It's difficult to say something about out of memory errors. 2GB should be more than enough. Have you verified in the Help -> About -> Configuration dialog that you really have 2GB?
/Nicklas On 2011-05-23 04:03, Irina 264 wrote: > Dear Team, > > I run Illumina plugin and had error: "Java heap space". I have increased > CATALINA OPTS=-Xmx2048m, however now I have the garbage collector problem: > > "Error: GC overhead limit exceeded" > > View job -- Run plugin: Illumina raw data importer > > java.lang.OutOfMemoryError: GC overhead limit exceeded > at org.hibernate.engine.EntityEntry.getEntityKey(EntityEntry.java:182) > at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:198) > at > org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898) > at org.hibernate.loader.Loader.loadSingleRow(Loader.java:327) > at > org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:254) > at > org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:123) > at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:66) > at net.sf.basedb.core.RawDataBatcher.<init>(RawDataBatcher.java:263) > at net.sf.basedb.core.RawDataBatcher.getNew(RawDataBatcher.java:104) > at net.sf.basedb.core.RawBioAssay.getRawDataBatcher(RawBioAssay.java:1119) > at > net.sf.basedb.plugins.IlluminaRawDataImporter.beginData(IlluminaRawDataImporter.java:520) > at > net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:691) > at > net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510) > at java.lang.Thread.run(Thread.java:636) > > Did I gave too much memory? > > Regards, > Irina > > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > > > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net ------------------------------------------------------------------------------ What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
