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[protege-discussion] Mac Leopard / Prompt problem was Re: Memory problem?
Karin.Verspoor at ucdenver.edu
Wed Feb 25 15:28:28 PST 2009
We have tracked down this problem. I'm posting again for the archives
in case anyone else runs across this.
Turns out there is a problem with the Mac look and feel on Leopard,
which gets triggered if your Protege project uses the Prompt plug-in.
This is manifested with the following exception:
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at edu.stanford.smi.protege.ui.ProjectMenuBar.paint(Unknown Source)
For now, for us, the solution is a workaround: remove the Prompt tab
from the project. If we need to use Prompt, we'll run Protege on
On Feb 25, 2009, at 2:47 PM, Karin Verspoor wrote:
> 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.
> 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
>> 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 ucdenver.edu / tel: (720) 279-4875 / campus: 4-3758
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