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https://issues.apache.org/jira/browse/JENA-546?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13778016#comment-13778016
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Mark Buquor commented on JENA-546:
----------------------------------
Thanks, Andy.
So far, I've hit this general stack/abort state every time. I also see the same
problem/stack with TDB 1.0.0. The top QueryIterTDB is always there. I'll let it
run overnight and see what it looks like in the morning.
It's easy to avoid this problem by modifying the query, but so far I've only
avoided the need to time out. This particular query was optimized for a
different SPARQL implementation. The person writing the query then moved to
TDB/ARQ and was in the process of optimizing this and other queries when he
noticed performance degrading. We found that this version of the query had been
executing for over 18 hours after query timeout. My understanding is that the
user has a version of this query that runs fine with TDB, but I'll pass your
suggestions along.
I've asked for authorization to share the dataset, but it's unlikely. I'll see
if we can get further with another query/dataset that has a similar timeout
problem.
> 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
> Attachments: query1.txt
>
>
> 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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