From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Jun 01 2012 - 08:57:23 CDT
On a related note, would it make sense to try and reorder atoms in
memory by neighborhood, to make memory accesses more regular and
increase cache hits?
On 1 June 2012 15:35, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Jun 1, 2012 at 7:52 AM, Florian Mrugalla
> <florian.mrugalla_at_uni-dortmund.de> 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,
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
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