KNIME freezes/crashes in 64-bit Linux

I use Red Hat 6.4 with KNIME 2.8.1, and during a long KNIME session I find that there’s a strong likelihood that opening a dialog box will freeze KNIME entirely, with some background activity still occurring but no option to save or configure anything. Even terminating the KNIME process fails.

Hi,

 

I get exactly the same problem in Kubuntu 64 bit (KDE graphical user interface), using KNIME 2.8.2 - opening certain dialogs (no apparent pattern) just causes it to eventually freeze & be unable to terminate KNIME, without using the kill -KILL [PID] command in the terminal.

 

I can't find any log files generated whenever it does this either.  Most confusing!

Ed.

If this happens, please issue a "jstack [pid]" and send the output. jstack is part of the JDK therefore you may need to install that first.

Hi,

Appologies for reviving an old thread. I am having the same issue with Knime freezing on Lubuntu 64bit. here is the output (attached) from jstack for the java process (stuck at 25% cpu). The knime process does not exist eventhough the knime window is still displayed. I'm testing if it is related to tightvnc but I appreciate any other input.

Thanks,

 

Fadi

This is indeed a very common occurrance. CV reader, sdf reader, xls reader just about anything gives the same freeze.  Is this related to the fast double clicking-freeze issue that was present earlier?

This is a bug in Java which will be fixed with the upcoming 1.7.0_60 release. KNIME 2.10 will use this Java version.

I am still having the same issue. Here is my jstack. Any help would be greatly apprecaited:

015-06-17 14:43:53
Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.60-b09 mixed mode):

"Attach Listener" daemon prio=10 tid=0x00007f03b8001000 nid=0x3efb waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"[ThreadPool Manager] - Idle Thread" daemon prio=10 tid=0x00007f0380004000 nid=0x3ecc in Object.wait() [0x00007f02b5099000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f1df0588> (a org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor)
    at java.lang.Object.wait(Object.java:503)
    at org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor.run(Executor.java:106)
    - locked <0x00000000f1df0588> (a org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor)

"SwingWorker-pool-2-thread-1" daemon prio=10 tid=0x00007f02dc152000 nid=0x3ec9 waiting on condition [0x00007f02b4c8f000]
   java.lang.Thread.State: WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000f1321968> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.park(Unknown Source)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source)
    at java.util.concurrent.LinkedBlockingQueue.take(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

"Thread-13" daemon prio=10 tid=0x00007f02a800a000 nid=0x3ec6 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"AWT-EventQueue-0" prio=10 tid=0x00007f03f9070000 nid=0x3ec2 waiting on condition [0x00007f02b5894000]
   java.lang.Thread.State: WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000f33af190> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.park(Unknown Source)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source)
    at java.awt.EventQueue.getNextEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)

"AWT-Shutdown" prio=10 tid=0x00007f03f906f800 nid=0x3ec1 in Object.wait() [0x00007f02b5793000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000effdb3d0> (a java.lang.Object)
    at java.lang.Object.wait(Object.java:503)
    at sun.awt.AWTAutoShutdown.run(Unknown Source)
    - locked <0x00000000effdb3d0> (a java.lang.Object)
    at java.lang.Thread.run(Unknown Source)

"TimerQueue" daemon prio=10 tid=0x00007f02dc08f800 nid=0x3ec0 waiting on condition [0x00007f02b519a000]
   java.lang.Thread.State: WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000f0692388> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.park(Unknown Source)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source)
    at java.util.concurrent.DelayQueue.take(Unknown Source)
    at javax.swing.TimerQueue.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

"Unknown Progress Timer" prio=10 tid=0x00007f03f8c7a800 nid=0x3ebc in Object.wait() [0x00007f035bffe000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000ed566460> (a java.util.ArrayList)
    at java.lang.Object.wait(Object.java:503)
    at org.knime.workbench.editor2.figures.ProgressFigure$UnknownProgressTimer.run(ProgressFigure.java:549)
    - locked <0x00000000ed566460> (a java.util.ArrayList)

"KNIME Sync Exec Dispatcher-1" daemon prio=10 tid=0x00007f03f8262800 nid=0x3ebb waiting on condition [0x00007f02fc154000]
   java.lang.Thread.State: WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000ecf5bc80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.park(Unknown Source)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source)
    at java.util.concurrent.LinkedBlockingQueue.take(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

"Worker-5" prio=10 tid=0x00007f036808f800 nid=0x3eb4 in Object.wait() [0x00007f02f4b5c000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f35ffa58> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    - locked <0x00000000f35ffa58> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:50)

"Worker-4" prio=10 tid=0x00007f036801d000 nid=0x3eb3 in Object.wait() [0x00007f02fc6a2000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f35ffa58> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    - locked <0x00000000f35ffa58> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:50)

"KNIME Progress Timer" daemon prio=10 tid=0x00007f0370041800 nid=0x3eac in Object.wait() [0x00007f02f74f9000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f3b72d78> (a java.util.TaskQueue)
    at java.util.TimerThread.mainLoop(Unknown Source)
    - locked <0x00000000f3b72d78> (a java.util.TaskQueue)
    at java.util.TimerThread.run(Unknown Source)

"ServerSpace Update Timer" daemon prio=10 tid=0x00007f03f94fb000 nid=0x3eab in Object.wait() [0x00007f02f76fc000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f3b73378> (a java.util.TaskQueue)
    at java.util.TimerThread.mainLoop(Unknown Source)
    - locked <0x00000000f3b73378> (a java.util.TaskQueue)
    at java.util.TimerThread.run(Unknown Source)

"SelectorThread" daemon prio=10 tid=0x00007f03f94bb000 nid=0x3eaa runnable [0x00007f02f77fd000]
   java.lang.Thread.State: RUNNABLE
    at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
    at sun.nio.ch.EPollArrayWrapper.poll(Unknown Source)
    at sun.nio.ch.EPollSelectorImpl.doSelect(Unknown Source)
    at sun.nio.ch.SelectorImpl.lockAndDoSelect(Unknown Source)
    - locked <0x00000000f3b75058> (a sun.nio.ch.Util$2)
    - locked <0x00000000f3b75048> (a java.util.Collections$UnmodifiableSet)
    - locked <0x00000000f3b75000> (a sun.nio.ch.EPollSelectorImpl)
    at sun.nio.ch.SelectorImpl.select(Unknown Source)
    at com.sun.corba.ee.impl.transport.SelectorImpl.run(SelectorImpl.java:283)

"AWT-XAWT" daemon prio=10 tid=0x00007f03f8e20000 nid=0x3e99 runnable [0x00007f0384ba4000]
   java.lang.Thread.State: RUNNABLE
    at sun.awt.X11.XToolkit.waitForEvents(Native Method)
    at sun.awt.X11.XToolkit.run(Unknown Source)
    at sun.awt.X11.XToolkit.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

"Java2D Disposer" daemon prio=10 tid=0x00007f03f8e10000 nid=0x3e98 in Object.wait() [0x00007f0384ca5000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f360fac0> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(Unknown Source)
    - locked <0x00000000f360fac0> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(Unknown Source)
    at sun.java2d.Disposer.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

"Bundle File Closer" daemon prio=10 tid=0x00007f03f8da2000 nid=0x3e97 in Object.wait() [0x00007f03847b9000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f3b84cf0> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at java.lang.Object.wait(Object.java:503)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    - locked <0x00000000f3b84cf0> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"Provisioning Event Dispatcher" daemon prio=10 tid=0x00007f03f8786800 nid=0x3e94 in Object.wait() [0x00007f038556f000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f34e8a10> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at java.lang.Object.wait(Object.java:503)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    - locked <0x00000000f34e8a10> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"Worker-JM" prio=10 tid=0x00007f03940a4800 nid=0x3e8e in Object.wait() [0x00007f0387ffe000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f35ffa80> (a java.util.ArrayList)
    at org.eclipse.core.internal.jobs.InternalWorker.run(InternalWorker.java:58)
    - locked <0x00000000f35ffa80> (a java.util.ArrayList)

"[Timer] - Main Queue Handler" daemon prio=10 tid=0x00007f0394053000 nid=0x3e8d in Object.wait() [0x00007f03a4189000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f3b85280> (a java.lang.Object)
    at org.eclipse.equinox.internal.util.impl.tpt.timer.TimerImpl.run(TimerImpl.java:141)
    - locked <0x00000000f3b85280> (a java.lang.Object)
    at java.lang.Thread.run(Unknown Source)

"Framework Event Dispatcher" daemon prio=10 tid=0x00007f039400a800 nid=0x3e8b in Object.wait() [0x00007f03a438b000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f3b853e8> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at java.lang.Object.wait(Object.java:503)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    - locked <0x00000000f3b853e8> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"Start Level Event Dispatcher" daemon prio=10 tid=0x00007f03f84ba000 nid=0x3e8a in Object.wait() [0x00007f03a448c000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f3b856a0> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at java.lang.Object.wait(Object.java:503)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    - locked <0x00000000f3b856a0> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"State Data Manager" daemon prio=10 tid=0x00007f03f84f0800 nid=0x3e89 waiting on condition [0x00007f03a6d51000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
    at java.lang.Thread.sleep(Native Method)
    at org.eclipse.osgi.internal.baseadaptor.StateManager.run(StateManager.java:297)
    at java.lang.Thread.run(Unknown Source)

"Framework Active Thread" prio=10 tid=0x00007f03f84a6800 nid=0x3e88 in Object.wait() [0x00007f03ac14c000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f33bd278> (a org.eclipse.osgi.framework.internal.core.Framework)
    at org.eclipse.osgi.framework.internal.core.Framework.run(Framework.java:1817)
    - locked <0x00000000f33bd278> (a org.eclipse.osgi.framework.internal.core.Framework)
    at java.lang.Thread.run(Unknown Source)

"Service Thread" daemon prio=10 tid=0x00007f03f8216000 nid=0x3e84 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=10 tid=0x00007f03f820f800 nid=0x3e83 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=10 tid=0x00007f03f820d000 nid=0x3e82 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=10 tid=0x00007f03f81e1800 nid=0x3e81 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=10 tid=0x00007f03f81c2000 nid=0x3e80 in Object.wait() [0x00007f03d63e2000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f3cd09c8> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(Unknown Source)
    - locked <0x00000000f3cd09c8> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(Unknown Source)
    at java.lang.ref.Finalizer$FinalizerThread.run(Unknown Source)

"Reference Handler" daemon prio=10 tid=0x00007f03f81c0000 nid=0x3e7f in Object.wait() [0x00007f03d64e3000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000f3cd0520> (a java.lang.ref.Reference$Lock)
    at java.lang.Object.wait(Object.java:503)
    at java.lang.ref.Reference$ReferenceHandler.run(Unknown Source)
    - locked <0x00000000f3cd0520> (a java.lang.ref.Reference$Lock)

"main" prio=10 tid=0x00007f03f800b800 nid=0x3e75 runnable [0x00007f03ff3de000]
   java.lang.Thread.State: RUNNABLE
    at org.eclipse.swt.internal.gtk.OS._g_main_context_acquire(Native Method)
    at org.eclipse.swt.internal.gtk.OS.g_main_context_acquire(OS.java:2445)
    at org.eclipse.swt.widgets.Display.sleep(Display.java:4270)
    at org.eclipse.ui.application.WorkbenchAdvisor.eventLoopIdle(WorkbenchAdvisor.java:364)
    at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2702)
    at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2665)
    at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2499)
    at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:679)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:668)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
    at org.knime.product.rcp.KNIMEApplication.start(KNIMEApplication.java:130)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1386)

"VM Thread" prio=10 tid=0x00007f03f81bb800 nid=0x3e7e runnable 

"GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f03f8021800 nid=0x3e76 runnable 

"GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f03f8023000 nid=0x3e77 runnable 

"GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f03f8025000 nid=0x3e78 runnable 

"GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f03f8027000 nid=0x3e79 runnable 

"GC task thread#4 (ParallelGC)" prio=10 tid=0x00007f03f8029000 nid=0x3e7a runnable 

"GC task thread#5 (ParallelGC)" prio=10 tid=0x00007f03f802b000 nid=0x3e7b runnable 

"GC task thread#6 (ParallelGC)" prio=10 tid=0x00007f03f802d000 nid=0x3e7c runnable 

"GC task thread#7 (ParallelGC)" prio=10 tid=0x00007f03f802e800 nid=0x3e7d runnable 

"VM Periodic Task Thread" prio=10 tid=0x00007f03f8223000 nid=0x3e85 waiting on condition 

JNI global references: 1347