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Question: Galaxy and GPU use
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gravatar for elaine.youngman
3.9 years ago by
elaine.youngman • 0
United States
elaine.youngman • 0 wrote:

I have been having some conversations with IT folks about server versus cluster installation of a local galaxy instance and the subject of GPU computing came up. I see a few of the aligners listed in the catalog of GPU-compliant programs, but not Galaxy as a whole. Can anyone give me an idea of whether Galaxy currently does or plans to incorporate GPU use? This is all very out of my knowledge depth - I routinely use Galaxy but know nothing about installation. (A search of this forum turned up discussions from 2011-2012, but I wondered about new developments on this front)

 
galaxy gpu processing • 706 views
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modified 3.9 years ago • written 3.9 years ago by elaine.youngman • 0
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gravatar for Bjoern Gruening
3.9 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

Galaxy is a framework that hides all the complexity of your cluster, but it is totally capable of using your entire cluster, also GPU nodes. It is just a matter of the correct configuration and the correct tools.

If you have further questions please don't hesitate to ask here!

Bjoern
ADD COMMENT • link written 3.9 years ago by Bjoern Gruening ♦ 5.1k
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gravatar for elaine.youngman
3.9 years ago by
elaine.youngman • 0
United States
elaine.youngman • 0 wrote:

Thanks Bjoern! That's good to know. This is probably not an easy question, but do you have any idea how many of the tools that can be included in a Galaxy install are currently programmed to use GPUs? It looks in the Nvidia catalog like it's just a few of the aligners, plus the GATK toolkit. I think the fundamental question here is whether GPUs would give us any advantage, as the department is comparing the advantages of paying for remote cluster use versus a local server equipped with some GPUs. I can get more details if that's helpful.
ADD COMMENT • link written 3.9 years ago by elaine.youngman • 0

I don't know exactly, sorry. GATK is integrated in Galaxy and actively maintained, not sure how to run it on GPUs.

ADD REPLY • link written 3.9 years ago by Bjoern Gruening ♦ 5.1k
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