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Overlap Output window crash
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Tobias

Joined: 26 Jan 2005
Posts: 580

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Link to postPosted: Sat May 17, 2008 5:22 amPost subject: Overlap Output window crash Reply with quote

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)
Tim
ChemAxon personnel
Joined: 05 Oct 2004
Posts: 1703

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Link to postPosted: Sat May 17, 2008 8:50 amPost subject: Reply with quote

I think the text output is too big and causes problems with memory.
I think we need to make this optional.

Tim
Tim
ChemAxon personnel
Joined: 05 Oct 2004
Posts: 1703

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Link to postPosted: Wed Jun 18, 2008 8:39 amPost subject: Reply with quote

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
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