Created
October 18, 2016 10:49
-
-
Save bdionne/c0bb93df41c51123b7f4e693750865cf to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Java-level deadlock detected | |
| This means that some threads are blocked waiting to enter a synchronization block or | |
| waiting to reenter a synchronization block after an Object.wait() call, where each thread | |
| owns one monitor while trying to obtain another monitor already held by another thread. | |
| Deadlock: | |
| AWT-EventQueue-0 is waiting to lock java.util.concurrent.locks.ReentrantReadWriteLock$NonfairSync@199666c5 which is held by Thread-4 | |
| Thread-4 is waiting to lock java.awt.Component$AWTTreeLock@60803f48 which is held by AWT-EventQueue-0 | |
| Thread stacks | |
| AWT-EventQueue-0 [WAITING] | |
| sun.misc.Unsafe.park(native method) | |
| java.util.concurrent.locks.LockSupport.park(LockSupport.java:175) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:836) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.doAcquireShared(AbstractQueuedSynchronizer.java:967) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireShared(AbstractQueuedSynchronizer.java:1283) | |
| java.util.concurrent.locks.ReentrantReadWriteLock$ReadLock.lock(ReentrantReadWriteLock.java:727) | |
| uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.getOntologyID(ConcurrentOWLOntologyImpl.java:123) | |
| org.protege.editor.owl.ui.renderer.OWLOntologyCellRenderer.getOntologyLabelText(OWLOntologyCellRenderer.java:51) | |
| org.protege.editor.owl.ui.renderer.OWLOntologyCellRenderer.getListCellRendererComponent(OWLOntologyCellRenderer.java:40) | |
| com.apple.laf.AquaComboBoxButton.doRendererPaint(AquaComboBoxButton.java:167) | |
| com.apple.laf.AquaComboBoxButton.paintComponent(AquaComboBoxButton.java:159) | |
| javax.swing.JComponent.paint(JComponent.java:1056) | |
| javax.swing.JComponent.paintChildren(JComponent.java:889) | |
| javax.swing.JComponent.paint(JComponent.java:1065) | |
| javax.swing.JComponent.paintChildren(JComponent.java:889) | |
| javax.swing.JComponent.paint(JComponent.java:1065) | |
| javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) | |
| javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) | |
| javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) | |
| javax.swing.RepaintManager.paint(RepaintManager.java:1272) | |
| javax.swing.JComponent._paintImmediately(JComponent.java:5158) | |
| javax.swing.JComponent.paintImmediately(JComponent.java:4969) | |
| javax.swing.RepaintManager$4.run(RepaintManager.java:831) | |
| javax.swing.RepaintManager$4.run(RepaintManager.java:814) | |
| java.security.AccessController.doPrivileged(native method) | |
| java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) | |
| javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) | |
| javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) | |
| javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) | |
| javax.swing.RepaintManager.access$1200(RepaintManager.java:64) | |
| javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) | |
| java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) | |
| java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) | |
| java.awt.EventQueue.access$500(EventQueue.java:97) | |
| java.awt.EventQueue$3.run(EventQueue.java:709) | |
| java.awt.EventQueue$3.run(EventQueue.java:703) | |
| java.security.AccessController.doPrivileged(native method) | |
| java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) | |
| java.awt.EventQueue.dispatchEvent(EventQueue.java:726) | |
| java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) | |
| java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) | |
| java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109) | |
| java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184) | |
| java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:229) | |
| java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:227) | |
| java.security.AccessController.doPrivileged(native method) | |
| java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:227) | |
| java.awt.Dialog.show(Dialog.java:1084) | |
| java.awt.Component.show(Component.java:1671) | |
| java.awt.Component.setVisible(Component.java:1623) | |
| java.awt.Window.setVisible(Window.java:1014) | |
| java.awt.Dialog.setVisible(Dialog.java:1005) | |
| gov.nih.nci.ui.dialog.TaskProgressDialog.run(TaskProgressDialog.java:149) | |
| gov.nih.nci.ui.dialog.BatchProcessingDialog.actionPerformed(BatchProcessingDialog.java:305) | |
| javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) | |
| javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) | |
| javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) | |
| javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) | |
| javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) | |
| java.awt.Component.processMouseEvent(Component.java:6533) | |
| javax.swing.JComponent.processMouseEvent(JComponent.java:3324) | |
| java.awt.Component.processEvent(Component.java:6298) | |
| java.awt.Container.processEvent(Container.java:2236) | |
| java.awt.Component.dispatchEventImpl(Component.java:4889) | |
| java.awt.Container.dispatchEventImpl(Container.java:2294) | |
| java.awt.Component.dispatchEvent(Component.java:4711) | |
| java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) | |
| java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) | |
| java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) | |
| java.awt.Container.dispatchEventImpl(Container.java:2280) | |
| java.awt.Window.dispatchEventImpl(Window.java:2746) | |
| java.awt.Component.dispatchEvent(Component.java:4711) | |
| java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) | |
| java.awt.EventQueue.access$500(EventQueue.java:97) | |
| java.awt.EventQueue$3.run(EventQueue.java:709) | |
| java.awt.EventQueue$3.run(EventQueue.java:703) | |
| java.security.AccessController.doPrivileged(native method) | |
| java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) | |
| java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) | |
| java.awt.EventQueue$4.run(EventQueue.java:731) | |
| java.awt.EventQueue$4.run(EventQueue.java:729) | |
| java.security.AccessController.doPrivileged(native method) | |
| java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) | |
| java.awt.EventQueue.dispatchEvent(EventQueue.java:728) | |
| java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) | |
| java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) | |
| java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109) | |
| java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184) | |
| java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:229) | |
| java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:227) | |
| java.security.AccessController.doPrivileged(native method) | |
| java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:227) | |
| java.awt.Dialog.show(Dialog.java:1084) | |
| java.awt.Component.show(Component.java:1671) | |
| java.awt.Component.setVisible(Component.java:1623) | |
| java.awt.Window.setVisible(Window.java:1014) | |
| java.awt.Dialog.setVisible(Dialog.java:1005) | |
| gov.nih.nci.ui.dialog.BatchProcessingDialog.init(BatchProcessingDialog.java:192) | |
| gov.nih.nci.ui.dialog.BatchProcessingDialog.<init>(BatchProcessingDialog.java:73) | |
| gov.nih.nci.ui.NCIToldOWLClassHierarchyViewComponent$2.actionPerformed(NCIToldOWLClassHierarchyViewComponent.java:81) | |
| org.protege.editor.core.ui.view.ViewActionAdapter.actionPerformed(ViewActionAdapter.java:46) | |
| javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) | |
| javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) | |
| javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) | |
| javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) | |
| javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) | |
| java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289) | |
| java.awt.Component.processMouseEvent(Component.java:6533) | |
| javax.swing.JComponent.processMouseEvent(JComponent.java:3324) | |
| java.awt.Component.processEvent(Component.java:6298) | |
| java.awt.Container.processEvent(Container.java:2236) | |
| java.awt.Component.dispatchEventImpl(Component.java:4889) | |
| java.awt.Container.dispatchEventImpl(Container.java:2294) | |
| java.awt.Component.dispatchEvent(Component.java:4711) | |
| java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) | |
| java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) | |
| java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) | |
| java.awt.Container.dispatchEventImpl(Container.java:2280) | |
| java.awt.Window.dispatchEventImpl(Window.java:2746) | |
| java.awt.Component.dispatchEvent(Component.java:4711) | |
| java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) | |
| java.awt.EventQueue.access$500(EventQueue.java:97) | |
| java.awt.EventQueue$3.run(EventQueue.java:709) | |
| java.awt.EventQueue$3.run(EventQueue.java:703) | |
| java.security.AccessController.doPrivileged(native method) | |
| java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) | |
| java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) | |
| java.awt.EventQueue$4.run(EventQueue.java:731) | |
| java.awt.EventQueue$4.run(EventQueue.java:729) | |
| java.security.AccessController.doPrivileged(native method) | |
| java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) | |
| java.awt.EventQueue.dispatchEvent(EventQueue.java:728) | |
| java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) | |
| java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) | |
| java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) | |
| java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) | |
| java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) | |
| java.awt.EventDispatchThread.run(EventDispatchThread.java:82) | |
| Thread-4 [BLOCKED; waiting to lock java.awt.Component$AWTTreeLock@60803f48] | |
| java.awt.Component.setFont(Component.java:1893) | |
| java.awt.Container.setFont(Container.java:1750) | |
| javax.swing.JComponent.setFont(JComponent.java:2754) | |
| org.protege.editor.owl.ui.renderer.OWLCellRenderer.setupFont(OWLCellRenderer.java:291) | |
| org.protege.editor.owl.ui.renderer.OWLCellRenderer.resetStyles(OWLCellRenderer.java:942) | |
| org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareTextPane(OWLCellRenderer.java:676) | |
| org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareRenderer(OWLCellRenderer.java:491) | |
| org.protege.editor.owl.ui.renderer.OWLCellRenderer.getTreeCellRendererComponent(OWLCellRenderer.java:377) | |
| org.protege.editor.owl.ui.tree.OWLObjectTreeCellRenderer.getTreeCellRendererComponent(OWLObjectTreeCellRenderer.java:38) | |
| javax.swing.plaf.basic.BasicTreeUI$NodeDimensionsHandler.getNodeDimensions(BasicTreeUI.java:2807) | |
| javax.swing.tree.AbstractLayoutCache.getNodeDimensions(AbstractLayoutCache.java:492) | |
| javax.swing.tree.VariableHeightLayoutCache$TreeStateNode.updatePreferredSize(VariableHeightLayoutCache.java:1360) | |
| javax.swing.tree.VariableHeightLayoutCache.createNodeAt(VariableHeightLayoutCache.java:782) | |
| javax.swing.tree.VariableHeightLayoutCache.treeNodesInserted(VariableHeightLayoutCache.java:491) | |
| javax.swing.plaf.basic.BasicTreeUI$Handler.treeNodesInserted(BasicTreeUI.java:3878) | |
| javax.swing.tree.DefaultTreeModel.fireTreeNodesInserted(DefaultTreeModel.java:517) | |
| javax.swing.tree.DefaultTreeModel.nodesWereInserted(DefaultTreeModel.java:314) | |
| javax.swing.tree.DefaultTreeModel.insertNodeInto(DefaultTreeModel.java:241) | |
| org.protege.editor.owl.ui.tree.OWLObjectTree.updateNode(OWLObjectTree.java:273) | |
| org.protege.editor.owl.ui.tree.OWLObjectTree.access$000(OWLObjectTree.java:54) | |
| org.protege.editor.owl.ui.tree.OWLObjectTree$1.nodeChanged(OWLObjectTree.java:105) | |
| org.protege.editor.owl.model.hierarchy.AbstractOWLObjectHierarchyProvider.fireNodeChanged(AbstractOWLObjectHierarchyProvider.java:239) | |
| org.protege.editor.owl.model.hierarchy.AssertedClassHierarchyProvider.notifyNodeChanges(AssertedClassHierarchyProvider.java:184) | |
| org.protege.editor.owl.model.hierarchy.AssertedClassHierarchyProvider.handleChanges(AssertedClassHierarchyProvider.java:160) | |
| org.protege.editor.owl.model.hierarchy.AssertedClassHierarchyProvider$$Lambda$135/1759670434.ontologiesChanged(unknown source) | |
| org.semanticweb.owlapi.model.DefaultChangeBroadcastStrategy.broadcastChanges(DefaultChangeBroadcastStrategy.java:38) | |
| uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.broadcastChanges(OWLOntologyManagerImpl.java:1490) | |
| uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:590) | |
| org.protege.editor.owl.model.OWLModelManagerImpl.applyChanges(OWLModelManagerImpl.java:694) | |
| gov.nih.nci.ui.NCIEditTab.createNewChild(NCIEditTab.java:1002) | |
| gov.nih.nci.utils.batch.BatchLoadTask.processTask(BatchLoadTask.java:57) | |
| gov.nih.nci.ui.dialog.TaskProgressDialog$BatchProc.run(TaskProgressDialog.java:230) | |
| Frozen threads found (potential deadlock) | |
| It seems that the following threads have not changed their stack for more than 10 seconds. | |
| These threads are possibly (but not necessarily!) in a deadlock or hung. | |
| process reaper <--- Frozen for at least 13m 18s | |
| java.lang.UNIXProcess$ProcessPipeInputStream.processExited() UNIXProcess.java:528 | |
| java.lang.UNIXProcess.lambda$initStreams$3() UNIXProcess.java:299 | |
| java.lang.UNIXProcess$$Lambda$7.run() | |
| java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor$Worker) ThreadPoolExecutor.java:1142 | |
| java.util.concurrent.ThreadPoolExecutor$Worker.run() ThreadPoolExecutor.java:617 | |
| java.lang.Thread.run() Thread.java:745 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment