From: Till S. <til...@tu...> - 2016-02-15 17:27:24
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Hi, glad to hear, that it works with the new version. THX for sharing the info, Till Am Montag, 15. Februar 2016, 11:27:25 schrieb Jing Lu: > Yes, you are right. The new version has no problem. > > > > Thanks, > Jing > > On Mon, Feb 15, 2016 at 8:25 AM, Till Schäfer <til...@tu... > > wrote: > > > Hi, > > the observed issue is not caused by the dataset size, but is a bug in the > > cdk library. Which version of SH are you using? The new SH version 2.6.0 > > has a new version of the cdk library. So if you are still using 2.5.1 or > > below, please try the new version. > > > > Regards, > > Till Schäfer > > > > Am Freitag, 12. Februar 2016, 12:17:55 CET schrieb Jing Lu: > > > Hi Scaffold Hunters, > > > > > > I have a dataset with >20,000 molecules. The software froze after loading > > > about 6,000 molecules and gave me the following error (part of the > > error). > > > > > > Is there any way to get around this? > > > > > > Thanks, > > > Jing > > > > > > ble.actionPerformed(SwingWorker.java:958) > > > at javax.swing.Timer.fireActionPerformed(Unknown Source) > > > at javax.swing.Timer$DoPostEvent.run(Unknown Source) > > > at java.awt.event.InvocationEvent.dispatch(Unknown Source) > > > at java.awt.EventQueue.dispatchEventImpl(Unknown Source) > > > at java.awt.EventQueue.access$500(Unknown Source) > > > at java.awt.EventQueue$3.run(Unknown Source) > > > at java.awt.EventQueue$3.run(Unknown Source) > > > at java.security.AccessController.doPrivileged(Native Method) > > > at > > > java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionP > > > rivilege(Unknown Source) > > > at java.awt.EventQueue.dispatchEvent(Unknown Source) > > > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown > > > Source) > > > at java.awt.EventDispatchThread.pumpEventsForFilter(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) > > > Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded > > > at java.lang.AbstractStringBuilder.<init>(Unknown Source) > > > at java.lang.StringBuffer.<init>(Unknown Source) > > > at > > org.openscience.cdk.silent.AtomType.toString(AtomType.java:366) > > > at org.openscience.cdk.silent.Atom.toString(Atom.java:386) > > > at java.lang.String.valueOf(Unknown Source) > > > at java.lang.StringBuilder.append(Unknown Source) > > > at > > > org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis$AuxiliaryG > > > raph.auxVertex1(SimpleCycleBasis.java:854) > > > at > > > org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis$AuxiliaryG > > > raph.edgesOf(SimpleCycleBasis.java:831) > > > at > > > org._3pq.jgrapht.traverse.CrossComponentIterator$UndirectedSpecifics. > > > edgesOf(Unknown Source) > > > at > > > org._3pq.jgrapht.traverse.CrossComponentIterator.addUnseenChildrenOf( > > > Unknown Source) > > > at org._3pq.jgrapht.traverse.CrossComponentIterator.next(Unknown > > > Source) > > > > > > at > > > org.openscience.cdk.graph.MinimalPathIterator.createShortestPathGraph > > > (MinimalPathIterator.java:143) > > > at > > > org.openscience.cdk.graph.MinimalPathIterator.<init>(MinimalPathItera > > > tor.java:78) > > > at > > > org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis.relevantCy > > > cles(SimpleCycleBasis.java:557) > > > at > > > org.openscience.cdk.ringsearch.cyclebasis.CycleBasis.relevantCycles(C > > > ycleBasis.java:239) > > > at > > > org.openscience.cdk.ringsearch.SSSRFinder.findRelevantRings(SSSRFinde > > > r.java:122) > > > at > > > edu.udo.scaffoldhunter.model.util.SVGGen.calcSVGString(SVGGen.java:16 > > > 0) > > > at > > edu.udo.scaffoldhunter.model.util.SVGGen.getSVG(SVGGen.java:107) > > > at > > > edu.udo.scaffoldhunter.model.dataimport.MergeIterator.newMolecule(Mer > > > geIterator.java:360) > > > at > > > edu.udo.scaffoldhunter.model.db.DbManagerHibernate.mergeMoleculesInto > > > DBbySMILES(DbManagerHibernate.java:2545) > > > at > > > edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBack > > > ground(Importer.java:426) > > > at > > > edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBack > > > ground(Importer.java:373) > > > at > > > edu.udo.scaffoldhunter.gui.util.SwingWorker$1.call(SwingWorker.java:3 > > > 18) > > > at java.util.concurrent.FutureTask.run(Unknown Source) > > > at > > > edu.udo.scaffoldhunter.gui.util.SwingWorker$2.run(SwingWorker.java:32 > > > 5) > > > at > > > edu.udo.scaffoldhunter.gui.util.SwingWorker.run(SwingWorker.java:362) > > > > > > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown > > Source) > > > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown > > > Source) > > > at java.lang.Thread.run(Unknown Source) > > > > > -- > > Dipl.-Inf. Till Schäfer > > TU Dortmund University > > Chair 11 - Algorithm Engineering > > Otto-Hahn-Str. 14 / Room 237 > > 44227 Dortmund, Germany > > > > e-mail: til...@cs... > > phone: +49(231)755-7706 > > fax: +49(231)755-7740 > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer > > pgp: > > https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79 > > -- Dipl.-Inf. Till Schäfer TU Dortmund University Chair 11 - Algorithm Engineering Otto-Hahn-Str. 14 / Room 237 44227 Dortmund, Germany e-mail: til...@cs... phone: +49(231)755-7706 fax: +49(231)755-7740 web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer pgp: https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79 |