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[protege-owl] Troubles saving 100k+ triples/10 mb+ project

David Kao dkao42 at
Mon Aug 25 14:05:24 PDT 2008

Hi Rune -

Generally speaking, if an operation such as 'save' or running a SWRL rule is
going to work, it will work in 10 minutes or less.  In my experience, if it
goes longer than that, it will almost always crash.  If you incrementally
add, eg individuals to find the limit with your available heap size, you
will notice that there is a step up when you exceed your memory limit in
operations times.

Regarding your problem, I have found that use of datatype properties limits
the number of individuals you can successfully manage quite a bit,
particularly strings.  This is most applicable for running SWRL operations,
but seems to apply to 'save' operations as well.  I believe there are some
garbage collection/heap management inefficiencies that come into play here,
as you can import hundreds of thousands of individuals via Datamaster, for
example, and manipulate them, but you will be unable to save.  It really
depends on the complexity of your ontology.  If you have relatively few
properties per individual, you will be able to use more individuals, etc.

I have tried running it on 64-bit JVMs via Windows but to no avail.  I am a
little unclear on how this works on the mac OS, as I have found Protege to
be quite buggy on Tiger/Leopard.  At any rate, larger JVMs don't help in
this situation, unfortunately.

Again, I would check your max heap size in the Protege.lax file (or the
startup options via the Protege tabs) to ~ 1.6 GB if your system can manage
it.  This is the only way that I have found to really increase the number of
individuals you can manage.


Rune Stilling wrote:
> Hi
> I changed the settings to "Experimental native writer" and this solved the
> problem. Now it takes 5 seconds to save the entire project.
> Using the old (none working) setting I got no errors in the log at all. On
> the mac I suspect something just makes the whole save process extremely
> slow. Maybe it will actually finish after a couple of hours. I can't tell.
> On the PC I couldn't find any errors either. The thing just chrashed.
> In the end I guess this is Jenas and not Protégés fault if I understand
> you right?
> Thanks for the help
> \Rune

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