[gmx-users] Re: Looking for GPU benchmarks

Justin Lemkul jalemkul at vt.edu
Mon Aug 27 13:48:40 CEST 2012

On 8/27/12 7:31 AM, Mathieu38 wrote:
> I have tried the basic approcah of taking some of the input files that are
> provided with the sources of Gromacs or on the website, and adding the line
> cutoff-scheme = Verlet
> in the grompp.mdp file
> However, I have not find a case where use of GPUs (2 MPI Tasks, 4 OpenMP
> Threads per MPI tasks, 2 GPUs) lead to a significant speed up, comparing to
> a CPU only version using 8 cores on a single node.
> I don't know if this is because GPU implementation is still not performant
> or if this is because my test cases are unappropriate.
> Any help here would be very much appreciated.

Have you pulled the correct development branch from the git repository?  The 
changes have not yet been merged into the release-4-6 branch, as they are still 
pending in the Gerrit review system.  If you're working with any of the source 
distributions from the website, those will not work.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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