[InterMine Dev] adding the GO source
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).
On 24/10/2011 17:46, JD Wong wrote:
> 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?
> dev mailing list
> dev at intermine.org
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