[gmx-users] Performance advice for newest Pascal architecture

Téletchéa Stéphane stephane.teletchea at univ-nantes.fr
Thu Mar 9 11:58:41 CET 2017

Dear colleagues,

We are willing to invest on nodes for GROMACS-specific calculations, and 
trying to best the best for our bucks (as everyone).

For now our decisions comes close to nodes using the following 

2 * Xeon E5-2630 v4
1 P100 or 2 * P5000 or 2 * K40
Cluster node interconnection: Intel OmniPath

Our system will will range from 50k to 200k atoms most of the time, 
using AMBER-99SB-ILDn, GROMCAS 2016.1 and above.

I am aware of various benchmark and recommandations like "Best Bang for 
your Bucks", but is there any reference (internal may be) for latest 
Pascal architecture, or any general advice against/for ?

Thanks a lot in advance for the feedback, if we are able to benchmark on 
our systems using the different setups above we'll share as possible by 
the upstream vendor the results.


Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein 
Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 
Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org

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