From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
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 http://norma.mbg.duth.gr/index.php?id=about:benchmarks:namdv28cudagtx460
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
http://norma.mbg.duth.gr/index.php?id=about:benchmarks:network 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, http://utopia.duth.gr/~glykos/
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