Out of memory and Error in module Clean2D during search

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

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

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

This problem should now be fixed in IJC 2.2.


Structures are converted to 2D if necessary prior to displaying in Marvin.