waiting on condition [0x00007fa5748ad000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SwingWorker-pool-1-thread-3" #29 daemon prio=5 os_prio=0 tid=0x00007fa570ca6800 nid=0x36d7 waiting on condition [0x00007fa574f59000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SwingWorker-pool-1-thread-2" #28 daemon prio=5 os_prio=0 tid=0x00007fa570d62000 nid=0x36d1 waiting on condition [0x00007fa576def000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"SizeSaver-1" #27 prio=6 os_prio=0 tid=0x00007fa570a55000 nid=0x36c6 waiting on condition [0x00007fa5767ed000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000006c9358df0> (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.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1081)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"Thread-5" #26 daemon prio=5 os_prio=0 tid=0x00007fa568002800 nid=0x36bd runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE

"jEdit server daemon [/home/eric/.jedit/server]" #16 daemon prio=5 os_prio=0 tid=0x00007fa570a4f800 nid=0x36c5 runnable [0x00007fa5768ee000]
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 org.gjt.sp.jedit.EditServer.run(EditServer.java:135)

"SwingWorker-pool-1-thread-1" #25 daemon prio=5 os_prio=0 tid=0x00007fa5709c2800 nid=0x36c3 waiting on condition [0x00007fa574dae000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x000000079e15bb50> (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:1074)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"DestroyJavaVM" #22 prio=5 os_prio=0 tid=0x00007fa5f400a000 nid=0x369b waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE

"Thread-3" #21 prio=1 os_prio=0 tid=0x00007fa5f56c7800 nid=0x36b8 waiting on condition [0x00007fa577af1000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at ise.plugin.bmp.BufferLocal$1.run(BufferLocal.java:107)

"TimerQueue" #17 daemon prio=5 os_prio=0 tid=0x00007fa5f4455800 nid=0x36b6 waiting on condition [0x00007fa577ffe000]
java.lang.Thread.State: TIMED_WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000006c90699d8> (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.DelayQueue.take(DelayQueue.java:223)
at javax.swing.TimerQueue.run(TimerQueue.java:174)
at java.lang.Thread.run(Thread.java:748)

"AWT-EventQueue-1" #14 prio=6 os_prio=0 tid=0x00007fa5f436b000 nid=0x36b3 runnable [0x00007fa57c7cc000]
java.lang.Thread.State: RUNNABLE
at org.GNOME.Accessibility.AtkWrapper.emitSignal(Native Method)
at org.GNOME.Accessibility.AtkWrapper$4.propertyChange(AtkWrapper.java:531)
at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
at javax.accessibility.AccessibleContext.firePropertyChange(AccessibleContext.java:768)
at javax.swing.JLabel.setText(JLabel.java:338)
at javax.swing.DefaultListCellRenderer.getListCellRendererComponent(DefaultListCellRenderer.java:151)
at org.gjt.sp.jedit.gui.BufferSwitcher$BufferCellRenderer.getListCellRendererComponent(BufferSwitcher.java:148)
at javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1361)
at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1311)
at javax.swing.plaf.basic.BasicListUI$Handler.valueChanged(BasicListUI.java:2623)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:164)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:211)
at javax.swing.DefaultListSelectionModel.changeSelection(DefaultListSelectionModel.java:405)
at javax.swing.DefaultListSelectionModel.changeSelection(DefaultListSelectionModel.java:415)
at javax.swing.DefaultListSelectionModel.setSelectionInterval(DefaultListSelectionModel.java:459)
at javax.swing.JList.setSelectedIndex(JList.java:2210)
at javax.swing.plaf.basic.BasicComboPopup.setListSelection(BasicComboPopup.java:1179)
at javax.swing.plaf.basic.BasicComboPopup.access$300(BasicComboPopup.java:63)
at javax.swing.plaf.basic.BasicComboPopup$Handler.itemStateChanged(BasicComboPopup.java:1008)
at javax.swing.JComboBox.fireItemStateChanged(JComboBox.java:1223)
at javax.swing.JComboBox.selectedItemChanged(JComboBox.java:1280)
at javax.swing.JComboBox.contentsChanged(JComboBox.java:1330)
at javax.swing.AbstractListModel.fireContentsChanged(AbstractListModel.java:118)
at javax.swing.DefaultComboBoxModel.setSelectedItem(DefaultComboBoxModel.java:93)
at javax.swing.JComboBox.setSelectedItem(JComboBox.java:576)
at org.gjt.sp.jedit.gui.BufferSwitcher$2.run(BufferSwitcher.java:126)
at org.gjt.sp.util.ThreadUtilities.runInDispatchThread(ThreadUtilities.java:62)
at org.gjt.sp.jedit.gui.BufferSwitcher.updateBufferList(BufferSwitcher.java:132)
at org.gjt.sp.jedit.EditPane.bufferRemoved(EditPane.java:732)
at org.gjt.sp.jedit.bufferset.BufferSet.removeBuffer(BufferSet.java:348)
at org.gjt.sp.jedit.bufferset.BufferSetManager._removeBuffer(BufferSetManager.java:324)
at org.gjt.sp.jedit.bufferset.BufferSetManager.handleEditPaneUpdate(BufferSetManager.java:71)
at sun.reflect.GeneratedMethodAccessor25.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.gjt.sp.jedit.EditBus.dispatch(EditBus.java:242)
at org.gjt.sp.jedit.EditBus.sendImpl(EditBus.java:281)
at org.gjt.sp.jedit.EditBus.access$200(EditBus.java:87)
at org.gjt.sp.jedit.EditBus$SendMessage.run(EditBus.java:461)
at org.gjt.sp.jedit.EditBus.send(EditBus.java:206)
at org.gjt.sp.jedit.EditPane.close(EditPane.java:855)
at org.gjt.sp.jedit.View.close(View.java:1502)
at org.gjt.sp.jedit.jEdit.closeView(jEdit.java:4552)
at org.gjt.sp.jedit.jEdit.exit(jEdit.java:2980)
at org.gjt.sp.jedit.jEdit.closeView(jEdit.java:4543)
at org.gjt.sp.jedit.jEdit.closeView(jEdit.java:2630)
at org.gjt.sp.jedit.View$WindowHandler.windowClosing(View.java:2239)
at java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:349)
at java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:349)
at java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:349)
at java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:349)
at java.awt.Window.processWindowEvent(Window.java:2054)
at javax.swing.JFrame.processWindowEvent(JFrame.java:305)
at java.awt.Window.processEvent(Window.java:2013)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
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:80)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at org.GNOME.Accessibility.AtkWrapper$5.dispatchEvent(AtkWrapper.java:700)
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)

"AWT-Shutdown" #15 prio=5 os_prio=0 tid=0x00007fa5f436e000 nid=0x36b2 in Object.wait() [0x00007fa57c8d0000]
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 <0x00000006c9069ea0> (a java.lang.Object)
at java.lang.Thread.run(Thread.java:748)

"process reaper" #13 daemon prio=10 os_prio=0 tid=0x00007fa5f42f5000 nid=0x36b1 waiting on condition [0x00007fa5b8089000]
java.lang.Thread.State: TIMED_WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000006c91936d8> (a java.util.concurrent.SynchronousQueue$TransferStack)
at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362)
at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1073)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

"AWT-XAWT" #12 daemon prio=6 os_prio=0 tid=0x00007fa5f42e7800 nid=0x36af runnable [0x00007fa591f91000]
java.lang.Thread.State: RUNNABLE
at sun.awt.X11.XToolkit.waitForEvents(Native Method)
at sun.awt.X11.XToolkit.run(XToolkit.java:568)
at sun.awt.X11.XToolkit.run(XToolkit.java:532)
at java.lang.Thread.run(Thread.java:748)

"Java2D Disposer" #10 daemon prio=10 os_prio=0 tid=0x00007fa5f42c6800 nid=0x36ae in Object.wait() [0x00007fa5924a9000]
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 <0x00000006c8c05c70> (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:748)

"Service Thread" #9 daemon prio=9 os_prio=0 tid=0x00007fa5f40e3800 nid=0x36ac runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE

"C1 CompilerThread3" #8 daemon prio=9 os_prio=0 tid=0x00007fa5f40be800 nid=0x36ab waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE

"C2 CompilerThread2" #7 daemon prio=9 os_prio=0 tid=0x00007fa5f40ba000 nid=0x36aa waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007fa5f40b8000 nid=0x36a9 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007fa5f40b5000 nid=0x36a8 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007fa5f40b3000 nid=0x36a7 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE

"Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007fa5f408b800 nid=0x36a6 in Object.wait() [0x00007fa5e0bbb000]
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 <0x00000006c8bce0e8> (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)

"Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007fa5f4087000 nid=0x36a5 in Object.wait() [0x00007fa5e0cbc000]
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 <0x00000006c9109238> (a java.lang.ref.Reference$Lock)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:153)

"VM Thread" os_prio=0 tid=0x00007fa5f407f800 nid=0x36a4 runnable

"GC task thread#0 (ParallelGC)" os_prio=0 tid=0x00007fa5f401f000 nid=0x369c runnable

"GC task thread#1 (ParallelGC)" os_prio=0 tid=0x00007fa5f4020800 nid=0x369d runnable

"GC task thread#2 (ParallelGC)" os_prio=0 tid=0x00007fa5f4022800 nid=0x369e runnable

"GC task thread#3 (ParallelGC)" os_prio=0 tid=0x00007fa5f4024000 nid=0x369f runnable

"GC task thread#4 (ParallelGC)" os_prio=0 tid=0x00007fa5f4026000 nid=0x36a0 runnable

"GC task thread#5 (ParallelGC)" os_prio=0 tid=0x00007fa5f4027800 nid=0x36a1 runnable

"GC task thread#6 (ParallelGC)" os_prio=0 tid=0x00007fa5f4029800 nid=0x36a2 runnable

"GC task thread#7 (ParallelGC)" os_prio=0 tid=0x00007fa5f402b000 nid=0x36a3 runnable

"VM Periodic Task Thread" os_prio=0 tid=0x00007fa5f40e6000 nid=0x36ad waiting on condition

JNI global references: 2913

Heap
PSYoungGen total 751616K, used 66499K [0x000000076cf00000, 0x000000079ef80000, 0x00000007c0000000)
eden space 730112K, 6% used [0x000000076cf00000,0x000000076fb10a80,0x0000000799800000)
from space 21504K, 99% used [0x000000079da80000,0x000000079ef604c0,0x000000079ef80000)
to space 31744K, 0% used [0x000000079b180000,0x000000079b180000,0x000000079d080000)
ParOldGen total 160256K, used 45116K [0x00000006c6c00000, 0x00000006d0880000, 0x000000076cf00000)
object space 160256K, 28% used [0x00000006c6c00000,0x00000006c980f100,0x00000006d0880000)
Metaspace used 30160K, capacity 31436K, committed 31744K, reserved 1077248K
class space used 3533K, capacity 4051K, committed 4096K, reserved 1048576K

The gnome.accessibility.atkwrapper stuff makes me think that either
a. you are using the gtk look and feel or
b. you are missing libatk-wrapper-java (sudo apt-get install libatk-wrapper-java)

Are you using metal look and feel?
Does installing this package do anything for you?

I'm using the metal look and feel. libatk-wrapper-java is already the newest version (0.33.3-13).