[InterMine Dev] adding the GO source

Richard Smith richard at flymine.org
Mon Oct 24 17:59:20 BST 2011


The GO source uses a library from OBO-Edit to calculate transitive
closure on the ontology (following relationships through the tree).

This is quite memory intensive so it may be that you need to allocate
some more RAM.  I think for us it takes ten minutes or less.

If you have haven't already, you can set an ANT_OPTS environment
variable to control how much memory is allocated to the Java process.

See the Java section here: http://intermine.org/wiki/Prerequisites

I would say you want -Xmx2048m as a minimum on a dev machine, much
more if your running large builds of a production database.  Our
newest servers have 96GB RAM so we set the Java memory to around
32GB (it doesn't need that much but helps performance).

Cheers,
Richard.



On 24/10/2011 17:46, JD Wong wrote:
> Hi,
>
> When I run project_build.pl <http://project_build.pl>, loading my
> 500,000 genes only takes 4 minutes, but loading the GO source (which
> references the most recent GO OBO release) takes 43 minutes
> consistently.  These sources are the first two, and are loaded in this
> order.  Is this wait typical?
>
> Thanks,
> -JD
>
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev




More information about the dev mailing list