[gmx-users] Performance difference when using Gromacs 5.0 with different vector instructions

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 19 23:19:02 CEST 2017


In short, yes. See
You should generally always use a GROMACS binary compiled for the highest
SIMD level supported by your hardware. Your mdrun .log file will advise you
when it observes that you are not.


On Thu, Oct 19, 2017 at 7:02 PM MING HA <mingtha at scarletmail.rutgers.edu>

> Hi all,
> I am running several resources using Gromacs 5.0 to run my simulations.
> On some resources, Gromacs is compiled using SSE4.1 SIMD instructions,
> while on others AVX_256 or AVX2_256 is used. While I don't find much of a
> performance difference between AVX_256 and AVX2_256 instructions, there
> is a large performance difference between resources that use SSE4.1 and
> AVX instructions. Specifically, resources using SSE4.1 are about 2-3x
> slower
> than those that use AVX.
> I'm kind of new to the SIMD instructions used by Gromacs, so I was
> wondering
> whether the instruction set is causing the large performance difference.
> Sincerely,
> Ming
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