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[protege-discussion] Memory problem?

Karin Verspoor Karin.Verspoor at ucdenver.edu
Wed Feb 25 13:47:11 PST 2009


Sorry to reply to myself, but I have some additional information which  
is pertinent.

I loaded a different .pprj file and noted the same greedy growth in  
virtual memory but in the case of that ontology did not see the  
strange GUI behavior.

So it seems like
(a) Protege may just standardly grab the maximum amount of memory it  
is offered, whether or not it needs it, and
(b) the strange GUI behavior I'm seeing has nothing to do with memory.

All three of the people in my group working on this ontology file are  
experiencing the same issue, and it is persistent. We are all working  
with Protege 3.3.1 build 430 on Macs.

My current guess is there may be a problem with our .pprj, .pins,  
or .pont files.  Is there a way to check the validity of these files?   
As I said, the project seems to load fine.  I have manually inspected  
them and can't find any unusual artifacts in them (at least not just  
glancing through them).  We work with them via a version control  
system (CVS) which shouldn't introduce any problems but is it possible  
that if somehow the 3 files got out of sync with each other that this  
would cause the problem?

I'm at a loss for how to proceed and would appreciate any input, or  
hearing from others who have witnessed this problem.

Karin

On Feb 25, 2009, at 11:30 AM, 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 ucdenver.edu / tel: (720) 279-4875 / campus: 4-3758





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