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

Pavel Klinov pavel.klinov at uni-ulm.de
Tue Nov 26 01:35:26 PST 2013


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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