[gmx-developers] KNL usage and mcdram
pall.szilard at gmail.com
Fri Sep 22 14:36:28 CEST 2017
No, it does not. IIRC, as Berk said, there were small differences when
using cache mode (as long as everything fits!), but you can also
configure it in flat mode and bind mdrun to the first NUMA region. For
all intents and purposes that should be as good as it gets.
You might want to also try huge pages and quadrant mode (I don't have
detailed data comment on the impact of these, but both of those have
been claimed to be beneficial).
On Fri, Sep 22, 2017 at 12:22 PM, Åke Sandgren
<ake.sandgren at hpc2n.umu.se> wrote:
> Ok, so gromacs doesn't explicitly use mcdram at least.
> On 09/22/2017 11:44 AM, Berk Hess wrote:
>> GROMACS simulations will usually completely fit in MCDRAM. So cache
>> configuration should be ok. I don't recall if there is some small
>> overhead to cache mode, in which case it would be better to use MCDRAM
>> as (the only) memory.
>> On 22/09/17 10:28 , Åke Sandgren wrote:
>>> Quick question, does gromacs currently take advantage of explicit use of
>>> mcdram on KNL nodes?
>>> I.e., when it's not configure as cache that is.
>>> Didn't see anything obvious during confiugure.
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: ake at hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
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