From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Mon Sep 22 2014 - 00:23:41 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?
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 <glykos_at_mbg.duth.gr> 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, http://utopia.duth.gr/~glykos/
Dr. Douglas R. Houston
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
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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