With a bigger heap, I ran longer, and then got the following. "GC
overhead limit exceeded" is described as a side effect of too many
little objects created too fast.
2012-06-12 19:03:41,093 [DefaultMessageListenerContainer-1] WARN TDB -
Transaction not commited or aborted: Transaction: 2335\
9 : Mode=WRITE : State=ACTIVE :
/data/benson/oap/dist/jug-dist/ris-install/bin/../data/
2012-06-12 19:03:41,099 [DefaultMessageListenerContainer-1] ERROR
com.basistech.jug.rdfdb.task.RdfdbTaskEndpoint - Failed to \
add generate RDF for b671a2b222c20fced4d1ed68096f2a97
java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.nio.HeapByteBuffer.asIntBuffer(HeapByteBuffer.java:366)
at com.hp.hpl.jena.tdb.base.buffer.PtrBuffer.<init>(PtrBuffer.java:47)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNodeMgr.formatBPTreeNode(BPTreeNodeMgr.java:259)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNodeMgr.overlay(BPTreeNodeMgr.java:204)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNodeMgr.access$000(BPTreeNodeMgr.java:36)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNodeMgr$Block2BPTreeNode.fromBlock(BPTreeNodeMgr.java:144)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNodeMgr$Block2BPTreeNode.fromBlock(BPTreeNodeMgr.java:119)
at
com.hp.hpl.jena.tdb.base.page.PageBlockMgr.getRead(PageBlockMgr.java:69)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNodeMgr.getRead(BPTreeNodeMgr.java:105)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.getMgrRead(BPTreeNode.java:166)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.get(BPTreeNode.java:154)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.findHere(BPTreeNode.java:422)
at
com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.recordsPageId(BPTreeNode.java:270)
at
com.hp.hpl.jena.tdb.index.bplustree.BPlusTree.iterator(BPlusTree.java:373)
at
com.hp.hpl.jena.tdb.index.bplustree.BPlusTree.iterator(BPlusTree.java:361)
at
com.hp.hpl.jena.tdb.index.TupleIndexRecord.findWorker(TupleIndexRecord.java:164)
at
com.hp.hpl.jena.tdb.index.TupleIndexRecord.findOrScan(TupleIndexRecord.java:84)
at
com.hp.hpl.jena.tdb.index.TupleIndexRecord.performFind(TupleIndexRecord.java:78)
at com.hp.hpl.jena.tdb.index.TupleIndexBase.find(TupleIndexBase.java:88)
at com.hp.hpl.jena.tdb.index.TupleTable.find(TupleTable.java:173)
at
com.hp.hpl.jena.tdb.nodetable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:169)
at
com.hp.hpl.jena.tdb.solver.StageMatchTuple.makeNextStage(StageMatchTuple.java:101)
at
com.hp.hpl.jena.tdb.solver.StageMatchTuple.makeNextStage(StageMatchTuple.java:44)
at
org.openjena.atlas.iterator.RepeatApplyIterator.hasNext(RepeatApplyIterator.java:49)
at
org.openjena.atlas.iterator.RepeatApplyIterator.hasNext(RepeatApplyIterator.java:46)
at org.openjena.atlas.iterator.Iter$4.hasNext(Iter.java:287)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIterPlainWrapper.hasNextBinding(QueryIterPlainWrapper.java:54)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:108)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:40)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:108)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:40)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:108)
On Tue, Jun 12, 2012 at 1:47 PM, Benson Margulies <[email protected]> wrote:
> I hit the problem I sent mail about most recently whilst trying to
> reproduce the following. Is there any reason to think that this is
> worse than TDB being unlucky enough to be the allocation straw that
> breaks the camel's back?
>
> java.lang.OutOfMemoryError: Java heap space
> at java.util.LinkedHashMap.createEntry(LinkedHashMap.java:424)
> at java.util.LinkedHashMap.addEntry(LinkedHashMap.java:406)
> at java.util.HashMap.put(HashMap.java:385)
> at
> sun.util.resources.OpenListResourceBundle.loadLookup(OpenListResourceBundle.java:118)
> at
> sun.util.resources.OpenListResourceBundle.loadLookupTablesIfNecessary(OpenListResourceBundle.java:97)
> at
> sun.util.resources.OpenListResourceBundle.handleGetObject(OpenListResourceBundle.java:58)
> at
> sun.util.resources.TimeZoneNamesBundle.handleGetObject(TimeZoneNamesBundle.java:59)
> at java.util.ResourceBundle.getObject(ResourceBundle.java:368)
> at java.util.ResourceBundle.getObject(ResourceBundle.java:371)
> at java.util.ResourceBundle.getStringArray(ResourceBundle.java:351)
> at
> sun.util.TimeZoneNameUtility.retrieveDisplayNames(TimeZoneNameUtility.java:100)
> at
> sun.util.TimeZoneNameUtility.retrieveDisplayNames(TimeZoneNameUtility.java:81)
> at java.util.TimeZone.getDisplayNames(TimeZone.java:399)
> at java.util.TimeZone.getDisplayName(TimeZone.java:350)
> at java.text.SimpleDateFormat.subFormat(SimpleDateFormat.java:1110)
> at java.text.SimpleDateFormat.format(SimpleDateFormat.java:899)
> at java.text.SimpleDateFormat.format(SimpleDateFormat.java:869)
> at java.text.DateFormat.format(DateFormat.java:316)
> at com.hp.hpl.jena.sparql.util.Utils.nowAsString(Utils.java:81)
> at com.hp.hpl.jena.sparql.util.Utils.nowAsString(Utils.java:76)
> at
> com.hp.hpl.jena.sparql.mgt.QueryEngineInfo.setLastQueryExecAt(QueryEngineInfo.java:61)
> at
> com.hp.hpl.jena.sparql.engine.QueryEngineBase.evaluate(QueryEngineBase.java:125)
> at
> com.hp.hpl.jena.sparql.engine.QueryEngineBase.createPlan(QueryEngineBase.java:99)
> at
> com.hp.hpl.jena.sparql.engine.QueryEngineBase.getPlan(QueryEngineBase.java:87)
> at
> com.hp.hpl.jena.sparql.engine.main.QueryEngineMain$1.create(QueryEngineMain.java:124)
> at
> com.hp.hpl.jena.sparql.graph.Reifier2.nodesReifTriple(Reifier2.java:142)
> at com.hp.hpl.jena.sparql.graph.Reifier2.getTriple(Reifier2.java:326)
> at com.hp.hpl.jena.sparql.graph.Reifier2.reifyAs(Reifier2.java:267)
> at
> com.hp.hpl.jena.rdf.model.impl.ReifiedStatementImpl.installInReifier(ReifiedStatementImpl.java:119)
> at
> com.hp.hpl.jena.rdf.model.impl.ReifiedStatementImpl.create(ReifiedStatementImpl.java:135)
> at
> com.hp.hpl.jena.rdf.model.impl.ModelReifier.createReifiedStatement(ModelReifier.java:111)
> at
> com.hp.hpl.jena.rdf.model.impl.ModelCom.createReifiedStatement(ModelCom.java:1151)
