Overlap Output window crash

Hi,


I downloaded 30k structures from PubChem (as Substances)


Import was fine and quick, the overlap output window


created a long list of overlapping numbers (each substance has


10 overlaps or more) and then crashed (no output anymore).


See error messages. Also there is still this weird flicker and the


massive text output in the output window. 1024 MByte was reserved


for memory and usually 256 MByte were used in the garbage collection window. The overlap calculation itself was not stopped.





Tobias





java.lang.OutOfMemoryError


at sun.misc.Unsafe.allocateMemory(Native Method)


at java.nio.DirectByteBuffer.<init>(Unknown Source)


at java.nio.ByteBuffer.allocateDirect(Unknown Source)


at sun.nio.ch.Util.getTemporaryDirectBuffer(Unknown Source)


at sun.nio.ch.IOUtil.read(Unknown Source)


at sun.nio.ch.FileChannelImpl.read(Unknown Source)


at org.netbeans.core.output2.FileMapStorage.getReadBuffer(FileMapStorage.java:316)


at org.netbeans.core.output2.AbstractLines.getText(AbstractLines.java:127)


at org.netbeans.core.output2.OutputDocument.getText(OutputDocument.java:208)


at javax.swing.text.PlainView.getLineWidth(Unknown Source)


at javax.swing.text.PlainView.updateDamage(Unknown Source)


at javax.swing.text.PlainView.insertUpdate(Unknown Source)


at javax.swing.plaf.basic.BasicTextUI$RootView.insertUpdate(Unknown Source)


at javax.swing.plaf.basic.BasicTextUI$UpdateHandler.insertUpdate(Unknown Source)


at org.netbeans.core.output2.OutputDocument.fireDocumentEvent(OutputDocument.java:532)


at org.netbeans.core.output2.OutputDocument.access$200(OutputDocument.java:64)


at org.netbeans.core.output2.OutputDocument$4.run(OutputDocument.java:453)


at org.openide.util.Mutex.doEvent(Mutex.java:1203)


at org.openide.util.Mutex.readAccess(Mutex.java:309)


at org.netbeans.core.output2.OutputDocument.stateChanged(OutputDocument.java:450)


at org.netbeans.core.output2.AbstractLines.run(AbstractLines.java:218)


at java.awt.event.InvocationEvent.dispatch(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)





java.io.IOException: Not enough storage is available to process this command


at sun.nio.ch.FileChannelImpl.map0(Native Method)


at sun.nio.ch.FileChannelImpl.map(Unknown Source)


at org.netbeans.core.output2.FileMapStorage.getReadBuffer(FileMapStorage.java:304)


at org.netbeans.core.output2.AbstractLines.getText(AbstractLines.java:127)


at org.netbeans.core.output2.OutputDocument.getText(OutputDocument.java:208)


at javax.swing.text.PlainView.getLineWidth(Unknown Source)


at javax.swing.text.PlainView.updateDamage(Unknown Source)


at javax.swing.text.PlainView.insertUpdate(Unknown Source)


at javax.swing.plaf.basic.BasicTextUI$RootView.insertUpdate(Unknown Source)


at javax.swing.plaf.basic.BasicTextUI$UpdateHandler.insertUpdate(Unknown Source)


at org.netbeans.core.output2.OutputDocument.fireDocumentEvent(OutputDocument.java:532)


at org.netbeans.core.output2.OutputDocument.access$200(OutputDocument.java:64)


at org.netbeans.core.output2.OutputDocument$4.run(OutputDocument.java:453)


at org.openide.util.Mutex.doEvent(Mutex.java:1203)


at org.openide.util.Mutex.readAccess(Mutex.java:309)


at org.netbeans.core.output2.OutputDocument.stateChanged(OutputDocument.java:450)


[catch] at org.netbeans.core.output2.AbstractLines.run(AbstractLines.java:218)


at java.awt.event.InvocationEvent.dispatch(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)

I think the text output is too big and causes problems with memory.


I think we need to make this optional.





Tim

We have added an option what allows the console output to be turned on/off during overlap analysis. This is present in the 2.3.1 update.





Tim