[Mulgara-general] Memory error during rdf load

Bill OConnor wtoconnor at gmail.com
Mon Aug 11 18:00:15 UTC 2008 

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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