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[protege-discussion] Mac Leopard / Prompt problem was Re: Memory problem?

Karin Verspoor Karin.Verspoor at
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 apple.laf.CUIAquaMenuPainter.paintMenuBarBackground
	at apple.laf.CUIAquaMenu.paintBackground(
	at apple.laf.CUIAquaMenuPainter.paintMenuItem
	at apple.laf.CUIAquaMenu.paintMenuItem(
	at javax.swing.plaf.basic.BasicMenuItemUI.paint
	at javax.swing.plaf.basic.BasicMenuItemUI.update
	at javax.swing.JComponent.paintComponent(
	at javax.swing.JComponent.paint(
	at javax.swing.JComponent.paintChildren(
	at javax.swing.JComponent.paint(
	at edu.stanford.smi.protege.ui.ProjectMenuBar.paint(Unknown Source)
	at javax.swing.JComponent._paintImmediately(
	at javax.swing.JComponent.paintImmediately(
	at javax.swing.RepaintManager.paintDirtyRegions
	at javax.swing.SystemEventQueueUtilities$
	at java.awt.event.InvocationEvent.dispatch(
	at java.awt.EventQueue.dispatchEvent(
	at java.awt.EventDispatchThread.pumpOneEventForHierarchy
	at java.awt.EventDispatchThread.pumpEventsForHierarchy
	at java.awt.EventDispatchThread.pumpEvents
	at java.awt.EventDispatchThread.pumpEvents

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  
another OS.


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.
> 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 / tel: (720) 279-4875 / campus: 4-3758

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