User 677b9c22ff
23-08-2008 07:03:19
Miklos,
there are several weird things happening with LibMCS 0.7.
It seems to have problems with metals Mn, Sn, I ,As and general
metals and all kinds of metal organics. The bad thing is that the error reporting is turned off(?). Or in some cases it never finishes. This is also true for the old NCI-10000 test set see old post
which could be finished under 2 minutes, but now never finishes (see the ZIP file with the several test cases)
If it looses its marbels it eats all the CPU cores and runs havoc.
(0)
The scroll bar error is very bad, after its finished and one clicks the molecule view and tries to click the right scroll bar, the whole thing starts growing like a homunculus. (since version 0.X)
(1)
nci-1000-short.smi
nci-1000-long.smi
as attached never finish to read. And 1000 molecules can be fisnished in less than 1 second usually.
(2)
NCI-10000-sort-desc.smi never finishes.
(3)
NCI-1000-asc and NCI-1000-desc (the same molecules, sorted according to their string length) give different cluster values
NCI-1000-asc.smi: top: 96 total cluster: 532
NCI-1000-desc.smi top: 99 total cluster: 567
One would expect to have the same cluster number for the same molecules. This is a bad error (I assume). It can be avoided
by sorting the SMILES according to their length, but I rather suspect a
programming error. I checked again, the molecules are exactly the same.
(X)
if you click the property during a run a NPE occurs
see below
(X+1)
scrolling through molecules -> NPE
(X+2)
If I remove the bracket molecules following times (standard start settings; Dual Quad Intel(R) Xeon(R) CPU X5460, 3.16GHz).
see addenum.
NCI-10000.smi (n=10000) : Clustering time : 4:15 min
NCI-10000-nobrackets.smi (n=8926) : Clustering time : 1:51 min
NCI-brackets.smi (n=1074) : Clustering time : 0:01 min
I don't know, but this looks like a) there are problematic molecules or b) it would be possible to randomly split the whole list and merge them later to obtain a speed-up.
(X+4)
I also runs with 18 threads but doesnt make use of all 8 CPU cores?
Sorry for reporting so many problems, I still like LibMCS :-)
Bye
Tobias
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listing molecules
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(edit times)
there are several weird things happening with LibMCS 0.7.
It seems to have problems with metals Mn, Sn, I ,As and general
metals and all kinds of metal organics. The bad thing is that the error reporting is turned off(?). Or in some cases it never finishes. This is also true for the old NCI-10000 test set see old post
which could be finished under 2 minutes, but now never finishes (see the ZIP file with the several test cases)
If it looses its marbels it eats all the CPU cores and runs havoc.
(0)
The scroll bar error is very bad, after its finished and one clicks the molecule view and tries to click the right scroll bar, the whole thing starts growing like a homunculus. (since version 0.X)
(1)
nci-1000-short.smi
nci-1000-long.smi
as attached never finish to read. And 1000 molecules can be fisnished in less than 1 second usually.
(2)
NCI-10000-sort-desc.smi never finishes.
(3)
NCI-1000-asc and NCI-1000-desc (the same molecules, sorted according to their string length) give different cluster values
NCI-1000-asc.smi: top: 96 total cluster: 532
NCI-1000-desc.smi top: 99 total cluster: 567
One would expect to have the same cluster number for the same molecules. This is a bad error (I assume). It can be avoided
by sorting the SMILES according to their length, but I rather suspect a
programming error. I checked again, the molecules are exactly the same.
(X)
if you click the property during a run a NPE occurs
see below
(X+1)
scrolling through molecules -> NPE
(X+2)
If I remove the bracket molecules following times (standard start settings; Dual Quad Intel(R) Xeon(R) CPU X5460, 3.16GHz).
see addenum.
NCI-10000.smi (n=10000) : Clustering time : 4:15 min
NCI-10000-nobrackets.smi (n=8926) : Clustering time : 1:51 min
NCI-brackets.smi (n=1074) : Clustering time : 0:01 min
I don't know, but this looks like a) there are problematic molecules or b) it would be possible to randomly split the whole list and merge them later to obtain a speed-up.
(X+4)
I also runs with 18 threads but doesnt make use of all 8 CPU cores?
Sorry for reporting so many problems, I still like LibMCS :-)
Bye
Tobias
Code: |
java.lang.NullPointerException at chemaxon.clustering.gui.JKMenuBar.actionPerformed(JKMenuBar.java:706) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(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) |
-----------------------------
listing molecules
Code: |
java.lang.IllegalArgumentException: No nodes with property:h_bond_donors at chemaxon.clustering.MGraph.getPropertySpecificValue(MGraph.java:1026) at chemaxon.clustering.MGraph.getPropertyMin(MGraph.java:1157) at chemaxon.clustering.gui.MWrapNode.getPropertyMin(MWrapNode.java:189) at chemaxon.clustering.gui.component.ChartPanel.initChart(ChartPanel.java:79) at chemaxon.clustering.gui.component.ChartPanel.<init>(ChartPanel.java:58) at chemaxon.clustering.gui.component.TreeTableModel.getValueAt(TreeTableModel.java:255) at chemaxon.clustering.gui.component.TreeTableSorter.getValueAt(TreeTableSorter.java:289) at javax.swing.JTable.getValueAt(JTable.java:1903) at javax.swing.JTable.prepareRenderer(JTable.java:3911) at chemaxon.clustering.gui.component.TreeTable.prepareRenderer(TreeTable.java:258) at javax.swing.plaf.basic.BasicTableUI.paintCell(BasicTableUI.java:2072) at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:1974) at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1897) at javax.swing.plaf.ComponentUI.update(ComponentUI.java:142) at javax.swing.JComponent.paintComponent(JComponent.java:743) at javax.swing.JComponent.paint(JComponent.java:1006) at javax.swing.JComponent.paintChildren(JComponent.java:843) at javax.swing.JComponent.paint(JComponent.java:1015) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:843) at javax.swing.JComponent.paint(JComponent.java:1015) at javax.swing.JComponent.paintChildren(JComponent.java:843) at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1021) at javax.swing.JComponent.paint(JComponent.java:1015) at javax.swing.JComponent.paintChildren(JComponent.java:843) at javax.swing.JComponent.paint(JComponent.java:1015) at javax.swing.JComponent.paintWithOffscreenBuffer(JComponent.java:4972) at javax.swing.JComponent.paintDoubleBuffered(JComponent.java:4925) at javax.swing.JComponent._paintImmediately(JComponent.java:4868) at javax.swing.JComponent.paintImmediately(JComponent.java:4675) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:451) at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:114) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEvent(EventQueue.java:461) at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149) at java.awt.EventDispatchThread.run(EventDispatchThread.java:110) |
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(edit times)