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https://issues.apache.org/jira/browse/JENA-546?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13776073#comment-13776073
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Andy Seaborne commented on JENA-546:
------------------------------------
What's the query? Please could you provide an example query (not a dump of some
large one!). Without the query, it's very hard to investigate as it would be
poking around guessing and even if one cause is found, it does not help
determine if there is a general issue.
> Query timeout not observed in OPTIONAL eval
> -------------------------------------------
>
> Key: JENA-546
> URL: https://issues.apache.org/jira/browse/JENA-546
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB
> Affects Versions: TDB 0.10.1
> Reporter: Mark Buquor
>
> We've found two queries so far that fail to time out in a reasonable time
> after the timeout elapses. The severity of the issue varies. In one case, the
> query completes without error ~30 minutes after it should have aborted. In
> the other case, the query runs indefinitely.
> Beyond wasted resources, the critical issue for us is that queries must
> reliably abort in order for TDB to flush the writeback queue. Failure to
> flush the queue leads to stack overflows and heap exhaustion.
> I haven't been able to isolate a testcase yet, but in both cases, the problem
> appears to be isolated to an OPTIONAL block. Running under the debugger, the
> process was suspended after the query should have aborted. I placed comments
> in the stack below to show 1) the last iterator in the stack with abortFlag
> == true and 2) the QueryIterPeek directly above it has abortIterator ==
> false. All iterators above the first comment have not been aborted, so it
> appears that the abort signal does not propagate sufficiently.
> I'm not sure if this affects ARQ in general. I'm filing this against TDB
> because the QueryIterTDB below the comments is the last to have
> requestCancel() called. Its killList includes the two IterAbortables directly
> above it. Nothing else above that QueryIterTDB is aborted.
> {noformat}
> Thread [main] (Suspended)
>
> com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.recordsPageId(com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode,
> com.hp.hpl.jena.tdb.base.record.Record) line: 277
>
> com.hp.hpl.jena.tdb.index.bplustree.BPlusTree.iterator(com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode,
> com.hp.hpl.jena.tdb.base.record.Record,
> com.hp.hpl.jena.tdb.base.record.Record) line: 378
>
> com.hp.hpl.jena.tdb.index.bplustree.BPlusTree.iterator(com.hp.hpl.jena.tdb.base.record.Record,
> com.hp.hpl.jena.tdb.base.record.Record) line: 366
>
> com.hp.hpl.jena.tdb.index.TupleIndexRecord.findWorker(org.apache.jena.atlas.lib.Tuple<com.hp.hpl.jena.tdb.store.NodeId>,
> boolean, boolean) line: 164
>
> com.hp.hpl.jena.tdb.index.TupleIndexRecord.findOrScan(org.apache.jena.atlas.lib.Tuple<com.hp.hpl.jena.tdb.store.NodeId>)
> line: 84
>
> com.hp.hpl.jena.tdb.index.TupleIndexRecord.performFind(org.apache.jena.atlas.lib.Tuple<com.hp.hpl.jena.tdb.store.NodeId>)
> line: 78
>
> com.hp.hpl.jena.tdb.index.TupleIndexRecord(com.hp.hpl.jena.tdb.index.TupleIndexBase).find(org.apache.jena.atlas.lib.Tuple<com.hp.hpl.jena.tdb.store.NodeId>)
> line: 91
>
> com.hp.hpl.jena.tdb.index.TupleTable.find(org.apache.jena.atlas.lib.Tuple<com.hp.hpl.jena.tdb.store.NodeId>)
> line: 197
>
> com.hp.hpl.jena.tdb.nodetable.NodeTupleTableConcrete.find(org.apache.jena.atlas.lib.Tuple<com.hp.hpl.jena.tdb.store.NodeId>)
> line: 169
>
> com.hp.hpl.jena.tdb.solver.StageMatchTuple.makeNextStage(com.hp.hpl.jena.tdb.solver.BindingNodeId)
> line: 91
>
> com.hp.hpl.jena.tdb.solver.StageMatchTuple.makeNextStage(java.lang.Object)
> line: 37
>
> com.hp.hpl.jena.tdb.solver.StageMatchTuple(org.apache.jena.atlas.iterator.RepeatApplyIterator<T>).hasNext()
> line: 49
> com.hp.hpl.jena.tdb.solver.SolverLib$IterAbortable<T>.hasNext() line:
> 193
> org.apache.jena.atlas.iterator.Iter$4.hasNext() line: 293
>
> com.hp.hpl.jena.tdb.solver.QueryIterTDB(com.hp.hpl.jena.sparql.engine.iterator.QueryIterPlainWrapper).hasNextBinding()
> line: 54
>
> com.hp.hpl.jena.tdb.solver.QueryIterTDB(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterDefaulting.hasNextBinding()
> line: 54
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterDefaulting(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.sparql.engine.main.iterator.QueryIterOptionalIndex(com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply).hasNextBinding()
> line: 81
>
> com.hp.hpl.jena.sparql.engine.main.iterator.QueryIterOptionalIndex(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
> #### abortIterator == false ####
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterPeek.hasNextBinding() line:
> 57
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterPeek(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
> org.apache.jena.atlas.iterator.Iter$4.hasNext() line: 293
>
> com.hp.hpl.jena.tdb.solver.StageMatchTuple(org.apache.jena.atlas.iterator.RepeatApplyIterator<T>).hasNext()
> line: 46
> #### abortFlag == true ####
> com.hp.hpl.jena.tdb.solver.SolverLib$IterAbortable<T>.hasNext() line: 193
>
> com.hp.hpl.jena.tdb.solver.StageMatchTuple(org.apache.jena.atlas.iterator.RepeatApplyIterator<T>).hasNext()
> line: 46
> com.hp.hpl.jena.tdb.solver.SolverLib$IterAbortable<T>.hasNext() line:
> 193
> org.apache.jena.atlas.iterator.Iter$4.hasNext() line: 293
>
> com.hp.hpl.jena.tdb.solver.QueryIterTDB(com.hp.hpl.jena.sparql.engine.iterator.QueryIterPlainWrapper).hasNextBinding()
> line: 54
>
> com.hp.hpl.jena.tdb.solver.QueryIterTDB(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterFilterExpr(com.hp.hpl.jena.sparql.engine.iterator.QueryIterProcessBinding).hasNextBinding()
> line: 60
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterFilterExpr(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterGroup$1.initializeIterator()
> line: 86
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterGroup$1(org.apache.jena.atlas.iterator.IteratorDelayedInitialization<T>).init()
> line: 40
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterGroup$1(org.apache.jena.atlas.iterator.IteratorDelayedInitialization<T>).hasNext()
> line: 50
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterGroup(com.hp.hpl.jena.sparql.engine.iterator.QueryIterPlainWrapper).hasNextBinding()
> line: 54
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterGroup(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterAssign(com.hp.hpl.jena.sparql.engine.iterator.QueryIterProcessBinding).hasNextBinding()
> line: 60
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterAssign(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> org.apache.jena.atlas.data.SortedDataBag<E>(org.apache.jena.atlas.data.AbstractDataBag<E>).addAll(java.util.Iterator<?
> extends E>) line: 74
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterSort$SortedBindingIterator.initializeIterator()
> line: 89
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterSort$SortedBindingIterator(org.apache.jena.atlas.iterator.IteratorDelayedInitialization<T>).init()
> line: 40
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterSort$SortedBindingIterator(org.apache.jena.atlas.iterator.IteratorDelayedInitialization<T>).hasNext()
> line: 50
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterSort(com.hp.hpl.jena.sparql.engine.iterator.QueryIterPlainWrapper).hasNextBinding()
> line: 54
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterSort(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterProject(com.hp.hpl.jena.sparql.engine.iterator.QueryIterConvert).hasNextBinding()
> line: 59
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterProject(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterSlice.hasNextBinding()
> line: 76
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIterSlice(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorCheck(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper).hasNextBinding()
> line: 40
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorCheck(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.tdb.solver.QueryEngineTDB$QueryIteratorMaterializeBinding(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper).hasNextBinding()
> line: 40
>
> com.hp.hpl.jena.tdb.solver.QueryEngineTDB$QueryIteratorMaterializeBinding(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorCloseable(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper).hasNextBinding()
> line: 40
>
> com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorCloseable(com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase).hasNext()
> line: 112
> com.hp.hpl.jena.sparql.engine.ResultSetStream.hasNext() line: 75
>
> com.hp.hpl.jena.sparql.resultset.ResultSetMem.<init>(com.hp.hpl.jena.query.ResultSet)
> line: 97
>
> com.hp.hpl.jena.query.ResultSetFactory.makeRewindable(com.hp.hpl.jena.query.ResultSet)
> line: 420
> com.hp.hpl.jena.sparql.resultset.TextOutput.write(java.io.PrintWriter,
> com.hp.hpl.jena.query.ResultSet, java.lang.String, java.lang.String,
> java.lang.String) line: 149
> com.hp.hpl.jena.sparql.resultset.TextOutput.write(java.io.OutputStream,
> com.hp.hpl.jena.query.ResultSet, java.lang.String, java.lang.String,
> java.lang.String) line: 132
> com.hp.hpl.jena.sparql.resultset.TextOutput.write(java.io.OutputStream,
> com.hp.hpl.jena.query.ResultSet) line: 120
>
> com.hp.hpl.jena.sparql.resultset.TextOutput.format(java.io.OutputStream,
> com.hp.hpl.jena.query.ResultSet) line: 67
> com.hp.hpl.jena.query.ResultSetFormatter.out(java.io.OutputStream,
> com.hp.hpl.jena.query.ResultSet, com.hp.hpl.jena.sparql.core.Prologue) line:
> 135
>
> com.hp.hpl.jena.query.ResultSetFormatter.out(com.hp.hpl.jena.query.ResultSet,
> com.hp.hpl.jena.query.Query) line: 83
> Rogue.test() line: 67
> {noformat}
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