[gmx-developers] Gromacs 5.0 benchmarks

[Kevin Chen]

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] On Behalf Of Mark Abraham
Sent: Thursday, July 7, 2016 5:46 AM
To: GROMACS developers <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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