OutOfMemoryError whilst loading large ontology   

I am getting an out of memory error whilst trying to load a Large ontology (~6 million lines of OWL). Any clues to why this might be? (I am assuming that this ontology is well within the limits of SHER's capability since it managed 300 million triples)

I can provide you with some details if required. Here's the trace:

Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

        at java.util.Arrays.copyOfRange(Arrays.java:3209)

        at java.lang.String.<init>(String.java:216)      

        at java.lang.StringBuffer.toString(StringBuffer.java:585)

        at org.eclipse.eodm.rdf.resource.parser.xml.RDFXMLParserImpl.checkStatementValid(RD

FXMLParserImpl.java:876)                                 

        at org.eclipse.eodm.rdf.resource.parser.xml.RDFXMLParserImpl.exportStatement(RDFXML

ParserImpl.java:752)                                     

        at org.eclipse.eodm.rdf.resource.parser.xml.RDFXMLParserImpl.addNodeElement(RDFXMLP

arserImpl.java:252)                                      

        at org.eclipse.eodm.rdf.resource.parser.xml.RDFXMLContentHandler.startElement(RDFXM

LContentHandler.java:149)                                

        at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)

        at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source)

        at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)

        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)                                 

        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)                                                       

        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)

        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)

        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)

        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)

        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)

        at org.eclipse.eodm.rdf.resource.parser.xml.RDFXMLParserImpl.parse(RDFXMLParserImpl.java:138)                                               

        at org.eclipse.eodm.owl.resource.parser.impl.OWLParserImpl.addOWLDocument(OWLParserImpl.java:550)                                           

        at com.ibm.iodt.sor.translator.EODMTranslator.addOWLDocument(EODMTranslator.java:899)                                                       

        at com.ibm.iodt.sor.OntologyStoreManager.addOWLDocument(OntologyStoreManager.java:220)                                                      

        at com.ibm.research.sher.utils.LoadForSHER.loadDocuments(LoadForSHER.java:79)

        at com.ibm.research.sher.utils.LoadForSHER.main(LoadForSHER.java:129)

I managed to get the ontology to load by splitting my ontology into multiple files. I found I had to include all the OWL class declarations at the beginning of each file.

This was successful. However running:

19 java -Xmx1024M com.ibm.research.sher.utils.QueryAnswering -ai rps rps-sher-config.cfg

Produced:

08-Nov-2008 23:25:11 com.ibm.research.sher.analysis.impl.ConsistencyChecker checkConsistency
INFO: SKIPPING CONSISTENCY CHECK since KB cannot entail contradictions
rps is consistent.

Which doesn't tell me where the contradiction might be. Any suggestions?

Ah, I had interpreted the message as "Since the ontology entails contradictions, SHER will not perform a consistency check". As you say, I suppose the constructs do not allow contradictions for this part of the ontology.

I'll let you know how I get on with querying...