NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree

From: Vlad Cojocaru (
Date: Tue Nov 30 2021 - 04:30:35 CST

Dear all,

We submitted a proposal to run some extensive atomistic simulations with
NAMD of systems ranging between 500 K to 2M atoms on a supercomputer
with  Intel Xeon Platinum 8160 processors and 100Gb Intel Omni-path
Full-Fat Tree interconnection.

Apparently, our project may fail the technical evaluation because during
our tests we did not achieve a 75 % parallel efficiency between 2 to 48
nodes (each node has 2 CPUs - 24 cores/CPU).  We have tested the NAMD
2.14 provided by default at the site and we do not know how this was
built. Looking at the NAMD benchmarks available for the Frontera
supercomputer (quite similar architecture if I understand it correctly
but for larger systems), it seems we should definitely achieve with NAMD
2.15 (maybe even 2.14) much better performance and parallel efficiency
up to 48/64 nodes on this architecture than we actually achieved in our

So, my reasoning is that probably the NAMD built by default was not
really carefully optimized.

I would appreciate if anyone who has experience with building and
optimizing NAMD on such an architecture could recommend any
compiler/MPI/configuration/options for building an NAMD with a better
performance and parallel efficiency. If I have some clear ideas about
how to optimize NAMD, maybe I could make the case for our project to not
fail the technical evaluation.

Thank you very much for any advice

Best wishes

Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at];!!DZ3fjg!ouau8vpkIDbQ8KrgRCSrc8Ng4YRHk1w7tQfeHsxoB5VnnkEQuC3CQj5uCvq0Gx8Paw$ 

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