[Pellet-users] Pellet stalling / OutOfMemory exceptions during classification

[Robert Davey]

In addition, we have another ontology that we are trying to classify,
and in this instance we have no problems with it loading (i.e. it loads
and classifies in a sensible time period).  However, when one wants do
any kind of operations involving individuals (e.g.
reasoner.getTypes(individual), or reasoner.getIndividuals()), it results
in an OutOfMemoryException after a good 30mins of processing.

Has there been any thoughts on why this may occur, or indeed to the
problem below? I can post up the ontology I mentioned if necessary.

Cheers

Rob

On Fri, 2007-11-16 at 09:17 +0000, Tony Burdett wrote:
> Hi guys,
> 
> I have a tool to generate ontologies that reflect explicit semantics of
> databases, and I'm having problems reasoning over the larger stuff.
> This particular example was generated from the Ensembl Human database.
> 
> Once I get over a certain size, I'm getting either OutOfMemory
> exceptions or else it's stalling altogether. I've tried reasoning over
> my ontology using both the java api and using the pellet command line
> jar, and I've tried it with both pellet 1.5 and 1.5.1 with no apparent
> difference. When i try and classify it from the command line using:
> 
> pellet -if homo_sapiens_core_47_36i.owl -c TREE -s off > output.txt
> 
> I set pellet.properties USE_CLASSIFICATION_MONITOR = swing and increased
> the -Xmx option to 1g, and the little progress bar rips straight up to
> around 60-70% and then completely stalls, before throwing an
> OutOfMemoryException. Any feedback on whats going on here would be
> really welcome. I've attached the ontology I'm using for reference.
> 
> Thanks,
> 
> Tony Burdett.
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-- 
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Dr. Rob Davey
NCYC / Institute of Food Research
Computational Biology / John Innes Centre
Norwich Research Park
Norwich, Norfolk, NR4 7HU

http://www.comparagrid.org/
http://cbr.jic.ac.uk/dicks/
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