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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
Mon Nov 25 17:16:03 PST 2013


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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