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

[Mark Abraham]

Yes, thus "always"

Mark

On Fri, 20 Oct 2017 00:19 MING HA <mingtha at scarletmail.rutgers.edu> wrote:

> Dear Mark,
>
>
> Thanks for the quick response. So, in general, running using AVX
> instructions will yield
> better performance than SSE4.1?
>
>
> Sincerely,
> Ming
>
> On Thu, Oct 19, 2017 at 5:18 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > In short, yes. See
> > http://manual.gromacs.org/documentation/2016.4/install-
> > guide/index.html#simd-support.
> > 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.
> >
> > Mark
> >
> > On Thu, Oct 19, 2017 at 7:02 PM MING HA <mingtha at scarletmail.rutgers.edu
> >
> > wrote:
> >
> > > 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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