[gmx-developers] KNL usage and mcdram

[Schulz, Roland]

Usually it is best to run with all in mcdram closely followed by using cache mode.
To run with all in mcdram use: "numactl -m1". For a few more tips about how to run on Xeon Phi you might want to look at:
https://software.intel.com/en-us/articles/recipe-building-and-running-gromacs-on-intel-processors

-----Original Message-----
From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of Åke Sandgren
Sent: Friday, September 22, 2017 6:27 AM
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] KNL usage and mcdram

Yeah, I'm running a longer benchmark series of the ion_channel case on all our different hw types. Just wanted to make sure I hadn't missed something when building the KNL version.

On 09/22/2017 02:36 PM, Szilárd Páll wrote:
> 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).
> 
> --
> Szilárd
> 
> 
> 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:
>>> Hi,
>>>
>>> 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.
>>>
>>> Cheers,
>>>
>>> Berk
>>>
>>> On 22/09/17 10:28 , Åke Sandgren wrote:
>>>> Hi!
>>>>
>>>> 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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--
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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