Dear all,
I am developing a set of nodes for database workflows. But I am having problems with the memory, having the following OutOfMemoryError error.
Also, I have noticed that zombie processes are maintained in the system when KNIME close. I can not kill these processes even with "sudo kill -9 [process_id]".
Could you give me some ideas of what can be happening?. Is there any document explaining how KNIME process the workflows? when daemons and processes are created and destructed?
Thank you very much in advance,
Roxana
!ENTRY org.eclipse.ui 4 0 2011-11-09 08:41:43.428
!MESSAGE Unhandled event loop exception
!STACK 0
org.eclipse.swt.SWTException: Failed to execute runnable (java.lang.OutOfMemoryError: PermGen space)
at org.eclipse.swt.SWT.error(SWT.java:4083)
at org.eclipse.swt.SWT.error(SWT.java:3998)
at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:137)
at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:3515)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3164)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2640)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2604)
at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2438)
at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:671)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:664)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:115)
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:369)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:619)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:574)
at org.eclipse.equinox.launcher.Main.run(Main.java:1407)
at org.eclipse.equinox.launcher.Main.main(Main.java:1383)
Caused by: java.lang.OutOfMemoryError: PermGen space
at com.sun.org.apache.xalan.internal.xsltc.dom.XSLTCDTMManager.getDTM(XSLTCDTMManager.java:338)
at com.sun.org.apache.xalan.internal.xsltc.dom.XSLTCDTMManager.getDTM(XSLTCDTMManager.java:234)
at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.getDOM(TransformerImpl.java:524)
at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:709)
at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:313)
at org.knime.workbench.helpview.NodeFactoryHTMLCreator.readFullDescription(NodeFactoryHTMLCreator.java:125)
at org.knime.workbench.helpview.DynamicNodeDescriptionCreator.addDescription(DynamicNodeDescriptionCreator.java:283)
at org.knime.workbench.helpview.HelpView.selectionChanged(HelpView.java:239)
at org.eclipse.ui.internal.AbstractSelectionService.fireSelection(AbstractSelectionService.java:156)
at org.eclipse.ui.internal.AbstractSelectionService$1.selectionChanged(AbstractSelectionService.java:62)
at org.eclipse.gef.ui.parts.AbstractEditPartViewer.fireSelectionChanged(AbstractEditPartViewer.java:247)
at org.eclipse.gef.ui.parts.AbstractEditPartViewer$1.run(AbstractEditPartViewer.java:131)
at org.eclipse.gef.SelectionManager.fireSelectionChanged(SelectionManager.java:127)
at org.eclipse.gef.SelectionManager.setSelection(SelectionManager.java:262)
at org.eclipse.gef.ui.parts.AbstractEditPartViewer.setSelection(AbstractEditPartViewer.java:751)
at org.knime.workbench.editor2.actions.delegates.AbstractEditorAction$SelectionRunnable.run(AbstractEditorAction.java:179)
at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:134)
at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:3515)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3164)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2640)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2604)
at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2438)
at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:671)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:664)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:115)
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:369)
Your error indicates that you are running out of PermGenSpace. I suspect, this happens if you start KNIME from within Eclipse while developing your nodes. You should add "-XX:MaxPermSize=192m" to the VM arguments then.
KNIME does not start any external daemons. It only uses Java threads. However, when OutOfMemoryErrors occurs sometimes the Java process becomes unresponding, especially when it is run in debug mode.