Re: Is there any point in running NAMD over an ethernet-linked cluster?

From: Nicholas M Glykos (
Date: Mon Sep 22 2014 - 03:40:59 CDT

> > Thank you very much for that, it is supremely helpful. I am going to try
> to replicate the various benchmarking tests you describe in your link. To
> that end, I wonder if you would be able to supply me with the 60,000-atom
> ionized.psf and heat_out.coor files you used so that my steps match yours
> as closely as possible?

I don't expect scaling problems to be protein-specific. We were getting
reasonable scaling with the ApoA1 benchmark distributed by NAMD
developers (see
for a more recent test with NAMD 2.8 + CUDA. The measurements stop at four
nodes because we only had four nodes with GPU's :-)

> > If not (you hint that your tests were done a long time ago), I wonder if
> you ever looked into total bandwidth usage in your tests? 64 minutes of
> simulation runtime across 2 of my nodes results in a total of 390GiB of
> data transferred between them (according to ifconfig) - this equates to
> about 100 MiB/sec. This is for my 80,000-atom system. Does this mean that
> my network bandwidth could indeed be saturating (100 MiB/sec being not far
> off 1Gbit/sec)? If this is true, it is not clear to me why the data
> transfer rate is so high in my case but not yours.

As Axel said, latency is probably more important. Have you benchmarked
your network with a tool like NetPIPE ? (see for an
example, this was again back in 2009, so there may be much better tools
around these days).

            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:52 CST