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

From: Douglas Houston (
Date: Mon Sep 22 2014 - 00:23:41 CDT

Hi Nicholas,

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?

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

I am starting to suspect that there is either something wrong with my
installation of NAMD (a bug perhaps), or with some aspect of my


Quoting Nicholas M Glykos <> on Sun, 21 Sep 2014
21:21:53 +0300 (EEST):

>> Can anyone on this mailing list tell me if they have successfully
>> noted a speed increase by running NAMD across an ethernet-linked
>> cluster vs. a single node?
> Sure. The following page is since the days of NAMD 2.6 using gigabit
> ethernet, Q6660 quads and a 60,000 atom system :
> We could (back in 2009) go to 8 nodes, but at that point the parallel
> efficiency had dropped to only ~45%.
> --
> 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,

Dr. Douglas R. Houston
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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