Re: Benefits of SandyBridge EP in NAMD2.9

From: Axel Kohlmeyer (
Date: Fri Jun 01 2012 - 08:35:37 CDT

On Fri, Jun 1, 2012 at 7:52 AM, Florian Mrugalla
<> wrote:
> Dear NAMD mailing list subscribers,
> Lately I thought wether NAMD2.9 benefits from the new
> avx instruction set present in the SandyBridge EP processors.
> If there is a benefit how large would you estimate the effect?
> Is one of the precompiled versions capable of using the avx instruction set
> or do I have to compile it from scratch?
> If I have to compile it for onself are there any suggestions on how to
> gain the most benefits from avx?
> According to the link beneath for arithmetic heavy processes there should
> be a substantial speedup.

but classical MD forcefields like CHARMM or Amber were
designed to have as little arithmetic as possible. performance
is much more governed by memory bandwidth and cache sizes
due to using neighbor lists and thus rather irregular memory
accesses than by floating point performance. if you were doing
linear algebra heavy stuff things would be different...

> Thanks in advance and Best Regards,
> Florian

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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