<div dir="ltr">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. <div>
<br></div><div>HTH,</div><div><br></div><div>Pavel </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Nov 26, 2013 at 2:16 AM, Paulo Picota <span dir="ltr"><<a href="mailto:ppicota@gmail.com" target="_blank">ppicota@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><p style="clear:both;vertical-align:baseline;line-height:18px;font-size:14px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;border:0px;padding:0px">

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:</p>

<h2 style="vertical-align:baseline;line-height:1.3;font-size:19px;font-family:'Trebuchet MS','Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;word-wrap:break-word;border:0px;padding:0px">

1</h2><p style="clear:both;vertical-align:baseline;line-height:18px;font-size:14px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;border:0px;padding:0px">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)</p>

<h2 style="vertical-align:baseline;line-height:1.3;font-size:19px;font-family:'Trebuchet MS','Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;word-wrap:break-word;border:0px;padding:0px">

java.lang.Thread.run(Thread.java:722)</h2><p style="clear:both;vertical-align:baseline;line-height:18px;font-size:14px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;border:0px;padding:0px">

2</p><p style="clear:both;vertical-align:baseline;line-height:18px;font-size:14px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;border:0px;padding:0px">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)</p>

<hr style="border:0px;color:rgb(221,221,221);background-color:rgb(221,221,221);min-height:1px;margin-bottom:20px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;font-size:14px;line-height:18px">
<p style="clear:both;vertical-align:baseline;line-height:18px;font-size:14px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;border:0px;padding:0px">
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.</p><p style="clear:both;vertical-align:baseline;line-height:18px;font-size:14px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;border:0px;padding:0px">

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.</p><p style="clear:both;vertical-align:baseline;line-height:18px;font-size:14px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;border:0px;padding:0px">

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.</p><p style="clear:both;vertical-align:baseline;line-height:18px;font-size:14px;font-family:Arial,'Liberation Sans','DejaVu Sans',sans-serif;margin:0px 0px 1em;border:0px;padding:0px">

how can I fix this issue? what are my options? Im new here but im ready to read a lot =) thnx everyone</p><br><br><div><div style="font-size:13px;font-family:Verdana,Arial,Helvetica,sans-serif">

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<td><strong><span style="color:rgb(255,0,0)">  |</span> Paulo A. Picota C.          </strong></td>
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<td><strong><span style="color:rgb(255,0,0)">  | </span></strong><span style="color:rgb(255,0,0)"><span style="color:rgb(0,0,0)">Ing. Sis. Computación     </span></span></td>
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<td><strong><span style="color:rgb(255,0,0)">  |</span> </strong>CCNA CNCO11876553  </td>
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<td><strong><span style="color:rgb(255,0,0)">  |</span></strong> Celular: 6426 9482<br>
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