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Old 02-12-2015, 09:39 AM   #13
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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Quote:
Originally Posted by thh32 View Post
We are trying to provide functional annotation to an assembly we have recently created. We are using 1 core per blast job as to allow as many as possible to get onto the server at once.
As Rick mentioned above that is probably not good since each of those jobs is trying to read the 30G database simultaneously on the same node.

Try using all cores on a physical server for one job with multiple threads (depending on the scheduler you should be able to ask it to run those threads on one physical machine) and see if that speeds things up. Logically it should, though I can't predict the drop in number from 30h per job (since you would still need to chunk through an equivalent number of jobs sequentially).

If you have access to a server with enough RAM you could try making a RAMdisk, cache the database there and do without disk access for index access part. Worth a try.
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