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stain / jena-docker

Docker image for Apache Jena riot
Apache License 2.0
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Error BlockMgrMapped.segmentAllocate #4

Closed ali3assi closed 6 years ago

ali3assi commented 7 years ago

Hello,

Im trying to parse a big file. The program runs very well and all it was ok. After 17h of runing i get the following exception:

com.hp.hpl.jena.tdb.base.file.FileException: BlockMgrMapped.segmentAllocate: Segment = 62 : Offset = 520093696 at com.hp.hpl.jena.tdb.base.file.BlockAccessMapped.allocSegment(BlockAccessMapped.java:229) at com.hp.hpl.jena.tdb.base.file.BlockAccessMapped.getByteBuffer(BlockAccessMapped.java:156) at com.hp.hpl.jena.tdb.base.file.BlockAccessMapped.allocate(BlockAccessMapped.java:84) at com.hp.hpl.jena.tdb.base.block.BlockMgrFileAccess.allocate(BlockMgrFileAccess.java:51) at com.hp.hpl.jena.tdb.base.block.BlockMgrBase.allocate(BlockMgrBase.java:44) at com.hp.hpl.jena.tdb.base.block.BlockMgrWrapper.allocate(BlockMgrWrapper.java:46) at com.hp.hpl.jena.tdb.base.block.BlockMgrFreeChain.allocate(BlockMgrFreeChain.java:48) at com.hp.hpl.jena.tdb.base.page.PageBlockMgr.create(PageBlockMgr.java:52) at com.hp.hpl.jena.tdb.index.bplustree.BPTreeRecordsMgr.create(BPTreeRecordsMgr.java:79) at com.hp.hpl.jena.tdb.index.bplustree.BPTreeRecords.create(BPTreeRecords.java:208) at com.hp.hpl.jena.tdb.index.bplustree.BPTreeRecords.split(BPTreeRecords.java:182) at com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.split(BPTreeNode.java:519) at com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.internalInsert(BPTreeNode.java:455) at com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.internalInsert(BPTreeNode.java:468) at com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.internalInsert(BPTreeNode.java:468) at com.hp.hpl.jena.tdb.index.bplustree.BPTreeNode.insert(BPTreeNode.java:212) at com.hp.hpl.jena.tdb.index.bplustree.BPlusTree.addAndReturnOld(BPlusTree.java:327) at com.hp.hpl.jena.tdb.index.bplustree.BPlusTree.add(BPlusTree.java:319) at com.hp.hpl.jena.tdb.store.tupletable.TupleIndexRecord.performAdd(TupleIndexRecord.java:62) at com.hp.hpl.jena.tdb.store.tupletable.TupleIndexBase.add(TupleIndexBase.java:64) at com.hp.hpl.jena.tdb.store.tupletable.TupleTable.add(TupleTable.java:96) at com.hp.hpl.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.addRow(NodeTupleTableConcrete.java:88) at com.hp.hpl.jena.tdb.store.TripleTable.add(TripleTable.java:58) at com.hp.hpl.jena.tdb.store.DatasetGraphTDB.addToDftGraph(DatasetGraphTDB.java:99) at com.hp.hpl.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:47) at com.hp.hpl.jena.sparql.core.GraphView.performAdd(GraphView.java:141) at com.hp.hpl.jena.tdb.store.GraphTDB.performAdd(GraphTDB.java:87) at com.hp.hpl.jena.graph.impl.GraphBase.add(GraphBase.java:202) at org.apache.jena.riot.system.StreamRDFLib$ParserOutputGraph.triple(StreamRDFLib.java:163) at org.apache.jena.riot.lang.LangTurtle.emit(LangTurtle.java:58) at org.apache.jena.riot.lang.LangTurtleBase.emitTriple(LangTurtleBase.java:488) at org.apache.jena.riot.lang.LangTurtleBase.objectList(LangTurtleBase.java:351) at org.apache.jena.riot.lang.LangTurtleBase.predicateObjectItem(LangTurtleBase.java:288) at org.apache.jena.riot.lang.LangTurtleBase.predicateObjectList(LangTurtleBase.java:269) at org.apache.jena.riot.lang.LangTurtleBase.triples(LangTurtleBase.java:250) at org.apache.jena.riot.lang.LangTurtleBase.triplesSameSubject(LangTurtleBase.java:191) at org.apache.jena.riot.lang.LangTurtle.oneTopLevelElement(LangTurtle.java:47) at org.apache.jena.riot.lang.LangTurtleBase.runParser(LangTurtleBase.java:90) at org.apache.jena.riot.lang.LangBase.parse(LangBase.java:42) at org.apache.jena.riot.RDFParserRegistry$ReaderRIOTLang.read(RDFParserRegistry.java:185) at org.apache.jena.riot.RDFDataMgr.process(RDFDataMgr.java:906) at org.apache.jena.riot.RDFDataMgr.parse(RDFDataMgr.java:687) at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:210) at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:143) at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:132) at org.apache.jena.riot.adapters.AdapterFileManager.readModelWorker(AdapterFileManager.java:283) at com.hp.hpl.jena.util.FileManager.readModel(FileManager.java:342) at de.dwslab.petar.walks.Connection.load_dumps(Connection.java:75) at de.dwslab.petar.walks.Connection.(Connection.java:49) at de.dwslab.petar.walks.SurfaceForms.main(SurfaceForms.java:285) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:282) at java.lang.Thread.run(Thread.java:745)

Im working on a SSH linux server. Any advice it appreciated. Thank you in advance

stain commented 6 years ago

You can increase the memory allocated to Jena with the Docker parameter -e JVM_ARGS=-Xmx2g (for 2 GB).

If you still have trouble, try running it outside Docker from the Jena Fuseki download and Oracle JDK 8 - then report back to Apache Jena if you still have trouble.

stain commented 6 years ago

Sorry I didn't spot this before, your traceback mentions com.hp.hpl.jena.graph.impl which indicates outdated Jena 2.x.

The latest Apache Jena download is 3.6.0 (which uses org.apache.jena.*)

Closing as out of scope for this Docker image.