Slow responsiveness and NullPointerException when closing Knime 3.0.1

lorenz · November 17, 2015, 2:23pm

When I run Knime 3.0.1 via X-Forwarding, the GUI tends to get slower and slower, independently of the RAM left. It happens more and more often that when I try to open a config window or dropdown box, it draws its background but no conent. For a few more times, it helps to close that window and to open it again. After a while, the only thing left to do is to close Knime.

When I close it, I get

!SESSION 2015-11-17 11:35:59.532 -----------------------------------------------
eclipse.buildId=unknown
java.version=1.8.0_60
java.vendor=Oracle Corporation
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_GB
Command-line arguments:  -os linux -ws gtk -arch x86_64

!ENTRY org.eclipse.core.runtime 4 0 2015-11-17 11:36:25.737
!MESSAGE Invalid input url:platform:/plugin/org.knime.ext.weka_3.7/icons/weka_splash_48.png
!STACK 0
java.io.IOException: Unable to resolve plug-in "platform:/plugin/org.knime.ext.weka_3.7/icons/weka_splash_48.png".
        at org.eclipse.core.internal.runtime.PlatformURLPluginConnection.parse(PlatformURLPluginConnection.java:65)
        at org.eclipse.core.internal.runtime.FindSupport.find(FindSupport.java:290)
        at org.eclipse.core.runtime.FileLocator.find(FileLocator.java:152)
        at org.eclipse.ui.plugin.AbstractUIPlugin.imageDescriptorFromPlugin(AbstractUIPlugin.java:713)
        at org.knime.product.KNIMESplashHandler.getSplashIcon(KNIMESplashHandler.java:300)
        at org.knime.product.KNIMESplashHandler.createUIImages(KNIMESplashHandler.java:332)
        at org.knime.product.KNIMESplashHandler.init(KNIMESplashHandler.java:222)
        at org.eclipse.ui.internal.Workbench$6.run(Workbench.java:834)
        at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
        at org.eclipse.ui.internal.Workbench.createSplashWrapper(Workbench.java:849)
        at org.eclipse.ui.internal.Workbench.access$5(Workbench.java:771)
        at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:628)
        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:132)
        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)
        at org.eclipse.equinox.launcher.Main.main(Main.java:1488)

!ENTRY org.eclipse.osgi 4 0 2015-11-17 14:15:24.311
!MESSAGE Application error
!STACK 1
org.eclipse.swt.SWTException: Failed to execute runnable (java.lang.NullPointerException)
        at org.eclipse.swt.SWT.error(SWT.java:4491)
        at org.eclipse.swt.SWT.error(SWT.java:4406)
        at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:138)
        at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:3794)
        at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3433)
        at org.eclipse.swt.widgets.Display.release(Display.java:3485)
        at org.eclipse.swt.graphics.Device.dispose(Device.java:248)
        at org.knime.product.rcp.KNIMEApplication.start(KNIMEApplication.java:148)
        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)
        at org.eclipse.equinox.launcher.Main.main(Main.java:1488)
Caused by: java.lang.NullPointerException
        at org.eclipse.ui.internal.e4.compatibility.SelectionService.getSelection(SelectionService.java:333)
        at org.eclipse.gef.ui.actions.SelectionAction.update(SelectionAction.java:125)
        at org.eclipse.gef.ui.parts.GraphicalEditor.updateActions(GraphicalEditor.java:458)
        at org.knime.workbench.editor2.WorkflowEditor.firePropertyChange(WorkflowEditor.java:2193)
        at org.knime.workbench.editor2.WorkflowEditor$14.run(WorkflowEditor.java:2948)
        at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
        at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:135)
        ... 18 more

!ENTRY org.eclipse.e4.ui.workbench 4 0 2015-11-17 14:15:24.381
!MESSAGE FrameworkEvent ERROR
!STACK 0
org.eclipse.e4.core.di.InjectionException: org.eclipse.swt.SWTException: Invalid thread access
        at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:68)
        at org.eclipse.e4.core.internal.di.InjectorImpl.processAnnotated(InjectorImpl.java:898)
        at org.eclipse.e4.core.internal.di.InjectorImpl.disposed(InjectorImpl.java:398)
        at org.eclipse.e4.core.internal.di.Requestor.disposed(Requestor.java:148)
        at org.eclipse.e4.core.internal.contexts.ContextObjectSupplier$ContextInjectionListener.update(ContextObjectSupplier.java:78)
        at org.eclipse.e4.core.internal.contexts.TrackableComputationExt.update(TrackableComputationExt.java:111)
        at org.eclipse.e4.core.internal.contexts.TrackableComputationExt.handleInvalid(TrackableComputationExt.java:74)
        at org.eclipse.e4.core.internal.contexts.EclipseContext.dispose(EclipseContext.java:174)
        at org.eclipse.e4.core.internal.contexts.EclipseContext.dispose(EclipseContext.java:159)
        at org.eclipse.e4.core.internal.contexts.osgi.EclipseContextOSGi.dispose(EclipseContextOSGi.java:106)
        at org.eclipse.e4.core.internal.contexts.osgi.EclipseContextOSGi.bundleChanged(EclipseContextOSGi.java:139)
        at org.eclipse.osgi.internal.framework.BundleContextImpl.dispatchEvent(BundleContextImpl.java:902)
        at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
        at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:148)
        at org.eclipse.osgi.internal.framework.EquinoxEventPublisher.publishBundleEventPrivileged(EquinoxEventPublisher.java:165)
        at org.eclipse.osgi.internal.framework.EquinoxEventPublisher.publishBundleEvent(EquinoxEventPublisher.java:75)
        at org.eclipse.osgi.internal.framework.EquinoxEventPublisher.publishBundleEvent(EquinoxEventPublisher.java:67)
        at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor.publishModuleEvent(EquinoxContainerAdaptor.java:102)
        at org.eclipse.osgi.container.Module.publishEvent(Module.java:466)
        at org.eclipse.osgi.container.Module.doStop(Module.java:624)
        at org.eclipse.osgi.container.Module.stop(Module.java:488)
        at org.eclipse.osgi.container.SystemModule.stop(SystemModule.java:186)
        at org.eclipse.osgi.internal.framework.EquinoxBundle$SystemBundle$EquinoxSystemModule$1.run(EquinoxBundle.java:159)
        at java.lang.Thread.run(Thread.java:745)
Caused by: org.eclipse.swt.SWTException: Invalid thread access
        at org.eclipse.swt.SWT.error(SWT.java:4491)
        at org.eclipse.swt.SWT.error(SWT.java:4406)
        at org.eclipse.swt.SWT.error(SWT.java:4377)
        at org.eclipse.swt.widgets.Display.error(Display.java:1186)
        at org.eclipse.swt.widgets.Display.checkDevice(Display.java:765)
        at org.eclipse.swt.widgets.Display.removeFilter(Display.java:3703)
        at org.eclipse.e4.ui.workbench.renderers.swt.MenuManagerRenderer.contextDisposed(MenuManagerRenderer.java:338)
        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.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:56)
        ... 23 more

lorenz · November 17, 2015, 3:20pm

Just had a crash of Knime while loading my workflow:

# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fa6d5800e76, pid=24642, tid=140355784980224
#
# JRE version: Java(TM) SE Runtime Environment (8.0_60-b27) (build 1.8.0_60-b27)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.60-b23 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libgdk-x11-2.0.so.0+0x20e76]  gdk_colormap_get_visual+0x16
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/maierlo/hs_err_pid24642.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.

Well, I guess that could refer to eclipse rather than Knime.

Iris · January 20, 2016, 10:26am

Hi Lorenz sorry for the late reply.

Does this problem still exist with 3.1 ?