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

Paulo Picota ppicota at gmail.com
Sun Nov 17 18:54:25 PST 2013


Hello,
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$IndexNode.<init>(Index.java:43)
    com.clarkparsia.pellet.rules.rete.Index$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 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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