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[protege-owl] Protege-owl] Ask for Technical Architecture of Protege server in your organisation and ways of solution

Brice Sommacal brice.sommacal at gmail.com
Wed Jul 28 01:25:54 PDT 2010


Hi Tania,

We are using Protege 3.4.4.
I'm going to send you the logs privately.

In the meantime, we made a script to re-boot Protege server when MySQL
timeout is reach.

Thanks,


Brice


2010/7/28 Tania Tudorache <tudorache at stanford.edu>

>  Hi Brice,
>
> Before answering each individual question, can you please tell us which
> version of Protege you are using?
>
> You should use Protege 3.4.4 or later (patch release is coming out soon).
> There was a problem in previous release with the DB connections, but in
> recent releases, Protege uses a connection pool for the database. If you
> send us a stack dump of your running server, we can see if it looks fine.
>
> I think you should see a connection for each project and for each import.
> If a project is performing a transaction, you will see more connections
> showing up, but they should also go away when the transaction is done. Tim
> can correct me, if I am wrong.
>
> Cheers,
> Tania
>
>
>
> On 07/27/2010 08:26 AM, Brice Sommacal wrote:
>
> Hello,
>
>  We are facing few weird things on our Protege-Server installation.
>
>  At the beginning, we were using protege server file based. Following
> admin's recommendation, we migrated to a mysql database.
>
>  (it's runnning well - no scalability problems)
>
>  At the moment, we set up the server on a virtual machine with 3Go of RAM
> et 2Go of swap.
> We are using about 20 Protégé Projects which are readable from a mysql
> database (protege) with the same user account.
>
>  We already put up the max_connection value of mysql connection to 200.
> (the default value was 100- it's thrown an error)
> I don't really understand why there is so much connection to the database.
> The most part of our ontologies import other ones.
>      > Do you think it may be because of that?
>
>  From the following command, I trace the access to mysql database: mysql
> -u XX -pXX protege -e "show processlist"
> In a day trime, we have about 170 conections working. But, when I get back
> to work in the morning, all the connections are gone!
> It seems that it's due to the timeout variable (eg.
> http://dev.mysql.com/doc/refman/5.0/en/server-system-variables.html#sysvar_wait_timeout
> )
>     > How are you handling this behavior in your organization?
>
>  I'm afraid that if we add new projects, our server will crash.
>
>       > what kind of machine do you use at Stanford? or other companies?
>  and how are defined the parameters?
>  (I'm expecting some technical details)
>
>
>  We think about several way of solution:
>      - Take time to modify code between Protege, MySql and repositories.
> (My preceding Email details that the changes are not propagated when
> modifying an imported ontology)
>
>       - Analyse how to use a triple store backend (Allegrograph) instead
> of a mysql database. (from a preceding post, I understood that it could take
> lots time to make this works)
>
>       - Analyse if a real server should be use instead of a vritual
> machine.
>
>
>       > Did the community already think about the issues?
>
>
>  Thanks for all the tips you could share with me,
> Best regards,
>
>
>  Brice
>
>
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