KNIME got stuck and doesn't respond when select some options of a node like confussion matrix, accuracy stadistic, etc

I created my project, configure the nodes, executed and everything works fine, but when I go to a node like "ARFF Reader" or "Scorer" or "Decision Tree Learner", etc and select some options like:

* ARFF Reader -> right click -> Data From ARFF

* Scorer -> right click -> Confussion Matrix or Accuracy stadistics

A window with the requested data is opened but then all knime stop working, is frozen, I can't select nodes or Open preferences, or changes to another workflow.

Any suggestions?

Screenshot 

 

Knime Version: 2.12.0 (also happend with 2.12.1)

 

OS: Ubuntu 15.04

$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 15.04
Release:	15.04
Codename:	vivid

 

Java:

$ java -version
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar 
java version "1.7.0_79"
OpenJDK Runtime Environment (IcedTea 2.5.6) (7u79-2.5.6-0ubuntu1.15.04.1)
OpenJDK 64-Bit Server VM (build 24.79-b02, mixed mode)

 

Command Line Output:

$ LANG='C' SWT_GTK3=0 knime_2.12.0/knime
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar 
No bp log location saved, using default.
[000:000] Cpu: 6.37.2, x4, 2133Mhz, 7781MB
[000:001] Computer model: Not available
Vector smash protection is enabled.
No bp log location saved, using default.
[000:000] Cpu: 6.37.2, x4, 2133Mhz, 7781MB
[000:000] Computer model: Not available
[000:000] Browser XEmbed support present: 1
[000:000] Browser toolkit is Gtk2.
[000:000] Using Gtk2 toolkit
[000:011] Warning(optionsfile.cc:30): Load: Could not open file, err=2
[000:011] No bp log location saved, using default.
[000:012] Cpu: 6.37.2, x4, 2133Mhz, 7781MB
[000:012] Computer model: Not available
[000:002] Warning(optionsfile.cc:30): Load: Could not open file, err=2
[000:002] No bp log location saved, using default.
[000:003] Cpu: 6.37.2, x4, 2133Mhz, 7781MB
[000:003] Computer model: Not available
[000:003] Browser XEmbed support present: 1
[000:003] Browser toolkit is Gtk2.
[000:003] Using Gtk2 toolkit
---Registering Weka Editors---

 

VisualVM: Thread Dump

2015-09-28 08:55:40
Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.60-b09 mixed mode):
 
"RMI TCP Connection(2)-127.0.0.1" daemon prio=10 tid=0x00007f3e20117000 nid=0x23f3 runnable [0x00007f3d93f38000]
   java.lang.Thread.State: RUNNABLE
    at java.net.SocketInputStream.socketRead0(Native Method)
    at java.net.SocketInputStream.read(Unknown Source)
    at java.net.SocketInputStream.read(Unknown Source)
    at java.io.BufferedInputStream.fill(Unknown Source)
    at java.io.BufferedInputStream.read(Unknown Source)
    - locked <0x00000007d89d9298> (a java.io.BufferedInputStream)
    at java.io.FilterInputStream.read(Unknown Source)
    at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(Unknown Source)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(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)
 
   Locked ownable synchronizers:
    - <0x00000007d875a3c0> (a java.util.concurrent.ThreadPoolExecutor$Worker)
 
"JMX server connection timeout 66" daemon prio=10 tid=0x00007f3e5c014800 nid=0x23f0 in Object.wait() [0x00007f3d94039000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000007d887b2d0> (a [I)
    at com.sun.jmx.remote.internal.ServerCommunicatorAdmin$Timeout.run(Unknown Source)
    - locked <0x00000007d887b2d0> (a [I)
    at java.lang.Thread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"RMI Scheduler(0)" daemon prio=10 tid=0x00007f3e5c012000 nid=0x23ef waiting on condition [0x00007f3d9413a000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000007d870f340> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.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)
 
   Locked ownable synchronizers:
    - None
 
"RMI TCP Connection(1)-127.0.0.1" daemon prio=10 tid=0x00007f3e200d4000 nid=0x23ee runnable [0x00007f3d9423b000]
   java.lang.Thread.State: RUNNABLE
    at java.net.SocketInputStream.socketRead0(Native Method)
    at java.net.SocketInputStream.read(Unknown Source)
    at java.net.SocketInputStream.read(Unknown Source)
    at java.io.BufferedInputStream.fill(Unknown Source)
    at java.io.BufferedInputStream.read(Unknown Source)
    - locked <0x00000007d8838d10> (a java.io.BufferedInputStream)
    at java.io.FilterInputStream.read(Unknown Source)
    at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(Unknown Source)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(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)
 
   Locked ownable synchronizers:
    - <0x00000007d8759e70> (a java.util.concurrent.ThreadPoolExecutor$Worker)
 
"RMI TCP Accept-0" daemon prio=10 tid=0x00007f3df002b800 nid=0x23ec runnable [0x00007f3d9433c000]
   java.lang.Thread.State: RUNNABLE
    at java.net.PlainSocketImpl.socketAccept(Native Method)
    at java.net.AbstractPlainSocketImpl.accept(Unknown Source)
    at java.net.ServerSocket.implAccept(Unknown Source)
    at java.net.ServerSocket.accept(Unknown Source)
    at sun.management.jmxremote.LocalRMIServerSocketFactory$1.accept(Unknown Source)
    at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(Unknown Source)
    at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"[ThreadPool Manager] - Idle Thread" daemon prio=10 tid=0x00007f3e1c5c2800 nid=0x23e9 in Object.wait() [0x00007f3d94841000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000007d82200b8> (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 <0x00000007d82200b8> (a org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor)
 
   Locked ownable synchronizers:
    - None
 
"TimerQueue" daemon prio=10 tid=0x00007f3e0813d000 nid=0x23e8 waiting on condition [0x00007f3d9443d000]
   java.lang.Thread.State: WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000007d812a5e0> (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)
 
   Locked ownable synchronizers:
    - <0x00000007d812a608> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
 
"Thread-16" daemon prio=10 tid=0x00007f3e5400b800 nid=0x23e6 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
 
   Locked ownable synchronizers:
    - None
 
"KNIME Memory Alert Distributor" daemon prio=10 tid=0x00007f3e0811d800 nid=0x23e5 in Object.wait() [0x00007f3d9453e000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000007d7f809b8> (a java.lang.Object)
    at java.lang.Object.wait(Object.java:503)
    at org.knime.core.data.util.memory.MemoryAlertSystem$3.run(MemoryAlertSystem.java:233)
    - locked <0x00000007d7f809b8> (a java.lang.Object)
 
   Locked ownable synchronizers:
    - None
 
"KNIME-TableIO-1" prio=10 tid=0x00007f3e08117800 nid=0x23e4 waiting on condition [0x00007f3d9463f000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000007e6af4778> (a java.util.concurrent.SynchronousQueue$TransferStack)
    at java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source)
    at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source)
    at java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source)
    at java.util.concurrent.SynchronousQueue.poll(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"Global KNIME Timer" prio=10 tid=0x00007f3e08100800 nid=0x23e3 in Object.wait() [0x00007f3d94740000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000007d7e6e1c0> (a java.util.TaskQueue)
    at java.lang.Object.wait(Object.java:503)
    at java.util.TimerThread.mainLoop(Unknown Source)
    - locked <0x00000007d7e6e1c0> (a java.util.TaskQueue)
    at java.util.TimerThread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"OutPortView-Updater-1" daemon prio=10 tid=0x00007f3e0808f000 nid=0x23e1 waiting on condition [0x00007f3d94e3a000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000007d79c3f00> (a java.util.concurrent.SynchronousQueue$TransferStack)
    at java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source)
    at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(Unknown Source)
    at java.util.concurrent.SynchronousQueue$TransferStack.transfer(Unknown Source)
    at java.util.concurrent.SynchronousQueue.poll(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.getTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"AWT-EventQueue-0" prio=10 tid=0x00007f3e809bd000 nid=0x23e0 waiting on condition [0x00007f3d94f3b000]
   java.lang.Thread.State: WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x0000000782c33490> (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)
 
   Locked ownable synchronizers:
    - None
 
"AWT-Shutdown" prio=10 tid=0x00007f3e809bc000 nid=0x23df in Object.wait() [0x00007f3d9b142000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000007809ab7a0> (a java.lang.Object)
    at java.lang.Object.wait(Object.java:503)
    at sun.awt.AWTAutoShutdown.run(Unknown Source)
    - locked <0x00000007809ab7a0> (a java.lang.Object)
    at java.lang.Thread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"Unknown Progress Timer" prio=10 tid=0x00007f3e80fca800 nid=0x23de in Object.wait() [0x00007f3e34137000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000007e6976718> (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 <0x00000007e6976718> (a java.util.ArrayList)
 
   Locked ownable synchronizers:
    - None
 
"KNIME Sync Exec Dispatcher-1" daemon prio=10 tid=0x00007f3e8143f800 nid=0x23dd waiting on condition [0x00007f3d978ab000]
   java.lang.Thread.State: WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000007e6af1e78> (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)
 
   Locked ownable synchronizers:
    - None
 
"Thread-9" prio=10 tid=0x00007f3df809d000 nid=0x23d7 waiting on condition [0x00007f3d97fee000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
    at java.lang.Thread.sleep(Native Method)
    at org.eclipse.equinox.internal.p2.updatechecker.UpdateChecker$UpdateCheckThread.run(UpdateChecker.java:67)
 
   Locked ownable synchronizers:
    - None
 
"Worker-4" prio=10 tid=0x00007f3df804d800 nid=0x23d6 in Object.wait() [0x00007f3d980ef000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000782cda900> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    - locked <0x0000000782cda900> (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)
 
   Locked ownable synchronizers:
    - None
 
"Worker-3" prio=10 tid=0x00007f3df802f800 nid=0x23d5 in Object.wait() [0x00007f3e0c105000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000782cda900> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    - locked <0x0000000782cda900> (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)
 
   Locked ownable synchronizers:
    - None
 
"Worker-2" prio=10 tid=0x00007f3df805d800 nid=0x23d4 in Object.wait() [0x00007f3e0d9ee000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000782cda900> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    - locked <0x0000000782cda900> (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)
 
   Locked ownable synchronizers:
    - None
 
"KNIME Progress Timer" daemon prio=10 tid=0x00007f3e1c01a000 nid=0x23ce in Object.wait() [0x00007f3d99b41000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000781c37e60> (a java.util.TaskQueue)
    at java.util.TimerThread.mainLoop(Unknown Source)
    - locked <0x0000000781c37e60> (a java.util.TaskQueue)
    at java.util.TimerThread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"ServerSpace Update Timer" daemon prio=10 tid=0x00007f3e81483800 nid=0x23cd in Object.wait() [0x00007f3d99c42000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000780a7abc8> (a java.util.TaskQueue)
    at java.util.TimerThread.mainLoop(Unknown Source)
    - locked <0x0000000780a7abc8> (a java.util.TaskQueue)
    at java.util.TimerThread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"SelectorThread" daemon prio=10 tid=0x00007f3e813f4000 nid=0x23cc runnable [0x00007f3d99d43000]
   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 <0x0000000780b3fe58> (a sun.nio.ch.Util$2)
    - locked <0x0000000780b3fe48> (a java.util.Collections$UnmodifiableSet)
    - locked <0x0000000780b35928> (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)
 
   Locked ownable synchronizers:
    - None
 
"Worker-1" prio=10 tid=0x00007f3df805f800 nid=0x23cb in Object.wait() [0x00007f3d99fe4000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000782cda900> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    - locked <0x0000000782cda900> (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)
 
   Locked ownable synchronizers:
    - None
 
"KNIME-Worker-1" daemon prio=10 tid=0x00007f3e80fb6000 nid=0x23c0 in Object.wait() [0x00007f3e0dcfa000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000780b40a78> (a java.lang.Object)
    at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:232)
    - locked <0x0000000780b40a78> (a java.lang.Object)
 
   Locked ownable synchronizers:
    - None
 
"KNIME-Worker-0" daemon prio=10 tid=0x00007f3e80fb5800 nid=0x23bf in Object.wait() [0x00007f3e0ddfb000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000780b632b8> (a java.lang.Object)
    at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:232)
    - locked <0x0000000780b632b8> (a java.lang.Object)
 
   Locked ownable synchronizers:
    - None
 
"pool-2-thread-1" prio=10 tid=0x00007f3e806ab000 nid=0x23bb waiting on condition [0x00007f3e0defc000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x0000000780785130> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.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)
 
   Locked ownable synchronizers:
    - None
 
"pool-1-thread-1" prio=10 tid=0x00007f3e8052b000 nid=0x23ba waiting on condition [0x00007f3e355d7000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x000000078079d150> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.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)
 
   Locked ownable synchronizers:
    - None
 
"Attach Listener" daemon prio=10 tid=0x00007f3e54001000 nid=0x23b9 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
 
   Locked ownable synchronizers:
    - None
 
"Provisioning Event Dispatcher" daemon prio=10 tid=0x00007f3e80a2c000 nid=0x23b4 in Object.wait() [0x00007f3e0e3af000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000782bcb1d8> (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 <0x0000000782bcb1d8> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)
 
   Locked ownable synchronizers:
    - None
 
"Worker-0" prio=10 tid=0x00007f3e8094b800 nid=0x23b3 in Object.wait() [0x00007f3e0e4b0000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000782cda900> (a org.eclipse.core.internal.jobs.WorkerPool)
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    - locked <0x0000000782cda900> (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)
 
   Locked ownable synchronizers:
    - None
 
"AWT-XAWT" daemon prio=10 tid=0x00007f3e808fe000 nid=0x23b1 runnable [0x00007f3e35980000]
   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)
 
   Locked ownable synchronizers:
    - None
 
"Java2D Disposer" daemon prio=10 tid=0x00007f3e808f3000 nid=0x23b0 in Object.wait() [0x00007f3e36cd0000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000780784fc8> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(Unknown Source)
    - locked <0x0000000780784fc8> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(Unknown Source)
    at sun.java2d.Disposer.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"Bundle File Closer" daemon prio=10 tid=0x00007f3e805ac000 nid=0x23ab in Object.wait() [0x00007f3e36858000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000007807126c0> (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 <0x00000007807126c0> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)
 
   Locked ownable synchronizers:
    - None
 
"Worker-JM" prio=10 tid=0x00007f3e200ac800 nid=0x23aa in Object.wait() [0x00007f3e36ace000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x000000078075a520> (a java.util.ArrayList)
    at org.eclipse.core.internal.jobs.InternalWorker.run(InternalWorker.java:58)
    - locked <0x000000078075a520> (a java.util.ArrayList)
 
   Locked ownable synchronizers:
    - None
 
"[Timer] - Main Queue Handler" daemon prio=10 tid=0x00007f3e20052800 nid=0x23a9 in Object.wait() [0x00007f3e36bcf000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000780b53ba8> (a java.lang.Object)
    at org.eclipse.equinox.internal.util.impl.tpt.timer.TimerImpl.run(TimerImpl.java:141)
    - locked <0x0000000780b53ba8> (a java.lang.Object)
    at java.lang.Thread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"Framework Event Dispatcher" daemon prio=10 tid=0x00007f3e2000e000 nid=0x23a7 in Object.wait() [0x00007f3e36dd1000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x000000078079e040> (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 <0x000000078079e040> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)
 
   Locked ownable synchronizers:
    - None
 
"Start Level Event Dispatcher" daemon prio=10 tid=0x00007f3e80402800 nid=0x23a6 in Object.wait() [0x00007f3e36ed2000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x000000078079e1b0> (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 <0x000000078079e1b0> (a org.eclipse.osgi.framework.eventmgr.EventManager$EventThread)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)
 
   Locked ownable synchronizers:
    - None
 
"State Data Manager" daemon prio=10 tid=0x00007f3e80404800 nid=0x23a5 waiting on condition [0x00007f3e36fd3000]
   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)
 
   Locked ownable synchronizers:
    - None
 
"Framework Active Thread" prio=10 tid=0x00007f3e803e0800 nid=0x23a4 in Object.wait() [0x00007f3e370d4000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000782b69d10> (a org.eclipse.osgi.framework.internal.core.Framework)
    at org.eclipse.osgi.framework.internal.core.Framework.run(Framework.java:1817)
    - locked <0x0000000782b69d10> (a org.eclipse.osgi.framework.internal.core.Framework)
    at java.lang.Thread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"Service Thread" daemon prio=10 tid=0x00007f3e8018c800 nid=0x23a0 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
 
   Locked ownable synchronizers:
    - None
 
"C2 CompilerThread1" daemon prio=10 tid=0x00007f3e80183800 nid=0x239f waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
 
   Locked ownable synchronizers:
    - None
 
"C2 CompilerThread0" daemon prio=10 tid=0x00007f3e80181800 nid=0x239e waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
 
   Locked ownable synchronizers:
    - None
 
"Signal Dispatcher" daemon prio=10 tid=0x00007f3e80160000 nid=0x239d runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
 
   Locked ownable synchronizers:
    - None
 
"Finalizer" daemon prio=10 tid=0x00007f3e80139000 nid=0x239c in Object.wait() [0x00007f3e7ab3a000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000782dcf030> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(Unknown Source)
    - locked <0x0000000782dcf030> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(Unknown Source)
    at java.lang.ref.Finalizer$FinalizerThread.run(Unknown Source)
 
   Locked ownable synchronizers:
    - None
 
"Reference Handler" daemon prio=10 tid=0x00007f3e80137000 nid=0x239b in Object.wait() [0x00007f3e7ac3b000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x0000000780baffa0> (a java.lang.ref.Reference$Lock)
    at java.lang.Object.wait(Object.java:503)
    at java.lang.ref.Reference$ReferenceHandler.run(Unknown Source)
    - locked <0x0000000780baffa0> (a java.lang.ref.Reference$Lock)
 
   Locked ownable synchronizers:
    - None
 
"main" prio=10 tid=0x00007f3e8000b800 nid=0x2395 runnable [0x00007f3e86c2e000]
   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:144)
    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)
 
   Locked ownable synchronizers:
    - None
 
"VM Thread" prio=10 tid=0x00007f3e80132800 nid=0x239a runnable 
 
"GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f3e80021000 nid=0x2396 runnable 
 
"GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f3e80023000 nid=0x2397 runnable 
 
"GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f3e80025000 nid=0x2398 runnable 
 
"GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f3e80027000 nid=0x2399 runnable 
 
"VM Periodic Task Thread" prio=10 tid=0x00007f3e80199800 nid=0x23a1 waiting on condition 
 
JNI global references: 904

The stack trace doesn't show any indication why the GUI should be frozen. What is the javaagent you are using maybe this is causing the problem?