Can the problem be that the jobagent does not get enough memory? CATALINA OPTS will only influence the BASE core server and if there are separate jobagent processed then these may need an increased memory setting? I may be completely off here but just a thought.
Jari On 2011-05-23 08.27, Nicklas Nordborg wrote: > 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 ------------------------------------------------------------------------------ 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
