[protege-owl] Memory leak?

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[protege-owl] Memory leak?

Mark Feblowitz
I noticed when I was configuring the new 3.2 release that, after a
few visits to the Owl... Preferences panel, Protege ran out of
memory. One of the things I was doing at the time was comparing the
multicolored icons against the default icons, so I switched them back
and forth a few times, exiting and re-entering the Preferences panel
a few times while looking at the icons. I did a few other things
involving the preferences panel. The Out of Memory error was a
surprise, since I did little other than loading an ontology file and
fiddling with the preferences.

Running Protege again, I did the same thing and watched the Windows
Task Manager to see the memory allocation shoot up from approx 36M to
well over 120M, just by opening the Preferences panel, changing the
icon presentation, and existing the panel.

Interestingly, I just did the same thing, with the same ontology. The
memory usage after the ontology load was 110M. I'm not sure how that
figure sank to 36M for the prior invocation. This time, switching the
icon presentation seemed to bump the memory usage by about 4M each
time the selection was switched, with no obvious reclamation afterward.

Does this sound normal?

BTW, the ontology file loaded is small and only contains abox
assertions, but it imports 17 other ontology files that contain, in
total, roughly 300 classes and 580 individuals. Not sure if this is a
factor in the memory consumption.


Mark

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Re: [protege-owl] Memory leak?

Tania Tudorache
Mark,

Thanks for the report. I did a quick profiling, and I did not see an
obvious memory leak. If you change the icons from default <->
multicolored, then the whole GUI and all tabs are reinitialized. This
means that one of the tabs might be responsible for this. In the
profiling, I could see that memory was allocated after exiting the OWL
Preferences panel, but it was also deallocated when I ran the garbage
collector. Anyway, from your tests, there are signs of a memory leak. We
will investigate this further.

It would be interesting to know what tabs you had activated when you did
this test.

Thanks,
Tania



Mark Feblowitz wrote:

> I noticed when I was configuring the new 3.2 release that, after a
> few visits to the Owl... Preferences panel, Protege ran out of
> memory. One of the things I was doing at the time was comparing the
> multicolored icons against the default icons, so I switched them back
> and forth a few times, exiting and re-entering the Preferences panel
> a few times while looking at the icons. I did a few other things
> involving the preferences panel. The Out of Memory error was a
> surprise, since I did little other than loading an ontology file and
> fiddling with the preferences.
>
> Running Protege again, I did the same thing and watched the Windows
> Task Manager to see the memory allocation shoot up from approx 36M to
> well over 120M, just by opening the Preferences panel, changing the
> icon presentation, and existing the panel.
>
> Interestingly, I just did the same thing, with the same ontology. The
> memory usage after the ontology load was 110M. I'm not sure how that
> figure sank to 36M for the prior invocation. This time, switching the
> icon presentation seemed to bump the memory usage by about 4M each
> time the selection was switched, with no obvious reclamation afterward.
>
> Does this sound normal?
>
> BTW, the ontology file loaded is small and only contains abox
> assertions, but it imports 17 other ontology files that contain, in
> total, roughly 300 classes and 580 individuals. Not sure if this is a
> factor in the memory consumption.
>
>
> Mark
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>
>  

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Re: [protege-owl] Memory leak?

Mark Feblowitz
Metadata, Owl Classes, Properties, Individuals, Forms, and Ontoviz.

Mark

At 06:05 PM 11/10/2006, Tania Tudorache wrote:

>Mark,
>
>Thanks for the report. I did a quick profiling, and I did not see an
>obvious memory leak. If you change the icons from default <->
>multicolored, then the whole GUI and all tabs are reinitialized. This
>means that one of the tabs might be responsible for this. In the
>profiling, I could see that memory was allocated after exiting the OWL
>Preferences panel, but it was also deallocated when I ran the garbage
>collector. Anyway, from your tests, there are signs of a memory leak. We
>will investigate this further.
>
>It would be interesting to know what tabs you had activated when you did
>this test.
>
>Thanks,
>Tania
>
>
>
>Mark Feblowitz wrote:
> > I noticed when I was configuring the new 3.2 release that, after a
> > few visits to the Owl... Preferences panel, Protege ran out of
> > memory. One of the things I was doing at the time was comparing the
> > multicolored icons against the default icons, so I switched them back
> > and forth a few times, exiting and re-entering the Preferences panel
> > a few times while looking at the icons. I did a few other things
> > involving the preferences panel. The Out of Memory error was a
> > surprise, since I did little other than loading an ontology file and
> > fiddling with the preferences.
> >
> > Running Protege again, I did the same thing and watched the Windows
> > Task Manager to see the memory allocation shoot up from approx 36M to
> > well over 120M, just by opening the Preferences panel, changing the
> > icon presentation, and existing the panel.
> >
> > Interestingly, I just did the same thing, with the same ontology. The
> > memory usage after the ontology load was 110M. I'm not sure how that
> > figure sank to 36M for the prior invocation. This time, switching the
> > icon presentation seemed to bump the memory usage by about 4M each
> > time the selection was switched, with no obvious reclamation afterward.
> >
> > Does this sound normal?
> >
> > BTW, the ontology file loaded is small and only contains abox
> > assertions, but it imports 17 other ontology files that contain, in
> > total, roughly 300 classes and 580 individuals. Not sure if this is a
> > factor in the memory consumption.
> >
> >
> > Mark
> >
> > _______________________________________________
> > protege-owl mailing list
> > [hidden email]
> > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> > Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
> >
> >
>
>_______________________________________________
>protege-owl mailing list
>[hidden email]
>https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
>Instructions for unsubscribing:
>http://protege.stanford.edu/doc/faq.html#01a.03

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Re: [protege-owl] Memory leak?

Mark Feblowitz
One other thought - with the 18 different ontologies loaded, there
are 18 different namespaces. If there is a problem with namespaces,
this may just be one more manifestation. I'll try this out for a
simple file and see whether the same problem occurs.

Mark


At 06:22 PM 11/10/2006, Mark Feblowitz wrote:

>Metadata, Owl Classes, Properties, Individuals, Forms, and Ontoviz.
>
>Mark
>
>At 06:05 PM 11/10/2006, Tania Tudorache wrote:
> >Mark,
> >
> >Thanks for the report. I did a quick profiling, and I did not see an
> >obvious memory leak. If you change the icons from default <->
> >multicolored, then the whole GUI and all tabs are reinitialized. This
> >means that one of the tabs might be responsible for this. In the
> >profiling, I could see that memory was allocated after exiting the OWL
> >Preferences panel, but it was also deallocated when I ran the garbage
> >collector. Anyway, from your tests, there are signs of a memory leak. We
> >will investigate this further.
> >
> >It would be interesting to know what tabs you had activated when you did
> >this test.
> >
> >Thanks,
> >Tania
> >
> >
> >
> >Mark Feblowitz wrote:
> > > I noticed when I was configuring the new 3.2 release that, after a
> > > few visits to the Owl... Preferences panel, Protege ran out of
> > > memory. One of the things I was doing at the time was comparing the
> > > multicolored icons against the default icons, so I switched them back
> > > and forth a few times, exiting and re-entering the Preferences panel
> > > a few times while looking at the icons. I did a few other things
> > > involving the preferences panel. The Out of Memory error was a
> > > surprise, since I did little other than loading an ontology file and
> > > fiddling with the preferences.
> > >
> > > Running Protege again, I did the same thing and watched the Windows
> > > Task Manager to see the memory allocation shoot up from approx 36M to
> > > well over 120M, just by opening the Preferences panel, changing the
> > > icon presentation, and existing the panel.
> > >
> > > Interestingly, I just did the same thing, with the same ontology. The
> > > memory usage after the ontology load was 110M. I'm not sure how that
> > > figure sank to 36M for the prior invocation. This time, switching the
> > > icon presentation seemed to bump the memory usage by about 4M each
> > > time the selection was switched, with no obvious reclamation afterward.
> > >
> > > Does this sound normal?
> > >
> > > BTW, the ontology file loaded is small and only contains abox
> > > assertions, but it imports 17 other ontology files that contain, in
> > > total, roughly 300 classes and 580 individuals. Not sure if this is a
> > > factor in the memory consumption.
> > >
> > >
> > > Mark
> > >
> > > _______________________________________________
> > > protege-owl mailing list
> > > [hidden email]
> > > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> > >
> > > Instructions for unsubscribing:
> > http://protege.stanford.edu/doc/faq.html#01a.03
> > >
> > >
> >
> >_______________________________________________
> >protege-owl mailing list
> >[hidden email]
> >https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> >Instructions for unsubscribing:
> >http://protege.stanford.edu/doc/faq.html#01a.03
>
>_______________________________________________
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>[hidden email]
>https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
>Instructions for unsubscribing:
>http://protege.stanford.edu/doc/faq.html#01a.03

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Re: [protege-owl] Memory leak?

Bert-14
Hi,

I just did a small test with an ontology I'm contructing.
It imports OWL-S and it contains only classes and restrictions.

On startup and loaded the OWL ontology  the java VM consumes according
to the MS task manager 76 MB.
When switching from the meta-data tab to the classes tab it consumes an
additional 3 MB.
Which I assume is because of a lazy loading process.
Now switching to another tab slightly increases the memory consumption.
Selecting back the classes tab, it consumes extra memory when starting
to browse the hiearchy.

So after 5 minutes of playing (doing no change) the memory consumption
increased to 82 MB.

It seems that the tabs are not releasing certain information. And that
is the reason, I believe,  my Protege session run out of memory  heap space
after a long editing session (I edit ontologies with a runnning version
of protege for days).

(my ontology consists about 110 classes and 80 properties according to
the metrics info)

best regards,

Bert




Mark Feblowitz wrote:

> One other thought - with the 18 different ontologies loaded, there
> are 18 different namespaces. If there is a problem with namespaces,
> this may just be one more manifestation. I'll try this out for a
> simple file and see whether the same problem occurs.
>
> Mark
>
>
> At 06:22 PM 11/10/2006, Mark Feblowitz wrote:
>  
>> Metadata, Owl Classes, Properties, Individuals, Forms, and Ontoviz.
>>
>> Mark
>>
>> At 06:05 PM 11/10/2006, Tania Tudorache wrote:
>>    
>>> Mark,
>>>
>>> Thanks for the report. I did a quick profiling, and I did not see an
>>> obvious memory leak. If you change the icons from default <->
>>> multicolored, then the whole GUI and all tabs are reinitialized. This
>>> means that one of the tabs might be responsible for this. In the
>>> profiling, I could see that memory was allocated after exiting the OWL
>>> Preferences panel, but it was also deallocated when I ran the garbage
>>> collector. Anyway, from your tests, there are signs of a memory leak. We
>>> will investigate this further.
>>>
>>> It would be interesting to know what tabs you had activated when you did
>>> this test.
>>>
>>> Thanks,
>>> Tania
>>>
>>>
>>>
>>> Mark Feblowitz wrote:
>>>      
>>>> I noticed when I was configuring the new 3.2 release that, after a
>>>> few visits to the Owl... Preferences panel, Protege ran out of
>>>> memory. One of the things I was doing at the time was comparing the
>>>> multicolored icons against the default icons, so I switched them back
>>>> and forth a few times, exiting and re-entering the Preferences panel
>>>> a few times while looking at the icons. I did a few other things
>>>> involving the preferences panel. The Out of Memory error was a
>>>> surprise, since I did little other than loading an ontology file and
>>>> fiddling with the preferences.
>>>>
>>>> Running Protege again, I did the same thing and watched the Windows
>>>> Task Manager to see the memory allocation shoot up from approx 36M to
>>>> well over 120M, just by opening the Preferences panel, changing the
>>>> icon presentation, and existing the panel.
>>>>
>>>> Interestingly, I just did the same thing, with the same ontology. The
>>>> memory usage after the ontology load was 110M. I'm not sure how that
>>>> figure sank to 36M for the prior invocation. This time, switching the
>>>> icon presentation seemed to bump the memory usage by about 4M each
>>>> time the selection was switched, with no obvious reclamation afterward.
>>>>
>>>> Does this sound normal?
>>>>
>>>> BTW, the ontology file loaded is small and only contains abox
>>>> assertions, but it imports 17 other ontology files that contain, in
>>>> total, roughly 300 classes and 580 individuals. Not sure if this is a
>>>> factor in the memory consumption.
>>>>
>>>>
>>>> Mark
>>>>
>>>> _______________________________________________
>>>> protege-owl mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>>
>>>> Instructions for unsubscribing:
>>>>        
>>> http://protege.stanford.edu/doc/faq.html#01a.03
>>>      
>>>>        
>>> _______________________________________________
>>> protege-owl mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>
>>> Instructions for unsubscribing:
>>> http://protege.stanford.edu/doc/faq.html#01a.03
>>>      
>> _______________________________________________
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>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
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>>    
>
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>  

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