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[protege-owl] Stack Overflow

Timothy Redmond tredmond at stanford.edu
Thu Jan 24 14:45:02 PST 2008


On Jan 24, 2008, at 5:40 AM, Kormann, Joseph wrote:

> No information from the group? I suspect it's the start-of-semester
> ramp-up lag.

Sorry to be somewhat out of touch.  The entire group is working  
overtime at the moment and it is very difficult to cover all of the  
bases.  Tania is working on a grant proposal (deadline in a few days),  
I am working on the parser-database inclusion-namespace branch (due at  
the end of February) and Jennifer is working on the web client.  All  
of these have a very short fuse.

So the upshot is that I apologize for being somewhat absent lately and  
hope that things are going ok.

> Here's related question: I don't get the stack overflow using the
> "RDF/XML" language type so I'm looking to use that for the problem  
> code.
> Is there a read or write method where it discovers the correct  
> language
> type, "RDF/XML" or "RDF/XML-ABBREV"? I want to have the piece of
> software that was throwing the stack be able to send it's OWL to  
> another
> program to interpret and do analysis.

I got the following from a conversation with Tania just a while ago.

The stack overflow turns out to be a difficult exception.  Tania  
studied it and didn't make too much progress.  It is happening in the  
Jena code but a priori this does not necessarily mean that it is a  
Jena bug.  However, some people have reported the same problem on the  
Jena forums.  The only answer given there was to try again with a  
larger stack size (-Xss not -Xmx) but it wasn't verified in our case.   
Tania thinks that perhaps the problem is that there is a very  
recursive procedure that would terminate but which is actually using  
up all the stack.  This is not usually the case with out of stack  
space exceptions but it may be the case here.

-Timothy



>
>
> Thanks.
>
>> -----Original Message-----
>> From: protege-owl-bounces at mailman.stanford.edu [mailto:protege-owl-
>> bounces at mailman.stanford.edu] On Behalf Of Kormann, Joseph
>> Sent: Tuesday, January 22, 2008 10:02 AM
>> To: User support for the Protege-OWL editor
>> Subject: Re: [protege-owl] Stack Overflow
>>
>> Follow-up. This only appears to occur when using the "RDF/XML-ABBREV"
>> language-type.
>>
>>> -----Original Message-----
>>> From: protege-owl-bounces at mailman.stanford.edu [mailto:protege-owl-
>>> bounces at mailman.stanford.edu] On Behalf Of Kormann, Joseph
>>> Sent: Tuesday, January 22, 2008 7:57 AM
>>> To: User support for the Protege-OWL editor
>>> Subject: [protege-owl] Stack Overflow
>>>
>>> Couldn't find it in the archives, so either I'm encountering a new
>> error
>>> or doing something wrong.
>>>
>>> I'm trying to save an OWL Model to a FileOutputStream. When the file
>>> gets to approx 22MB, I receive a java.lang.StackOverflowError.
>>>
>>> We're starting to fiddle with the Java VM Stack variables, however
> if
>> we
>>> don't have to, that would be preferred.
>>>
>>> Any suggestions?
>>>
>>> Code snippet:
>>> FileOutputStream os = null;
>>>        try {
>>>            os = new FileOutputStream("c:/outPut.owl");
>>>
>>>            owlModel.setWriterSettings(new
>>> ProtegeWriterSettings(owlModel));
>>>
>>>            owlModel.getOntModel().write(os, "RDF/XML-ABBREV");
>>>        } catch (Throwable th) {
>>>            System.out.println("Caught throwable exception");
>>>            System.out.println(th.getMessage());
>>>            th.printStackTrace();
>>>        }
>>>
>>> Exception:
>>> ava.lang.StackOverflowError
>>>        at java.util.regex.Pattern.access$000(Pattern.java:595)
>>>        at java.util.regex.Pattern$All.match(Pattern.java:4076)
>>>        at java.util.regex.Pattern$Curly.match0(Pattern.java:4218)
>>>        at java.util.regex.Pattern$Curly.match(Pattern.java:4202)
>>>        at
> java.util.regex.Pattern$GroupHead.match(Pattern.java:4575)
>>>        at java.util.regex.Pattern$Single.match(Pattern.java:3314)
>>>        at
> java.util.regex.Pattern$GroupHead.match(Pattern.java:4575)
>>>        at java.util.regex.Pattern$Branch.match(Pattern.java:4535)
>>> 	....
>>>
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