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List: beowulf
Subject: Re: [Beowulf] GPU-HMMer for interested people
From: Joe Landman <landman () scalableinformatics ! com>
Date: 2008-12-17 15:51:00
Message-ID: 49491FE4.4050402 () scalableinformatics ! com
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Hi Olli-Pekka
Olli-Pekka Lehto wrote:
> Joe Landman wrote:
> > Hi folks
> >
> > GPU-HMMer (part of the MPI-HMMer effort) has just been
> > announced/released at http://www.mpihmmer.org
> >
> > MPI-HMMer has itself been improved with parallel-IO and better
> > scalability features. JP has measured some large number (about 180x)
> > over single cores on a cluster for the MPI run.
> >
> > Enjoy!
> >
> > Joe
> >
>
> Hi Joe,
>
> Looks quite promising. Here are results from a simple real-world test case:
>
> GPU: Dual GTX280, each with 1GB RAM
> CPU: Single Intel Core2 quad Q9550 2.83GHz
>
> hmmsearch 4 threads sorted: 274.49s
> hmmsearch 4 threads unsorted: 254.23s
> cuda_hmmsearch unsorted 407.85s
> cuda_hmmsearch sorted: 62.69s
> cuda_hmmsearch sorted 2 simultaneous runs: 78.23s 80.79s
>
> Remarks:
>
> -Running hmmsort to sort the sequence database is critical to obtain
> reasonable performance from cuda_hmmsearch. However, the regular
> hmmsearch is slightly slower with the sorted database.
>
> -Running two simultaneous runs assigned to different GPUs on a dual-GPU
> quad-core system yields some performance penalty, but is still quite
> feasible.
>
> -I used the parameters THREADSIZE=320 BLOCKSIZE=64. I'm not completely
> sure if these are the optimum values for GTX280. Any better suggestions?
I'd suggest subscribing/posting to the mpihmmer list
(http://lists.scalableinformatics.com/mailman/listinfo/mpihmmer) so we
don't clutter beowulf with this.
JP could likely tell you more about the appropriate sizing for GTX280.
We have a pair of GTX260's in the lab that some runs were done on.
Could you describe your run a bit more (sequence queries, hmm size,
database and size)? On the mpihmmer list though ...
Thanks!
Joe
>
> Regards,
> Olli-Pekka
--
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web : http://www.scalableinformatics.com
http://jackrabbit.scalableinformatics.com
phone: +1 734 786 8423 x121
fax : +1 866 888 3112
cell : +1 734 612 4615
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