[Mulgara-general] Memory error during rdf load
Bill OConnor
wtoconnor at gmail.com
Wed Aug 13 17:59:39 UTC 2008
Hello,
Any more ideas about how I might fix some of these problems?
On Mon, Aug 11, 2008 at 11:00 AM, Bill OConnor <wtoconnor at gmail.com> wrote:
> Hello,
>
> Thanks for responding.
>
> I am running a 32 bit version of Ubuntu on a AMD 64 bit processor. I would
> assume the JVM
> that is running is 32 bit. The 64 bit operating systems have given me
> compatibility problems
> in the past so I generally try to avoid it. The system has 1 GB physical
> and 3 GB swap.
>
> I launched Mulgara with the default settings.The load process takes around
> 7 hours before it fails.
> I restarted Mulgara and attempted another load and got the following error
> on the client side. It seems to
> behave differently depending on whether a previous load has failed.
>
> org.mulgara.query.QueryException: Unable to load
> file:/home/wto/Projects/dmoz/t2.rdf into rmi://localhost/server1#content2
> at
> org.mulgara.resolver.DatabaseSession.execute(DatabaseSession.java:726)
> at
> org.mulgara.resolver.DatabaseSession.setModel(DatabaseSession.java:562)
> at
> org.mulgara.server.rmi.SessionWrapperRemoteSession.setModel(SessionWrapperRemoteSession.java:123)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:322)
> at sun.rmi.transport.Transport$1.run(Transport.java:177)
> at java.security.AccessController.doPrivileged(Native Method)
> at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
> at
> sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
> at
> sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
> at
> sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
> at java.lang.Thread.run(Thread.java:636)
> at
> sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:255)
> at
> sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:233)
> at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:142)
> at org.mulgara.server.rmi.RemoteSessionImpl_Stub.setModel(Unknown
> Source)
> at
> org.mulgara.server.rmi.RemoteSessionWrapperSession.setModel(RemoteSessionWrapperSession.java:166)
> at org.mulgara.query.operation.Load.doTx(Load.java:101)
> at
> org.mulgara.query.operation.DataInputTx.sendMarshalledData(DataInputTx.java:111)
> at org.mulgara.query.operation.Load.execute(Load.java:79)
> at
> org.mulgara.itql.ItqlInterpreterBean.load(ItqlInterpreterBean.java:707)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
> at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:226)
> at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:899)
> at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:740)
> at
> org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:765)
> at
> org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:753)
> at
> org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:167)
> at itql.run(itql.groovy:23)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
> at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:226)
> at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:899)
> at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:740)
> at
> org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:777)
> at
> org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:757)
> at
> org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:402)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
> at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:226)
> at
> groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:1094)
> at
> org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:748)
> at
> org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:167)
> at itql.main(itql.groovy)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
> at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:226)
> at
> groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:1094)
> at
> org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:748)
> at
> groovy.lang.GroovyShell.runMainOrTestOrRunnable(GroovyShell.java:244)
> at groovy.lang.GroovyShell.run(GroovyShell.java:218)
> at groovy.lang.GroovyShell.run(GroovyShell.java:147)
> at groovy.ui.GroovyMain.processOnce(GroovyMain.java:493)
> at groovy.ui.GroovyMain.run(GroovyMain.java:308)
> at groovy.ui.GroovyMain.process(GroovyMain.java:294)
> at groovy.ui.GroovyMain.processArgs(GroovyMain.java:111)
> at groovy.ui.GroovyMain.main(GroovyMain.java:92)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:101)
> at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:130)
> Caused by: org.mulgara.query.QueryException:
> org.mulgara.query.MulgaraTransactionException: Transaction rollback
> triggered
> at
> org.mulgara.resolver.MulgaraInternalTransaction.implicitRollback(MulgaraInternalTransaction.java:516)
> at
> org.mulgara.resolver.MulgaraInternalTransaction.execute(MulgaraInternalTransaction.java:627)
> at
> org.mulgara.resolver.DatabaseSession.execute(DatabaseSession.java:723)
> at
> org.mulgara.resolver.DatabaseSession.setModel(DatabaseSession.java:562)
> at
> org.mulgara.server.rmi.SessionWrapperRemoteSession.setModel(SessionWrapperRemoteSession.java:123)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:322)
> at sun.rmi.transport.Transport$1.run(Transport.java:177)
> at java.security.AccessController.doPrivileged(Native Method)
> at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
> at
> sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
> at
> sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
> at
> sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
> at java.lang.Thread.run(Thread.java:636)
> Caused by: org.mulgara.query.QueryException:
> org.mulgara.resolver.spi.ResolverException: Unable to read input statements
> at
> org.mulgara.resolver.store.StatementStoreResolver.modifyModel(StatementStoreResolver.java:381)
> at
> org.mulgara.resolver.InternalResolver.modifyModel(InternalResolver.java:164)
> at
> org.mulgara.resolver.SetModelOperation.execute(SetModelOperation.java:153)
> at
> org.mulgara.resolver.MulgaraInternalTransaction.execute(MulgaraInternalTransaction.java:623)
> ... 17 more
> Caused by: org.mulgara.query.QueryException:
> org.mulgara.query.TuplesException: Exception while reading
> file:/home/wto/Projects/dmoz/t2.rdf
> at org.mulgara.content.rdfxml.Parser.checkForException(Parser.java:525)
> at
> org.mulgara.content.rdfxml.Parser.getBufferFromQueue(Parser.java:559)
> at org.mulgara.content.rdfxml.Parser.getTriple(Parser.java:540)
> at
> org.mulgara.content.rdfxml.RDFXMLStatements.next(RDFXMLStatements.java:389)
> at
> org.mulgara.resolver.store.StatementStoreResolver.modifyModel(StatementStoreResolver.java:353)
> ... 20 more
> Caused by: java.lang.IllegalArgumentException: blockId: -14155777 of
> 7892698
> at
> org.mulgara.store.xa.MappedBlockFile.readBlock(MappedBlockFile.java:261)
> at
> org.mulgara.store.xa.ManagedBlockFile$Phase.readBlock(ManagedBlockFile.java:382)
> at org.mulgara.store.xa.AVLNode.init(AVLNode.java:1144)
> at org.mulgara.store.xa.AVLNode.<init>(AVLNode.java:142)
> at org.mulgara.store.xa.AVLNode.newInstance(AVLNode.java:180)
> at org.mulgara.store.xa.AVLNode.getChildNode_N(AVLNode.java:1116)
> at org.mulgara.store.xa.AVLNode.getRightChildNode_N(AVLNode.java:1097)
> at org.mulgara.store.xa.AVLNode.findDown(AVLNode.java:304)
> at org.mulgara.store.xa.AVLFile$Phase.find(AVLFile.java:361)
> at
> org.mulgara.store.stringpool.xa.XAStringPoolImpl$Phase.findGNode(XAStringPoolImpl.java:1636)
> at
> org.mulgara.store.stringpool.xa.XAStringPoolImpl.findGNode(XAStringPoolImpl.java:376)
> at
> org.mulgara.resolver.StringPoolSession.localizeSPObject(StringPoolSession.java:556)
> at
> org.mulgara.resolver.StringPoolSession.localize(StringPoolSession.java:467)
> at
> org.mulgara.resolver.StringPoolSession.localizePersistent(StringPoolSession.java:209)
> at
> org.mulgara.resolver.store.StatementStoreResolver.localizePersistent(StatementStoreResolver.java:451)
> at
> org.mulgara.resolver.PersistentResolverSession.localize(PersistentResolverSession.java:97)
> at org.mulgara.content.rdfxml.Parser.toLocalNode(Parser.java:458)
> at org.mulgara.content.rdfxml.Parser.statement(Parser.java:347)
> at com.hp.hpl.jena.rdf.arp.ARPResource.tripleLit(ARPResource.java:190)
> at com.hp.hpl.jena.rdf.arp.ARPResource.triple(ARPResource.java:172)
> at
> com.hp.hpl.jena.rdf.arp.ARPResource.setPredObject(ARPResource.java:146)
> at
> com.hp.hpl.jena.rdf.arp.ARPResource.setPredicateObject(ARPResource.java:127)
> at
> com.hp.hpl.jena.rdf.arp.ParserSupport.createTriple(ParserSupport.java:319)
> at
> com.hp.hpl.jena.rdf.arp.RDFParser.propertyEltIdAndValue(RDFParser.java:692)
> at com.hp.hpl.jena.rdf.arp.RDFParser.propertyElt(RDFParser.java:647)
> at com.hp.hpl.jena.rdf.arp.RDFParser.typedNode(RDFParser.java:984)
> at com.hp.hpl.jena.rdf.arp.RDFParser.description(RDFParser.java:429)
> at com.hp.hpl.jena.rdf.arp.RDFParser.obj(RDFParser.java:346)
> at com.hp.hpl.jena.rdf.arp.RDFParser.rdf(RDFParser.java:326)
> at com.hp.hpl.jena.rdf.arp.RDFParser.root(RDFParser.java:1371)
> at com.hp.hpl.jena.rdf.arp.RDFParser.embeddedFile(RDFParser.java:1364)
> at com.hp.hpl.jena.rdf.arp.ARPFilter.parse(ARPFilter.java:312)
> at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:291)
> at org.mulgara.content.rdfxml.Parser.run(Parser.java:308)
>
>
>
> On Mon, Aug 11, 2008 at 8:54 AM, Paul Gearon <gearon at ieee.org> wrote:
>
>> Do you know if you are running Mulgara in 32 bit or 64 bit mode? The
>> answers are different, depending on what mode you're in.
>>
>> Regards,
>> Paul Gearon
>>
>> On Mon, Aug 11, 2008 at 12:18 AM, Bill OConnor <wtoconnor at gmail.com>
>> wrote:
>> > 2008-08-10 11:15:32,522 WARN TripleWriteThread - Exception during abort
>> of
>> > TripleWriteThread:
>> > /home/wto/Projects/dmoz/server1/xaStatementStore/xa.g_3120
>> > java.lang.OutOfMemoryError
>> > at sun.misc.Unsafe.allocateMemory(Native Method)
>> > at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:117)
>> > at java.nio.ByteBuffer.allocateDirect(ByteBuffer.java:305)
>> > at org.mulgara.store.xa.Block.newInstance(Block.java:168)
>> > at
>> org.mulgara.store.xa.IOBlockFile.allocateBlock(IOBlockFile.java:138)
>> > at org.mulgara.store.xa.IOBlockFile.readBlock(IOBlockFile.java:152)
>> > at
>> >
>> org.mulgara.store.xa.ManagedBlockFile$Phase.readBlock(ManagedBlockFile.java:382)
>> > at
>> >
>> org.mulgara.store.statement.xa.TripleAVLFile$Phase.syncAddTriple(TripleAVLFile.java:857)
>> > at
>> >
>> org.mulgara.store.statement.xa.TripleAVLFile$Phase.syncAddTriples(TripleAVLFile.java:706)
>> > at
>> >
>> org.mulgara.store.statement.xa.TripleWriteThread.run(TripleWriteThread.java:155)
>> > 2008-08-10 11:15:32,522 WARN TripleWriteThread - Exception during abort
>> of
>> > TripleWriteThread:
>> > /home/wto/Projects/dmoz/server1/xaStatementStore/xa.g_3201
>> > java.lang.OutOfMemoryError
>> > at sun.misc.Unsafe.allocateMemory(Native Method)
>> > at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:117)
>> > at java.nio.ByteBuffer.allocateDirect(ByteBuffer.java:305)
>> > at org.mulgara.store.xa.Block.newInstance(Block.java:168)
>> > at
>> org.mulgara.store.xa.IOBlockFile.allocateBlock(IOBlockFile.java:138)
>> > at org.mulgara.store.xa.IOBlockFile.readBlock(IOBlockFile.java:152)
>> > at
>> >
>> org.mulgara.store.xa.ManagedBlockFile$Phase.readBlock(ManagedBlockFile.java:382)
>> > at
>> >
>> org.mulgara.store.statement.xa.TripleAVLFile$Phase.syncAddTriple(TripleAVLFile.java:857)
>> > at
>> >
>> org.mulgara.store.statement.xa.TripleAVLFile$Phase.syncAddTriples(TripleAVLFile.java:706)
>> > at
>> >
>> org.mulgara.store.statement.xa.TripleWriteThread.run(TripleWriteThread.java:155)
>> > 2008-08-10 22:17:02,985 ERROR Parser - Error, 20364240, column 9: {E213}
>> > Connection refused to host: 127.0.1.1; nested exception is:
>> > java.net.ConnectException: Connection refused
>> > com.hp.hpl.jena.rdf.arp.ParseException: {E213} Connection refused to
>> host:
>> > 127.0.1.1; nested exception is:
>> > java.net.ConnectException: Connection refused
>> > at
>> com.hp.hpl.jena.rdf.arp.ARPFilter.parseWarning(ARPFilter.java:559)
>> > Hello,
>> >
>> > I have been experimenting with Mulgara by trying to load the dmoz open
>> > directory project. I believe that I have fixed
>> > most of the invalid URI problems I was experiencing. However after
>> several
>> > hours of loading a 2 Gig rdf it fails with the following stack.
>> >
>> > The client side never returns with an error.
>> >
>> > Anybody have any suggestion were I should go from here?
>> >
>> >
>> > at com.hp.hpl.jena.rdf.arp.ARPFilter.parseWarning(ARPFilter.java:552)
>> > at
>> >
>> com.hp.hpl.jena.rdf.arp.ParserSupport.saxException(ParserSupport.java:183)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.saxEx(RDFParser.java:260)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.oneWhite(RDFParser.java:248)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.white1(RDFParser.java:172)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.white(RDFParser.java:137)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.zwhite(RDFParser.java:132)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.typedNode(RDFParser.java:985)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.description(RDFParser.java:429)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.obj(RDFParser.java:346)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.rdf(RDFParser.java:326)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.root(RDFParser.java:1371)
>> > at
>> com.hp.hpl.jena.rdf.arp.RDFParser.embeddedFile(RDFParser.java:1364)
>> > at com.hp.hpl.jena.rdf.arp.ARPFilter.parse(ARPFilter.java:312)
>> > at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:291)
>> > at org.mulgara.content.rdfxml.Parser.run(Parser.java:308)
>> > 2008-08-10 22:17:03,209 ERROR Parser - Fatal error, line -1, column -1:
>> > {E300} Error recovery failed.
>> > com.hp.hpl.jena.rdf.arp.ParseException: {E300} Error recovery failed.
>> > at
>> com.hp.hpl.jena.rdf.arp.RDFParser.error_recovery(RDFParser.java:1961)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.description(RDFParser.java:437)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.obj(RDFParser.java:346)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.rdf(RDFParser.java:326)
>> > at com.hp.hpl.jena.rdf.arp.RDFParser.root(RDFParser.java:1371)
>> > at
>> com.hp.hpl.jena.rdf.arp.RDFParser.embeddedFile(RDFParser.java:1364)
>> > at com.hp.hpl.jena.rdf.arp.ARPFilter.parse(ARPFilter.java:312)
>> > at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:291)
>> > at org.mulgara.content.rdfxml.Parser.run(Parser.java:308)
>> >
>> >
>> > _______________________________________________
>> > Mulgara-general mailing list
>> > Mulgara-general at mulgara.org
>> > http://mulgara.org/mailman/listinfo/mulgara-general
>> >
>> >
>> _______________________________________________
>> Mulgara-general mailing list
>> Mulgara-general at mulgara.org
>> http://mulgara.org/mailman/listinfo/mulgara-general
>>
>
>
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