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[protege-discussion] Memory problem?

Jonathan Carter jonathan.carter at
Wed Feb 25 13:42:53 PST 2009

Hi Karin,

Are you using the Mac look-and-feel or the default one? I've been  
using the Mac look-and-feel for some time with no issues. I've not yet  
had to up the memory and I've been using ontologies with 1000's of  
Does it behave normally with other Protege projects - e.g. the  
examples that are supplied with Protege?

I've seen Protege allocate memory like this when running as the  
Protege Server in a multi-user set up on Windows but has been stable.

Are you seeing Java out of memory exceptions in the Protege logs or  
the Mac console? If not, given the size of your ontology, I would  
suggest returning the -Xmx setting back to something smaller, e.g. - 
Xmx512m, so that Protege isn't taking all your memory.

Hope this helps


Jonathan Carter - Head of Technical Architecture
Enterprise Architecture Solutions Ltd

Assess your EA maturity at:

On 25 Feb 2009, at 18:30, Karin Verspoor wrote:

> 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
> -- 
> 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
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at
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