From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 01 2012 - 09:04:52 CDT
On Fri, Jun 1, 2012 at 9:57 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> 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?
absolutely. the speedup can be quite drastic.
> 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.
-- 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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