"Potential deadlock in AWT Event Queue detected" when working with large table

Hi,

I am working on KNIME 3.2.1 with 16G heap space, manipulating a matrix containing 300 rows and 125000 columns. Very often KNIME gives a deadlock error and freezes, and most of the times I have to kill the process from the task manager - at the bottom you'll find the trace taken from the log file after it recovered by itself.

Do you have any clue on what's happening?

Thanks,

Sonia

 

2016-10-17 11:57:38,362 : WARN  : pool-2-thread-1 : KNIMEApplication$4 :  :  : Potential deadlock in AWT Event Queue detected. Full thread dump will follow as debug ouput.

2016-10-17 11:57:38,362 : DEBUG : pool-2-thread-1 : KNIMEApplication$4 :  :  : "KNIME-TableIO-2" Id=103 TIMED_WAITING on java.util.concurrent.SynchronousQueue$TransferStack@7a838ec5
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.SynchronousQueue$TransferStack@7a838ec5
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
    at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362)
    at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1066)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"Worker-17" Id=102 TIMED_WAITING on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:52)

"OutPortView-Updater-3" Id=101 TIMED_WAITING on java.util.concurrent.SynchronousQueue$TransferStack@2cf55d3a
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.SynchronousQueue$TransferStack@2cf55d3a
    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:1066)
    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)

"Worker-16" Id=100 TIMED_WAITING on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:52)

"Worker-14" Id=98 TIMED_WAITING on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:52)

"KNIME Memory Alert Distributor" Id=86 WAITING on java.lang.Object@77f6aa8f
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.Object@77f6aa8f
    at java.lang.Object.wait(Object.java:502)
    at org.knime.core.data.util.memory.MemoryAlertSystem$3.run(MemoryAlertSystem.java:270)

"AWT-EventQueue-0" Id=81 RUNNABLE
    at java.util.ArrayList.indexOf(ArrayList.java:317)
    at java.util.ArrayList.contains(ArrayList.java:300)
    at org.knime.core.node.util.filter.NameFilterPanel.update(NameFilterPanel.java:611)
    at org.knime.core.node.util.filter.NameFilterPanel.setNameFilter(NameFilterPanel.java:839)
    at org.knime.core.node.util.filter.column.DataColumnSpecFilterPanel.loadConfiguration(DataColumnSpecFilterPanel.java:184)
    at org.knime.base.node.preproc.filter.column.DataColumnSpecFilterNodeDialogPane.loadSettingsFrom(DataColumnSpecFilterNodeDialogPane.java:94)
    at org.knime.core.node.NodeDialogPane.loadSettingsFrom(NodeDialogPane.java:564)
    at org.knime.core.node.NodeDialogPane.callDerivedLoadSettingsFrom(NodeDialogPane.java:473)
    at org.knime.core.node.NodeDialogPane$3.run(NodeDialogPane.java:426)
    at org.knime.core.node.util.ViewUtils$3.run(ViewUtils.java:351)
    at org.knime.core.node.util.ViewUtils$2.run(ViewUtils.java:153)
    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)

"AWT-Shutdown" Id=82 WAITING on java.lang.Object@7fa0eb8e
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.Object@7fa0eb8e
    at java.lang.Object.wait(Object.java:502)
    at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295)
    at java.lang.Thread.run(Thread.java:745)

"KNIME-WFM-Parent-Notifier" Id=79 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@31d8c7be
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@31d8c7be
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
    at java.util.concurrent.ArrayBlockingQueue.take(ArrayBlockingQueue.java:403)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"TimerQueue" Id=78 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@15abfccc
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@15abfccc
    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:171)
    at java.lang.Thread.run(Thread.java:745)

    Number of locked synchronizers = 1
    - java.util.concurrent.locks.ReentrantLock$NonfairSync@73b8b1d8

"Unknown Progress Timer" Id=71 WAITING on java.util.ArrayList@6daf996c
    at java.lang.Object.wait(Native Method)
    -  waiting on java.util.ArrayList@6daf996c
    at java.lang.Object.wait(Object.java:502)
    at org.knime.workbench.editor2.figures.ProgressFigure$UnknownProgressTimer.run(ProgressFigure.java:554)

"KNIME Sync Exec Dispatcher-1" Id=70 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@1abd5650
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@1abd5650
    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)

"[ThreadPool Manager] - Idle Thread" Id=66 WAITING on org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor@2cbd12ae
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor@2cbd12ae
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor.run(Executor.java:106)

"KNIME Progress Updater" Id=63 TIMED_WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@66bac669
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@66bac669
    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)

"Thread-8" Id=54 TIMED_WAITING
    at java.lang.Thread.sleep(Native Method)
    at org.eclipse.equinox.internal.p2.updatechecker.UpdateChecker$UpdateCheckThread.run(UpdateChecker.java:68)

"EventAdmin Async Event Dispatcher Thread" Id=52 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@774f572b
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@774f572b
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"pool-3-thread-3" Id=49 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    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)

"pool-3-thread-2" Id=48 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    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)

"pool-3-thread-1" Id=47 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    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)

"ServerSpace Update Timer" Id=44 TIMED_WAITING on java.util.TaskQueue@435cda7e
    at java.lang.Object.wait(Native Method)
    -  waiting on java.util.TaskQueue@435cda7e
    at java.util.TimerThread.mainLoop(Timer.java:552)
    at java.util.TimerThread.run(Timer.java:505)

"Java indexing" Id=36 WAITING on org.eclipse.jdt.internal.core.search.indexing.IndexManager@7365c5f2
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.jdt.internal.core.search.indexing.IndexManager@7365c5f2
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.jdt.internal.core.search.processing.JobManager.run(JobManager.java:382)
    at java.lang.Thread.run(Thread.java:745)

"pool-2-thread-1" Id=32 RUNNABLE
    at sun.management.ThreadImpl.dumpThreads0(Native Method)
    at sun.management.ThreadImpl.dumpAllThreads(ThreadImpl.java:446)
    at org.knime.core.util.GUIDeadlockDetector.createStacktrace(GUIDeadlockDetector.java:162)
    at org.knime.core.util.GUIDeadlockDetector$CheckTask.run(GUIDeadlockDetector.java:145)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
    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)

    Number of locked synchronizers = 1
    - java.util.concurrent.ThreadPoolExecutor$Worker@3d53e876

"pool-1-thread-1" Id=31 TIMED_WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7e1e32ba
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7e1e32ba
    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)

"Provisioning Event Dispatcher" Id=30 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@7dafaf8d
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@7dafaf8d
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"AWT-Windows" Id=26 RUNNABLE (in native)
    at sun.awt.windows.WToolkit.eventLoop(Native Method)
    at sun.awt.windows.WToolkit.run(WToolkit.java:306)
    at java.lang.Thread.run(Thread.java:745)

"Java2D Disposer" Id=24 WAITING on java.lang.ref.ReferenceQueue$Lock@5805056c
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.ref.ReferenceQueue$Lock@5805056c
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    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)

"Bundle File Closer" Id=23 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@51211cb
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@51211cb
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"EMF Reference Cleaner" Id=22 WAITING on java.lang.ref.ReferenceQueue$Lock@a967831
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.ref.ReferenceQueue$Lock@a967831
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
    at org.eclipse.emf.common.util.CommonUtil$1ReferenceClearingQueuePollingThread.run(CommonUtil.java:70)

"Worker-JM" Id=18 WAITING on java.util.ArrayList@a456d29
    at java.lang.Object.wait(Native Method)
    -  waiting on java.util.ArrayList@a456d29
    at org.eclipse.core.internal.jobs.InternalWorker.run(InternalWorker.java:59)

"[Timer] - Main Queue Handler" Id=17 TIMED_WAITING on java.lang.Object@7a1b2768
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.Object@7a1b2768
    at org.eclipse.equinox.internal.util.impl.tpt.timer.TimerImpl.run(TimerImpl.java:141)
    at java.lang.Thread.run(Thread.java:745)

"Start Level: Equinox Container: 60b432c2-5694-0016-1df5-88f44e40f4e7" Id=15 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@1d7e3af2
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@1d7e3af2
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"Framework Event Dispatcher: Equinox Container: 60b432c2-5694-0016-1df5-88f44e40f4e7" Id=14 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@6f12fda9
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@6f12fda9
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"Active Thread: Equinox Container: 60b432c2-5694-0016-1df5-88f44e40f4e7" Id=12 TIMED_WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@56fc478a
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@56fc478a
    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)

"Attach Listener" Id=5 RUNNABLE

"Signal Dispatcher" Id=4 RUNNABLE

"Finalizer" Id=3 WAITING on java.lang.ref.ReferenceQueue$Lock@77f14459
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.ref.ReferenceQueue$Lock@77f14459
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
    at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"Reference Handler" Id=2 WAITING on java.lang.ref.Reference$Lock@54720da8
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.ref.Reference$Lock@54720da8
    at java.lang.Object.wait(Object.java:502)
    at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)

"main" Id=1 RUNNABLE
    at org.eclipse.swt.internal.win32.OS.WaitMessage(Native Method)
    at org.eclipse.swt.widgets.Display.sleep(Display.java:4728)
    at org.knime.core.node.util.ViewUtils.invokeAndWaitInEDT(ViewUtils.java:164)
    at org.knime.core.node.NodeDialogPane.internalLoadSettingsFrom(NodeDialogPane.java:432)
    at org.knime.core.node.Node.getDialogPaneWithSettings(Node.java:2000)
    at org.knime.core.node.workflow.NativeNodeContainer.getDialogPaneWithSettings(NativeNodeContainer.java:1103)
    at org.knime.core.node.workflow.NodeContainer.getDialogPaneWithSettings(NodeContainer.java:949)
    at org.knime.workbench.ui.wrapper.WrappedNodeDialog.<init>(WrappedNodeDialog.java:133)
    at org.knime.workbench.editor2.editparts.NodeContainerEditPart.openNodeDialog(NodeContainerEditPart.java:820)
    at org.knime.workbench.editor2.editparts.NodeContainerEditPart.openDialog(NodeContainerEditPart.java:729)
    at org.knime.workbench.editor2.editparts.NodeContainerEditPart.performRequest(NodeContainerEditPart.java:331)
    at org.eclipse.gef.tools.SelectEditPartTracker.performOpen(SelectEditPartTracker.java:194)
    at org.eclipse.gef.tools.SelectEditPartTracker.handleDoubleClick(SelectEditPartTracker.java:137)
    at org.knime.workbench.editor2.WorkflowSelectionDragEditPartsTracker.handleDoubleClick(WorkflowSelectionDragEditPartsTracker.java:112)
    at org.eclipse.gef.tools.AbstractTool.mouseDoubleClick(AbstractTool.java:1069)
    at org.eclipse.gef.tools.SelectionTool.mouseDoubleClick(SelectionTool.java:527)
    at org.eclipse.gef.EditDomain.mouseDoubleClick(EditDomain.java:231)
    at org.eclipse.gef.ui.parts.DomainEventDispatcher.dispatchMouseDoubleClicked(DomainEventDispatcher.java:291)
    at org.eclipse.draw2d.LightweightSystem$EventHandler.mouseDoubleClick(LightweightSystem.java:518)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:196)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4362)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1113)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4180)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3769)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$4.run(PartRenderingEngine.java:1127)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:337)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1018)
    at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:156)
    at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:654)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:337)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:598)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
    at org.knime.product.rcp.KNIMEApplication.start(KNIMEApplication.java:137)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:380)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:235)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:669)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:608)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1515)

 

 

Mh, something for official support - quite the handsomely sized dataset there! :)

-E

 

125 thousand columns(!) isn't quite the average data set. This is a lot of meta data and the stack trace suggests that it's busy updating UI components (it's a list in the UI with 125k elements -- this isn't a simple task).

You may get further using the "wide data" nodes that are part of labs. They combine all the numeric features into a single column.