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
>
>
>
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------------------------------------------------------------------------------
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
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