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Out of memory and Error in module Clean2D during search
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TobiasKind
Joined: 26 Jan 2005
Posts: 301


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Post subject: Out of memory and Error in module Clean2D during search
Link to postPosted: Tue Oct 23, 2007 11:44 pm  Reply with quote
Hi,
I prevoisly reported a problem with the same error
using probably faulty structures in a MW restricted search
see http://www.chemaxon.com/forum/viewpost13675.html

The same error occurred during a substructure search with SMARTS.
The memory settings were set from 356 MByte to 1024 MByte and during the search only 128 MByte were used. I use the latest updated version 2.1.

Tobias

INFO [com.im.df.impl.db.DBSchemaUtilities]: Created ConnectionHandler
INFO [com.im.df.query.ui.AdvancedQueryUIBuilder]: single click
INFO [com.im.df.query.ui.AdvancedQueryUIBuilder]: Node is OK. Checking whole tree
internal error: cannot recognize clipboard data format
WARNING [org.openide.filesystems.Ordering]: Not all children in OptionsDialog/ marked with the position attribute: [Actions, Advanced, PreviewExamples, com-im-ijc-core-options-CTFavouritesOptionsCategory.instance], but some are: [Advanced.instance]
INFO [com.im.df.impl.db.DBSchemaUtilities]: Created ConnectionHandler
INFO [com.im.df.chem.JChemStructureSearcher]: Executing JChemSearch
Sceeening found 8,772 matches and took 15ms.
Atom by atom matching reduced this to 6,854 hits. Total time was 703.SEVERE [global]
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Unknown Source)
at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5037)
at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5016)
at chemaxon.marvin.common.swing.MolPanel.endHourglass(MolPanel.java:3671)
at chemaxon.marvin.common.swing.MolPanel.molLoaded(MolPanel.java:4472)
at chemaxon.marvin.view.swing.ViewPanel.molLoaded(ViewPanel.java:2599)
at chemaxon.marvin.view.swing.ViewPanel.setM(ViewPanel.java:1657)
at chemaxon.marvin.beans.MViewPane.setM(MViewPane.java:462)
at com.im.ijc.renderers.impl.StructureRenderer.getWidgetCellRendererComponent(StructureRenderer.java:262)
at com.im.ijc.renderers.impl.StructureRenderer.getTableCellRendererComponent(StructureRenderer.java:190)
at javax.swing.JTable.prepareRenderer(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paintCell(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paintCells(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paint(Unknown Source)
at javax.swing.plaf.ComponentUI.update(Unknown Source)
at javax.swing.JComponent.paintComponent(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintWithOffscreenBuffer(Unknown Source)
at javax.swing.JComponent.paintDoubleBuffered(Unknown Source)
at javax.swing.JComponent._paintImmediately(Unknown Source)
at javax.swing.JComponent.paintImmediately(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
[catch] 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)
SEVERE [global]
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Unknown Source)
at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5037)
at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5016)
at chemaxon.marvin.common.swing.MolPanel.endHourglass(MolPanel.java:3671)
at chemaxon.marvin.common.swing.MolPanel.molLoaded(MolPanel.java:4472)
at chemaxon.marvin.view.swing.ViewPanel.molLoaded(ViewPanel.java:2599)
at chemaxon.marvin.view.swing.ViewPanel.setM(ViewPanel.java:1657)
at chemaxon.marvin.beans.MViewPane.setM(MViewPane.java:462)
at com.im.ijc.renderers.impl.StructureRenderer.getWidgetCellRendererComponent(StructureRenderer.java:262)
at com.im.ijc.renderers.impl.StructureRenderer.getTableCellRendererComponent(StructureRenderer.java:190)
at javax.swing.JTable.prepareRenderer(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paintCell(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paintCells(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paint(Unknown Source)
at javax.swing.plaf.ComponentUI.update(Unknown Source)
at javax.swing.JComponent.paintComponent(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JViewport.paintViewDoubleBuffered(Unknown Source)
at javax.swing.JViewport.paintView(Unknown Source)
at javax.swing.JViewport.flushViewDirtyRegion(Unknown Source)
at javax.swing.JViewport.setViewPosition(Unknown Source)
at javax.swing.ViewportLayout.layoutContainer(Unknown Source)
at java.awt.Container.layout(Unknown Source)
at java.awt.Container.doLayout(Unknown Source)
at java.awt.Container.validateTree(Unknown Source)
at java.awt.Container.validateTree(Unknown Source)
at java.awt.Container.validate(Unknown Source)
at javax.swing.RepaintManager.validateInvalidComponents(Unknown Source)
at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
[catch] 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)
Error in module Clean2D
SEVERE [global]
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Unknown Source)
at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5037)
at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5016)
at chemaxon.marvin.common.swing.MolPanel.endHourglass(MolPanel.java:3671)
at chemaxon.marvin.common.swing.MolPanel.molLoaded(MolPanel.java:4472)
at chemaxon.marvin.view.swing.ViewPanel.molLoaded(ViewPanel.java:2599)
at chemaxon.marvin.view.swing.ViewPanel.setM(ViewPanel.java:1657)
at chemaxon.marvin.beans.MViewPane.setM(MViewPane.java:462)
at com.im.ijc.renderers.impl.StructureRenderer.getWidgetCellRendererComponent(StructureRenderer.java:262)
at com.im.ijc.renderers.impl.StructureRenderer.getTableCellRendererComponent(StructureRenderer.java:190)
at javax.swing.JTable.prepareRenderer(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paintCell(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paintCells(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paint(Unknown Source)
at javax.swing.plaf.ComponentUI.update(Unknown Source)
at javax.swing.JComponent.paintComponent(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JViewport.paintViewDoubleBuffered(Unknown Source)
at javax.swing.JViewport.paintView(Unknown Source)
at javax.swing.JViewport.flushViewDirtyRegion(Unknown Source)
at javax.swing.JViewport.setViewPosition(Unknown Source)
at javax.swing.ViewportLayout.layoutContainer(Unknown Source)
at java.awt.Container.layout(Unknown Source)
at java.awt.Container.doLayout(Unknown Source)
at java.awt.Container.validateTree(Unknown Source)
at java.awt.Container.validateTree(Unknown Source)
at java.awt.Container.validate(Unknown Source)
at javax.swing.JViewport.validateView(Unknown Source)
at javax.swing.JViewport.scrollRectToVisible(Unknown Source)
at javax.swing.JComponent.scrollRectToVisible(Unknown Source)
at com.im.ijc.widgets.table.WBTable$2.run(WBTable.java:297)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
[catch] 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)
Error in module Clean2D
SEVERE [global]
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Unknown Source)
at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5037)
at chemaxon.marvin.common.swing.MolPanel.initCursor(MolPanel.java:5016)
at chemaxon.marvin.common.swing.MolPanel.endHourglass(MolPanel.java:3671)
at chemaxon.marvin.common.swing.MolPanel.molLoaded(MolPanel.java:4472)
at chemaxon.marvin.view.swing.ViewPanel.molLoaded(ViewPanel.java:2599)
at chemaxon.marvin.view.swing.ViewPanel.setM(ViewPanel.java:1657)
at chemaxon.marvin.beans.MViewPane.setM(MViewPane.java:462)
at com.im.ijc.renderers.impl.StructureRenderer.getWidgetCellRendererComponent(StructureRenderer.java:262)
at com.im.ijc.renderers.impl.StructureRenderer.getTableCellRendererComponent(StructureRenderer.java:190)
at javax.swing.JTable.prepareRenderer(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paintCell(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paintCells(Unknown Source)
at javax.swing.plaf.basic.BasicTableUI.paint(Unknown Source)
at javax.swing.plaf.ComponentUI.update(Unknown Source)
at javax.swing.JComponent.paintComponent(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JViewport.paintViewDoubleBuffered(Unknown Source)
at javax.swing.JViewport.paintView(Unknown Source)
at javax.swing.JViewport.flushViewDirtyRegion(Unknown Source)
at javax.swing.JViewport.setViewPosition(Unknown Source)
at javax.swing.ViewportLayout.layoutContainer(Unknown Source)
at java.awt.Container.layout(Unknown Source)
at java.awt.Container.doLayout(Unknown Source)
at java.awt.Container.validateTree(Unknown Source)
at java.awt.Container.validateTree(Unknown Source)
at java.awt.Container.validate(Unknown Source)
at javax.swing.RepaintManager.validateInvalidComponents(Unknown Source)
at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
[catch] 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)
Error in module Clean2D
tdudgeon
Joined: 05 Oct 2004
Posts: 577
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Post subject:
Link to postPosted: Thu Oct 25, 2007 10:05 am  Reply with quote
We are looking into this.
From what we understand it happens when structures are being displayed in the grid view.
And those structures are probably in smiles/smarts format, as the error is coming from when 2D coordinate generation is needed?

Is this correct?
Are you able to send us the data so that we can use it to reproduce the problem? (send privately not to the forum).
tdudgeon at chemaxon dot com


Thanks
TobiasKind
Joined: 26 Jan 2005
Posts: 301


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Post subject:
Link to postPosted: Wed Oct 31, 2007 10:30 pm  Reply with quote
Hi Tim,
this issue is resolved in Marvin 05.pre-alpha version
and has something to do with the Mview or the Sketcher.
http://www.chemaxon.com/shared/alpha/marvin/examples/applets/example-sketch1.1.html
Product Version: MarvinSketch 5.0.0alpha13
Build Date: 2007-10-26
Operating System: x86 Windows XP 5.1
Java: Sun Microsystems Inc. Java 1.5.0_06
Memory: 63.6M maximum, 27.8M total, 4.9M free
Environment: Trusted Applet (with administrator rights)
Browser: sun.plugin 1.1

This version does not give the Clean2D error, but all prior versions do.
Tobias
tdudgeon
Joined: 05 Oct 2004
Posts: 577
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Post subject:
Link to postPosted: Tue Jan 15, 2008 3:04 pm  Reply with quote
This problem should now be fixed in IJC 2.2.
Structures are converted to 2D if necessary prior to displaying in Marvin.
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