Pellet size Error

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Pellet size Error

walaa
Hello, 
i'm trying to d reasoning with Pellet 2.0.0 in Protege 5 on a 18875 KB file. I got this error message: "... Uncaught Exception in thread 'AWT-EventQueue-0' java.lang.OutOfMemoryError: Java heap space... "

What is the max size of file supported by Pellet in Protege??

best regards, 
Walaa

_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
Reply | Threaded
Open this post in threaded view
|

Re: Pellet size Error

Lorenz Buehmann
File size doesn't matter at all but more the number of OWL axioms and it's complexity. You could try to increase the heap space and use a newer Pellet version.

Hello, 
i'm trying to d reasoning with Pellet 2.0.0 in Protege 5 on a 18875 KB file. I got this error message: "... Uncaught Exception in thread 'AWT-EventQueue-0' java.lang.OutOfMemoryError: Java heap space... "

What is the max size of file supported by Pellet in Protege??

best regards, 
Walaa


_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
Reply | Threaded
Open this post in threaded view
|

Re: Pellet size Error

Rafael Gonçalves
In reply to this post by walaa
Hi Walaa,

It looks like Protege hasn't been allocated enough memory to reason over the ontology. What distribution of Protege are you using (platform-independent or operating system-specific, and which OS)?

Cheers,
Rafael

On Jun 23, 2016, at 03:43, Walaa Karakich <[hidden email]> wrote:

Hello, 
i'm trying to d reasoning with Pellet 2.0.0 in Protege 5 on a 18875 KB file. I got this error message: "... Uncaught Exception in thread 'AWT-EventQueue-0' java.lang.OutOfMemoryError: Java heap space... "

What is the max size of file supported by Pellet in Protege??

best regards, 
Walaa
_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev

_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
Reply | Threaded
Open this post in threaded view
|

Re: Pellet size Error

walaa
In reply to this post by walaa


Hi , 

thank you all. I just want to give you a feedback about the error. 
Concerning Pellet: i'm using the version of Pellet plugin for Protégé what i get by checking plugins in Protégé. I tried installing Pellet 2.3 manuell but it didn't work.  
Concerning the Ontology: 
i' m unfortunately not allowed to transfer the information inside. There are coins and other objects from the nomisma.org project that are not yet published.Here i 'm sending you  a version with the public coins but this version differ at size and complexity from the other one. The objective of my work is to test data quality and do some data validation with Protégé and SWRL on Linked Open Data and simultaneously to experience how far can we go with data validation on the basis of using Protégé and swrltab.  
I tried some other reasoners but i didn't got any inferred information from my swrl rules.
The problem of over size seems to be in association with the owl "AllDifferent" because when i set all individuals to be different individuals i got the " GC Overhead Limit exceeded" - message in my log file even if i use the smaller public version(attatchement). Setting all individuals to be different with over 8000 Object considerably increased the complexity and number of axioms in the ontology and led to the error.  In my case i don't really need all individuals to be different but just some and this solve now my problem with the smaller file.
It would be useful and practical if the selection options in 
Protégé can be improved: for example bei setting Different Individuals specially when you have to choose 50 over 8000 individuals to be different. 

Best regards, 
Walaa



2016-06-25 21:03 GMT+02:00 <[hidden email]>:
Send protege-dev mailing list submissions to
        [hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
        https://mailman.stanford.edu/mailman/listinfo/protege-dev
or, via email, send a message with subject or body 'help' to
        [hidden email]

You can reach the person managing the list at
        [hidden email]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of protege-dev digest..."


Today's Topics:

   1. ProtegeCache directory (Nico Matentzoglu)
   2. Re: ProtegeCache directory (Rafael Gon?alves)
   3. Re: Pellet size Error (Lorenz B., Rafael Goncalves )
      (Rafael Gon?alves)
   4. Re: Pellet size Error (Lorenz B., Rafael Goncalves ) (Simon Spero)


----------------------------------------------------------------------

Message: 1
Date: Fri, 24 Jun 2016 19:40:20 +0000
From: Nico Matentzoglu <[hidden email]>
To: "[hidden email]" <[hidden email]>
Subject: [protege-dev] ProtegeCache directory
Message-ID:
        <CAMWhPOcw_u-Abo=[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hey all,

I was recently hitting my disk space limit, and I just found out why: I had
almost 2000 directories of the
form ProtegeCache-47202886-ff28-443d-a212-1b5c843d439e in my local temp
directory. Those took up more than 65 GB in space.. I dont know whether
they were generated by my IDE (protege plugin dev) or by Protege itself. Do
you know why they were not ever cleaned up?

All best!
Nico
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/protege-dev/attachments/20160624/dede8b21/attachment-0001.html>

------------------------------

Message: 2
Date: Fri, 24 Jun 2016 13:15:30 -0700
From: Rafael Gon?alves <[hidden email]>
To: Developer support for WebProtege and Protege Desktop
        <[hidden email]>
Subject: Re: [protege-dev] ProtegeCache directory
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi Nico,

These folders are indeed generated by Protege. I filed an issue for this: https://github.com/protegeproject/protege/issues/461 <https://github.com/protegeproject/protege/issues/461>.

Cheers,
Rafael

> On Jun 24, 2016, at 12:40, Nico Matentzoglu <[hidden email]> wrote:
>
> Hey all,
>
> I was recently hitting my disk space limit, and I just found out why: I had almost 2000 directories of the form ProtegeCache-47202886-ff28-443d-a212-1b5c843d439e in my local temp directory. Those took up more than 65 GB in space.. I dont know whether they were generated by my IDE (protege plugin dev) or by Protege itself. Do you know why they were not ever cleaned up?
>
> All best!
> Nico
> _______________________________________________
> protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/protege-dev/attachments/20160624/1cfde3eb/attachment-0001.html>

------------------------------

Message: 3
Date: Fri, 24 Jun 2016 13:30:53 -0700
From: Rafael Gon?alves <[hidden email]>
To: Developer support for WebProtege and Protege Desktop
        <[hidden email]>
Subject: Re: [protege-dev] Pellet size Error (Lorenz B., Rafael
        Goncalves )
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Have you tried using the latest version of Pellet (2.3, I believe)? Also, did you try other reasoners? Could you send us the ontology file so we can test it out?

Cheers,
Rafael

> On Jun 24, 2016, at 05:23, Walaa Karakich <[hidden email]> wrote:
>
> Thanks for answering.
> I increased the heap size to 6 GB in the run.bat file but Pellet still not working . I'm using protege 5 for windows on a 64 bit system.
> Message in Log file and Nb of Axioms ... as screenshot.
> Turning-off the GC Overhead Limit with -XX:-UseGCOverheadLimit in run.bat file also didn't help.
> Auto update for Pellet doesn't work likewise manual.
>
> Best regards,
> Walaa
> <pellet_after_increasing_heap.PNG><axioms.PNG>_______________________________________________
> protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/protege-dev/attachments/20160624/cf92f547/attachment-0001.html>

------------------------------

Message: 4
Date: Fri, 24 Jun 2016 16:50:03 -0400
From: Simon Spero <[hidden email]>
To: Developer support for WebProtege and Protege Desktop
        <[hidden email]>
Subject: Re: [protege-dev] Pellet size Error (Lorenz B., Rafael
        Goncalves )
Message-ID:
        <CADE8KM6V6ttdeHG4OaDf5BRnzn=[hidden email]>
Content-Type: text/plain; charset="utf-8"

I'd also suggest starting the virtual machine with "-XX:+PrintGC", which
prints basic GC activity to the console. That will give you a sign of when
memory is starting to disappear.

I  would also add the "-XX:HeapDumpOnOutOfMemoryError" flag, which will
generate a heap dump when you run out of memory, which will show where the
memory is being used.
This dump can be analyzed using tools like the Eclipse foundation's MAT.
On Jun 24, 2016 4:30 PM, "Rafael Gon?alves" <[hidden email]>
wrote:

> Have you tried using the latest version of Pellet (2.3, I believe)? Also,
> did you try other reasoners? Could you send us the ontology file so we can
> test it out?
>
> Cheers,
> Rafael
>
> On Jun 24, 2016, at 05:23, Walaa Karakich <[hidden email]>
> wrote:
>
> Thanks for answering.
> I increased the heap size to 6 GB in the run.bat file but Pellet still not
> working . I'm using protege 5 for windows on a 64 bit system.
> Message in Log file and Nb of Axioms ... as screenshot.
> Turning-off the GC Overhead Limit with -XX:-UseGCOverheadLimit in run.bat
> file also didn't help.
> Auto update for Pellet doesn't work likewise manual.
>
> Best regards,
> Walaa
> <pellet_after_increasing_heap.PNG><axioms.PNG>
> _______________________________________________
> protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
>
>
>
> _______________________________________________
> protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/protege-dev/attachments/20160624/ef072c40/attachment-0001.html>

------------------------------

Subject: Digest Footer

_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev


------------------------------

End of protege-dev Digest, Vol 29, Issue 18
*******************************************



_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev

ontology_with_public_coins_and_typeSeriesItem.owl (2M) Download Attachment