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
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