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Posted to dev@jena.apache.org by "Damien Obrist (Jira)" <ji...@apache.org> on 2019/09/12 15:07:00 UTC
[jira] [Commented] (JENA-1758) Exception when preparing InfModel
after TDB loading operation
[ https://issues.apache.org/jira/browse/JENA-1758?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16928617#comment-16928617 ]
Damien Obrist commented on JENA-1758:
-------------------------------------
h2. Investigation
Playing around I have observed the following:
* when catching the exception and trying to prepare the model a second time, the call succeeded and no exception was thrown
* when sleep for a few seconds after the loading and before preparing the model, the call succeeded and no exception was thrown at all
So I suspected that, even though the loading is complete, something must still be going on in the background.
Next I tried to close and reopen the dataset after the loading, in order to make sure that potential pending writes are terminated and have been flushed to disk:
{code:java}
TDBInternal.expel(dataset.asDatasetGraph());
dataset = TDB2Factory.connectDataset(path);
infModel = ModelFactory.createInfModel(reasoner, unionModel);
Txn.executeRead(dataset, infModel::prepare);
{code}
This lead to the following exception:
{noformat}
org.apache.jena.atlas.lib.InternalErrorException: BlockMgrFileAccess : already closed
at org.apache.jena.dboe.base.block.BlockMgrFileAccess.checkNotClosed(BlockMgrFileAccess.java:78)
at org.apache.jena.dboe.base.block.BlockMgrFileAccess.allocLimit(BlockMgrFileAccess.java:150)
at org.apache.jena.dboe.base.block.BlockMgrWrapper.allocLimit(BlockMgrWrapper.java:87)
at org.apache.jena.dboe.base.page.PageBlockMgr.allocLimit(PageBlockMgr.java:45)
at org.apache.jena.dboe.trans.bplustree.BPlusTree._commitPrepare(BPlusTree.java:544)
at org.apache.jena.dboe.trans.bplustree.BPlusTree._commitPrepare(BPlusTree.java:73)
at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.commitPrepare(TransactionalComponentLifecycle.java:98)
at org.apache.jena.dboe.transaction.txn.TransactionCoordinator.lambda$executePrepare$12(TransactionCoordinator.java:687)
at java.util.ArrayList.forEach(ArrayList.java:1257)
at org.apache.jena.dboe.transaction.txn.TransactionCoordinator.executePrepare(TransactionCoordinator.java:685)
at org.apache.jena.dboe.transaction.txn.Transaction.prepare(Transaction.java:151)
at org.apache.jena.dboe.transaction.txn.Transaction.commit(Transaction.java:160)
at org.apache.jena.tdb2.loader.main.DataToTuples.action(DataToTuples.java:139)
at org.apache.jena.tdb2.loader.main.DataToTuples.lambda$startBulk$0(DataToTuples.java:101)
at java.lang.Thread.run(Thread.java:748)
Exception in thread "Thread-67" java.lang.NullPointerException
at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.getDataState(TransactionalComponentLifecycle.java:251)
at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.abort(TransactionalComponentLifecycle.java:126)
at org.apache.jena.dboe.transaction.txn.SysTrans.abort(SysTrans.java:45)
at org.apache.jena.dboe.transaction.txn.Transaction.lambda$null$10(Transaction.java:189)
at java.util.ArrayList.forEach(ArrayList.java:1257)
at org.apache.jena.dboe.transaction.txn.Transaction.lambda$abort$$11(Transaction.java:189)
at org.apache.jena.dboe.transaction.txn.TransactionCoordinator.executeAbort(TransactionCoordinator.java:726)
at org.apache.jena.dboe.transaction.txn.Transaction.abort$(Transaction.java:189)
at org.apache.jena.dboe.transaction.txn.Transaction.abort(Transaction.java:181)
at org.apache.jena.tdb2.loader.main.DataToTuples.action(DataToTuples.java:142)
at org.apache.jena.tdb2.loader.main.DataToTuples.lambda$startBulk$0(DataToTuples.java:101)
at java.lang.Thread.run(Thread.java:748)
{noformat}
This shows that {{DataToTuples}} is the culprit still running after the loading operation has returned.
> Exception when preparing InfModel after TDB loading operation
> -------------------------------------------------------------
>
> Key: JENA-1758
> URL: https://issues.apache.org/jira/browse/JENA-1758
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
> Affects Versions: Jena 3.12.0
> Reporter: Damien Obrist
> Priority: Major
>
> h2. Exception
> I'm loading a few million triples into a TDB2 dataset. I'm using a custom loader (extending {{LoaderMain}}), since the triples being loaded are generated by a separate application and streamed in over HTTP.
> After the loading is done, I try to reset an {{InfModel}} to recompute the inference taking into account the new triples, but I encounter the following exception:
> {noformat}
> org.apache.jena.atlas.RuntimeIOException: Out of bounds: (limit 32834204)32834205
> at org.apache.jena.atlas.io.IO.exception(IO.java:254)
> at org.apache.jena.dboe.trans.data.TransBinaryDataFile.checkRead(TransBinaryDataFile.java:190)
> at org.apache.jena.dboe.trans.data.TransBinaryDataFile.read(TransBinaryDataFile.java:184)
> at org.apache.jena.tdb2.store.nodetable.TReadAppendFileTransport.read(TReadAppendFileTransport.java:71)
> at org.apache.thrift.transport.TTransport.readAll(TTransport.java:86)
> at org.apache.thrift.protocol.TCompactProtocol.readByte(TCompactProtocol.java:637)
> at org.apache.thrift.protocol.TCompactProtocol.readFieldBegin(TCompactProtocol.java:543)
> at org.apache.jena.riot.thrift.wire.RDF_IRI$RDF_IRIStandardScheme.read(RDF_IRI.java:318)
> at org.apache.jena.riot.thrift.wire.RDF_IRI$RDF_IRIStandardScheme.read(RDF_IRI.java:311)
> at org.apache.jena.riot.thrift.wire.RDF_IRI.read(RDF_IRI.java:258)
> at org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:319)
> at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224)
> at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213)
> at org.apache.thrift.TUnion.read(TUnion.java:138)
> at org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:80)
> at org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
> at org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52)
> at org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:197)
> at org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:108)
> at org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:52)
> at org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:66)
> at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:112)
> at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:108)
> at org.apache.jena.tdb2.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:53)
> at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:270)
> at org.apache.jena.atlas.iterator.IteratorWrapper.next(IteratorWrapper.java:36)
> at org.apache.jena.tdb2.store.IteratorTxnTracker.next(IteratorTxnTracker.java:43)
> at java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1812)
> at java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294)
> at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206)
> at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:169)
> at java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300)
> at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681)
> at org.apache.jena.atlas.iterator.Iter$2.hasNext(Iter.java:265)
> at org.apache.jena.atlas.iterator.Iter.hasNext(Iter.java:903)
> at org.apache.jena.atlas.iterator.Iter$1.hasNext(Iter.java:192)
> at org.apache.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
> at org.apache.jena.reasoner.rulesys.impl.RETEEngine.fastInit(RETEEngine.java:155)
> at org.apache.jena.reasoner.rulesys.FBRuleInfGraph.prepare(FBRuleInfGraph.java:471)
> at org.apache.jena.rdf.model.impl.InfModelImpl.prepare(InfModelImpl.java:87)
> ...
> {noformat}
> h2. Code
> I tried to come up with a minimal example but wasn't able to reproduce the issue outside of my more involved application environment, where the issue occurs consistently. It seems to depend on a specific timing, the number of triples being loaded, the inference rules used etc.
> The code looks roughly like this:
> {code:java}
> // initialize
> Dataset dataset = TDB2Factory.connectDataset(path);
> Model unionModel = dataset.getNamedModel("urn:x-arq:UnionGraph");
> InfModel infModel = ModelFactory.createInfModel(reasoner, unionModel);
> Txn.executeRead(dataset, infModel::prepare);
> // load
> InputStream inputStream = // incoming HTTP stream
> DataLoader loader = new CustomLoader(LoaderPlans.loaderPlanParallel, dataset.asDatasetGraph);
> loader.startBulk();
> try {
> RDFDataMgr.parse(loader.stream(), inputStream, RDFLanguages.NQUADS);
> loader.finishBulk();
> } catch (RuntimeException e) {
> loader.finishException(e);
> throw e;
> }
> // reset model to recompute inference
> Txn.executeRead(dataset, () -> {
> model.reset();
> model.prepare();
> });
> {code}
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