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big databases

Keith Bradnam krb at sanger.ac.uk
Mon Oct 14 02:47:06 EST 2002

> I'm interested in trading war stories and tips about how to deal with
> big ACEDB databases.  GrainGenes recently got big and we're feeling like
> we're bumping our head.  database/block*.wrm is about 2.5 GB.  Mainly
> due to 500K Sequence records.
> Today I added a small new .ace file and ran into a Unix "too many open files"
> error, where the default limit is 64.  I increased the limit and loaded the
> file, no problem.  But then I wondered if increasing the size of the
> block*.wrm files wasn't a better solution.  
> Fifty files are defined in the distribution (4_9i) wspec, 50000 bytes each
> (except the first two).  So I changed them to 100000 and reinitialized.
> The result to report is that the time for reloading the database improved
> from 7.5 hr to 4.25.  (On a Sun Ultra10, 300MHz, 1 GB RAM, ca. 450 MB memory
> used by the ACEDB process during loading.)

Any word from the acedb guys as to whether they fully endorse
this??? I.e. would there be any unforseen side effects (slower access
times maybe?).

I'll try to test this with our large database at some time and will report
back any speed gains in loading time.


~  Keith Bradnam - WormBase group: http://www.wormbase.org/
~  The Wellcome Trust Sanger Institute,
~  Hinxton, Cambridge, CB10 1SA, UK.  Tel: 01223 494922

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