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[protege-discussion] Undelivered Mail Returned to Sender

Congmin min marlonmin at gmail.com
Fri Sep 8 11:22:38 PDT 2006


Hi, Tania:
   Thank you for your suggestions. Now I believe what i need to do is
increasing my RAM. This is my computer configuration.

  Intel(R) Pentium(R) 4 CPU 3.40GHz
  stepping        : 3
  cpu MHz         : 3391.627
--------------------------------------------------------------------
                   total       used       free     shared    buffers
cached
Mem:           996        340        655          0         15        181
-/+ buffers/cache:        143        853
Swap:         1898          0       1897

I need to increase my RAM (only 655 MB available currently), at least double
it. And then it should work.

Actually I ever tried to use Jena API to directly populate the Protege OWL
Database, it was also stuck somewhere.

anyway, thanks for your help and have a good weekend.

On 9/8/06, Tania Tudorache <tudorache at stanford.edu> wrote:
>
> My computer configuration is similar to Raj's (Intel Pentium M, 2.2GHz,
> 2GB RAM) . With 700MB of heap size I could load the 300.000 classes
> ontology in memory.
>
> Anyway, the idea is that at some point, you will reach the limit of the
> heap space that Java can allocate (I think it is 1.6 GB on Windows), so
> you won't be able to load into memory a huge ontology. That is why you
> have to use the OWL db backend.
>
> Of course, everything depends on the scenario that you have. If you
> start to develop a new ontology, and you know that it will be huge, then
> you should start with a project using the OWL db backend. In this case,
> you don't have any limitation on the size of the ontology.
>
> If you already have a big OWL ontology as a file and you want to import
> it into an OWL db, so that you can use it with the OWL db backend, there
> are some solutions:
> 1. If you don't have enough memory, you can ask somebody (with enough
> memory) to load the owl file in Protege and convert it into a db project
> (this is a one time job). And he/she can get you a db dump that you can
> then use.
> 2. Ideally, you could use a converter that takes an OWL file and
> converts it directly to an OWL db without loading it completely in
> memory. We are working on this, but I cannot give you an exact date when
> it will be released.
>
> Tania
>
>
> Mudunuri, Raj wrote:
>
> >Hi Congmin,
> >
> >I have 2G RAM, where I have allocated 1G of heap space for Protege... It
> took around 100 secs to load all the triples, then for around 50 secs it did
> nothing (looked dead) and then the UI came into normal stage... so, totally
> it took around 150 secs in my system to load your ontology with 300,000
> concepts... mine is an Intel Pentium D, with 2.8 GHz and 2 GB RAM...
> >
> >Cheers,
> >Raj
> >
> >
> >
> >-----Ursprüngliche Nachricht-----
> >Von: protege-discussion-bounces at lists.stanford.edu [mailto:
> protege-discussion-bounces at lists.stanford.edu] Im Auftrag von Congmin min
> >Gesendet: Freitag, 8. September 2006 04:43
> >An: tudorache at stanford.edu; User support for Core Protege and the
> Protege-Frames editor
> >Betreff: Re: [protege-discussion] Undelivered Mail Returned to Sender
> >
> >Tania:
> >
> >   Could you let me know how large is your CPU and physical MEMORY? I
> >increased the heap size to 1GB, but had the same problem. Probably I
> should
> >install more CPU and RAM. When I try loading, the backround message
> showed
> >that everything has been loaded into memory compeletely, but it just
> didn't
> >come out on the Protege UI. And then looks dead.
> >
> >Thanks,
> >congmin
> >
> >On 9/7/06, Tania Tudorache <tudorache at stanford.edu> wrote:
> >
> >
> >>Congmin,
> >>
> >>I did receive your email. Indeed this is a problem, that you have to
> >>first load the OWL file in memory and then to export it to an OWL
> >>database. We are looking at ways on how to do a streaming writing to the
> >>database directly.
> >>
> >>Until then, you need to increase the heap size, if you need to
> >>accomodate very large ontologies.
> >>
> >>Tania
> >>
> >>Congmin min wrote:
> >>
> >>
> >>
> >>>Hi, Tania:
> >>>
> >>>      I am attaching three files for your testing:
> >>>      The .tar.gz contains three owl files I generated. Both are very
> >>>simple owl files, only containing one class and a number of instances
> >>>of this class. This is just for testing purpose. And three files are
> >>>quite small: about 8 MB, 5 MB and 3 MB.
> >>>
> >>>     test.200000.owl: one 'Concept' class and 120000 instances of it
> >>>      test.120000.owl: one 'Concept' class and 120000 instances of it
> >>>      test.50000.owl: one 'Concept' class and 50000 instances of it
> >>>
> >>>   On my computer I can load test.50000.owl within 2 minutes,
> >>>test.120000 within 5 minutes, but can't load test.200000.owl (I waited
> >>>for 30 minutes). My computer has about 1GB memory.
> >>>
> >>>   If your computer is more powerful than mine, you can use the little
> >>>test.cc to generate an ontology with more than 200000 instances of a
> >>>class, (you only need to pass a 'number'  you want at the command line
> >>>when executing 'a.out' ) and then test agin.
> >>>
> >>>   If I am not doing something wrong, it looks like Protege doen't
> >>>allow a class to have a certain number of instances; otherwise, it
> >>>would have difficluty in loading the file. This is true to database
> >>>option.
> >>>
> >>> If you received this email, please kindly let me know.
> >>>Thank you
> >>>
> >>>
> >>>
> >>>
> >>>On 9/7/06, *Mail Delivery System* < MAILER-DAEMON at lists.stanford.edu
> >>><mailto:MAILER-DAEMON at lists.stanford.edu>> wrote:
> >>>
> >>>    This is the Postfix program at host mailman.stanford.edu
> >>>    <http://mailman.stanford.edu>.
> >>>
> >>>    I'm sorry to have to inform you that your message could not
> >>>    be delivered to one or more recipients. It's attached below.
> >>>
> >>>    For further assistance, please send mail to <postmaster>
> >>>
> >>>    If you do so, please include this problem report. You can
> >>>    delete your own text from the attached returned message.
> >>>
> >>>                            The Postfix program
> >>>
> >>>    <protege-discussion at mailman.stanford.edu
> >>>    <mailto:protege-discussion at mailman.stanford.edu>>: mail forwarding
> >>>    loop for
> >>>         protege-discussion at mailman.stanford.edu
> >>>    <mailto:protege-discussion at mailman.stanford.edu>
> >>>
> >>>
> >>>    Final-Recipient: rfc822; protege-discussion at mailman.stanford.edu
> >>>    <mailto:protege-discussion at mailman.stanford.edu>
> >>>    Action: failed
> >>>    Status: 5.0.0
> >>>    Diagnostic-Code: X-Postfix; mail forwarding loop for
> >>>        protege-discussion at mailman.stanford.edu
> >>>    <mailto:protege-discussion at mailman.stanford.edu>
> >>>
> >>>
> >>>
> >>>    ---------- Forwarded message ----------
> >>>    From: "Congmin min" < marlonmin at gmail.com
> >>>    <mailto:marlonmin at gmail.com>>
> >>>    To: protege-discussion at lists.Stanford.EDU
> >>>    <mailto:protege-discussion at lists.Stanford.EDU>
> >>>    Date: Wed, 6 Sep 2006 14:54:26 -0500
> >>>    Subject: [protege-discussion] Number of Instances of one class can
> >>>    not be large??
> >>>    I am doing some experiments and seems to find another BUG. To
> >>>    officially
> >>>    report that, I want to ask:
> >>>
> >>>    Is there any restrictions on the number of instances of one class?
> >>>
> >>>
> >>The
> >>
> >>
> >>>    problem I have now is that once the number of instances of one
> >>>    class exceeds
> >>>    a certain number, Protege failed to load the OWL File, although
> >>>    the file is
> >>>    pretty small, just several MBs. It is not a memory issue.
> >>>
> >>>    Thanks for any info.
> >>>    _______________________________________________
> >>>    protege-discussion mailing list
> >>>    protege-discussion at lists.stanford.edu
> >>>    <mailto:protege-discussion at lists.stanford.edu>
> >>>    https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> >>>    <https://mailman.stanford.edu/mailman/listinfo/protege-discussion>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>_______________________________________________
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> >>
> >>
> >>
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