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[protege-discussion] Memory problem?

Karin Verspoor Karin.Verspoor at
Wed Feb 25 10:30:30 PST 2009

Protege version: 3.3.1
Platform: Mac OSX

Several of my colleagues and I are experiencing a problem where if we  
load a particular ontology that we are working on, the ontology loads  
fine (no errors) but the Protege GUI begins to behave oddly -- the  
menus disappear/reappear as we mouse over them, we can't access  
particular menu items.  I went in to the properties and upped the Java  
VM parameters to -Xmx2000M and if I watch top as I start up Protege I  
see that Protege grows very rapidly to fill up the full 2GB in virtual  
memory.  If I set that number higher, it clearly tries to take more  
memory but is shut down by the OS (I only have 2GB of RAM on this  
machine, so this makes sense) and crashes.

This ontology is very small (< 50 concepts) and I can't imagine for  
the life of me why it would need so much memory.  So I think there  
must be some sort of memory leak or perhaps a circular reference  
(which I can't see).  Has anyone experienced this?  Any advice or  
something I can look for?


Karin Verspoor, PhD
Research Assistant Professor
Center for Computational Pharmacology, University of Colorado Denver
PO Box 6511, MS 8303, Aurora, CO 80045 USA
karin.verspoor at / tel: (720) 279-4875 / campus: 4-3758

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