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[p4-feedback] Protege 4.2 - OutOfMemoryError: Java heap space on large number of Individuals in an OWL ontology

Paulo Picota ppicota at gmail.com
Tue Nov 26 06:42:54 PST 2013


Dear mr. Pavel

Thanks for the help. I will look into the pellet mailing list and try
running it from shell.

question, what do you mean by Pellet OOM ??


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2013/11/26 Pavel Klinov <pavel.klinov at uni-ulm.de>

> It looks like Pellet OOMs when reasoning with SWRL rules. This issue per
> se has little to do with Protege (you may double check by running Pellet
> from the shell). You may ask on the Pellet's mailing list, perhaps some
> remodeling will simplify reasoning.
>
> HTH,
>
> Pavel
>
>
> On Tue, Nov 26, 2013 at 2:16 AM, Paulo Picota <ppicota at gmail.com> wrote:
>
>> Im very new to the use of protege and working with ontologies. Im
>> creating a lil program to chek firewall rules and i have come across the
>> following error while trying to run Pellet resoner, 2 different errors in
>> the log:
>>  1
>>
>> Error 1 Logged at Sun Nov 17 21:49:48 COT 2013 OutOfMemoryError: Java
>> heap space
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.(Index.java:43)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:55)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index.add(Index.java:173)
>> com.clarkparsia.pellet.rules.rete.BetaNode.join(BetaNode.java:131)
>> com.clarkparsia.pellet.rules.rete.Interpreter.processBetaNodes(Interpreter.java:109)
>> com.clarkparsia.pellet.rules.rete.Interpreter.run(Interpreter.java:236)
>> com.clarkparsia.pellet.rules.ContinuousRulesStrategy.applyRete(ContinuousRulesStrategy.java:179)
>> com.clarkparsia.pellet.rules.ContinuousRulesStrategy.complete(ContinuousRulesStrategy.java:291)
>> org.mindswap.pellet.ABox.isConsistent(ABox.java:1423)
>> org.mindswap.pellet.ABox.isConsistent(ABox.java:1260)
>> org.mindswap.pellet.KnowledgeBase.consistency(KnowledgeBase.java:1987)
>> org.mindswap.pellet.KnowledgeBase.isConsistent(KnowledgeBase.java:2061)
>> org.mindswap.pellet.KnowledgeBase.ensureConsistency(KnowledgeBase.java:2075)
>> org.mindswap.pellet.KnowledgeBase.classify(KnowledgeBase.java:2083)
>> com.clarkparsia.pellet.owlapiv3.PelletReasoner.precomputeInferences(PelletReasoner.java:1067)
>> org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.precompute(OWLReasonerManagerImpl.java:417)
>> org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:356)
>>  java.lang.Thread.run(Thread.java:722)
>>
>> 2
>>
>> Error 2 Logged at Sun Nov 17 21:50:37 COT 2013 OutOfMemoryError: Java
>> heap space java.util.HashMap.createEntry(HashMap.java:869)
>> java.util.HashMap.addEntry(HashMap.java:856)
>> java.util.HashMap.put(HashMap.java:484)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:56)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index$IndexNode.add(Index.java:58)
>> com.clarkparsia.pellet.rules.rete.Index.add(Index.java:173)
>> com.clarkparsia.pellet.rules.rete.BetaNode.join(BetaNode.java:131)
>> com.clarkparsia.pellet.rules.rete.Interpreter.processBetaNodes(Interpreter.java:109)
>> com.clarkparsia.pellet.rules.rete.Interpreter.run(Interpreter.java:236)
>> com.clarkparsia.pellet.rules.ContinuousRulesStrategy.applyRete(ContinuousRulesStrategy.java:179)
>> com.clarkparsia.pellet.rules.ContinuousRulesStrategy.complete(ContinuousRulesStrategy.java:291)
>> org.mindswap.pellet.ABox.isConsistent(ABox.java:1423)
>> org.mindswap.pellet.ABox.isConsistent(ABox.java:1260)
>> org.mindswap.pellet.KnowledgeBase.consistency(KnowledgeBase.java:1987)
>> org.mindswap.pellet.KnowledgeBase.isConsistent(KnowledgeBase.java:2061)
>> com.clarkparsia.pellet.owlapiv3.PelletReasoner.isConsistent(PelletReasoner.java:849)
>> org.protege.editor.owl.model.inference.OWLReasonerManagerImpl.getReasonerStatus(OWLReasonerManagerImpl.java:236)
>> org.protege.editor.owl.model.OWLWorkspace.updateReasonerStatus(OWLWorkspace.java:750)
>> org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:351)
>> org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:140)
>> org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:253)
>> org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:818)
>> org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner$1.run(OWLReasonerManagerImpl.java:430)
>> java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251)
>> java.awt.EventQueue.dispatchEventImpl(EventQueue.java:721)
>> java.awt.EventQueue.access$200(EventQueue.java:103)
>> java.awt.EventQueue$3.run(EventQueue.java:682)
>> java.awt.EventQueue$3.run(EventQueue.java:680)
>> java.security.AccessController.doPrivileged(Native Method)
>> ------------------------------
>>
>> i have been reading and I have changed the JVM memory to almost 3GB which
>> is the maximum amount on my laptop. I have double cheked all the data type
>> are acording to design.
>>
>> In my corrent ontology Im using SWRL rules and i got about 1300 and some
>> individuals and the .owl file is 5.31Mb. Im running a 64bit windows 7.
>>
>> Im thinking that the main issue is that my laptop cannot run this large
>> ontology. is there any way I could be wrong? I have seen some places where
>> they say that this error msg might be misleading.
>>
>> how can I fix this issue? what are my options? Im new here but im ready
>> to read a lot =) thnx everyone
>>
>>
>>               *  | Paulo A. Picota C.          *  *  | *Ing. Sis.
>> Computación       *  | *CCNA CNCO11876553    *  |* Celular: 6426 9482
>>
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