[gmx-developers] Gromacs 5.0 benchmarks

[Schulz, Roland]

Hi Kevin,

I uploaded the master branch with those two changes under code review, plus a work-around for ICC 17beta to github.  You can download this version as
https://codeload.github.com/rolandschulz/gromacs/zip/knl

Besides the general performance tips you might want to try:

-          If you benchmark on a single node try to use only OpenMP with a single MPI rank

-          Or use 4 OpenMP and the appropriate number of MPI ranks (both for single node as well as multiple nodes)

-          Use 2 way Hyper threading (2 thread / core)

-          Try ICC17beta

-          Use "numactl -m1" when using Flat mode

Let me know if you have any other questions.

Roland


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 Kevin Chen
Sent: Friday, July 15, 2016 7:27 AM
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] Gromacs 5.0 benchmarks

Hi Roland,

Thanks for getting back to us.  Yes, it will be great if you could share the latest Gromacs development with all available improvements. In the meantime, we will give 2016RC a try first.

Best,

Kevin



From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of Schulz, Roland
Sent: Thursday, July 14, 2016 12:22 PM
To: gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>
Subject: Re: [gmx-developers] Gromacs 5.0 benchmarks

Hi Kevin,

GROMACS 2016 has already a lot of KNL optimizations included. Including AVX512(+ER) and OpenMP scaling improvements. The RC is out ftp://ftp.gromacs.org/pub/gromacs/gromacs-2016-rc1.tar.gz. Additionally there are further improvements publically available in the code-review system which will be included in the 2017 version such as
https://gerrit.gromacs.org/#/c/5841/
https://gerrit.gromacs.org/#/c/6004/

If you want to test a version with all available KNL improvements included feel free to contact me.

Roland

From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of Kevin Chen
Sent: Thursday, July 14, 2016 7:51 AM
To: gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>
Subject: Re: [gmx-developers] Gromacs 5.0 benchmarks

Hi Mark,

Thanks for getting back to me! Here at TACC, we are trying to do some Gromacs benchmarking on Stampede and the Stampede 1.5 (our latest KNL machine) and try to publish the results on conferences/ tutorials. We could easily make some systems for that purpose. However, we feel it's always better to get the "official" ones from the developer. As such, it will be great if you could share those files with us.

Speaking of KNL, at TACC we have received first 500 nodes from intel a couple month ago. Those nodes will eventually become the Stampede 1.5 and hopefully be in production later this year. So I was wondering, if you guys have any plan on testing/optimizing Gromacs code no KNLs in the near future?

Best,

Kevin Chen



From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of Mark Abraham
Sent: Thursday, July 7, 2016 5:46 AM
To: GROMACS developers <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>
Subject: Re: [gmx-developers] Gromacs 5.0 benchmarks

Hi,

Yes we've had a few requests for these. I can share e.g. the .tpr files easily enough but attempting to reproduce them requires driver scripts to scan parameters, etc. and I don't have time right now to make those usable in the hands of others on arbitrary HPC platforms and job schedulers. What's the purpose of the benchmarking? Are you better served by getting examples of actual .tpr files used by your users, and using those?

Mark

On Thu, Jul 7, 2016 at 12:43 PM Vedran Miletić <vedran at miletic.net<mailto:vedran at miletic.net>> wrote:
On 07/06/2016 05:54 PM, Kevin Chen wrote:
> Dear GROMACS developers,
>
> We are currently in the process of benchmarking GROMACS5.1.2 on our
> local HPC systems. There are some nice results posted online
> (http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf). I
> was wondering if anybody can kindly share the files (such as, pdbs,
> mdps, tops and tprs) used for those tests? We'd like to see if we could
> reproduce any of those results.
>
>
>
> Thank you in advance!
>
>
>
> Kevin Chen
>

Hi Kevin,

for benchmarking, the following files may be what you are looking for:
ftp://ftp.gromacs.org/pub/benchmarks/

Regards,
Vedran

--
Vedran Miletić
vedran.miletic.net<http://vedran.miletic.net>
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