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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 07:43:03 PST 2013


On Tue, Nov 26, 2013 at 3:42 PM, Paulo Picota <ppicota at gmail.com> wrote:

> 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 ??
>

"Pellet OOMs" is an abbreviation for "Pellet throws an out of memory (OOM)
error"

Cheers,
Pavel


>
>
>               *  | Paulo A. Picota C.          *  *  | *Ing. Sis.
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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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>>>
>>>
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