From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Fri Jul 10 2009 - 10:01:59 CDT
Hi Xavier,
A very quick note to say that on our toy-cluster (8 quads, gigabit) our
current best-performing combination is UDP-SMP-ICC compiled from source
using icc, Version 11.0, Build 20081105 (but keep in mind that this is the
only icc version we have tried, I'm not trying to compare 11.0 with 11.1).
See http://norma.mbg.duth.gr/index.php?id=about:benchmarks:namdv27b1 if
you care for more details.
Nicholas
On Fri, 10 Jul 2009, Xavier Deupi wrote:
> Hi everybody,
>
> We have installed the the NAMD_2.7b1_Linux-x86_64-TCP binaries in a 64-bit
> Intel Xeon processors cluster with 16GB memory and a 10Gbit ethernet
> connection.
>
> We plan to simulate a system consisting of ~100.000 atoms, and we have been
> doing some tests (see below). It seems that the scalability degrades
> significantly going from 32 to 64 processors. I have no experience in NAMD, so
> are these values within the expected behavior of NAMD?
>
> Also, it seems that the current binaries have not been compiled with the last
> version (11.1) of the Intel compilers. Am I right? If so, do you think that
> recompiling with this version would result in a noticeable increase of
> performance?
>
> Thanks,
>
> Xavier
>
> P.S. Performance so far:
>
> 8 procs WallClock: 800.417664
> 16 procs WallClock: 500.420837 x1.60
> 32 procs WallClock: 342.890442 x2.33
> 64 procs WallClock: 298.141724 x2.68
>
>
> Xavier Deupi
> Laboratory of Computational Medicine
> Biostatistics Unit. School of Medicine
> Universitat Autonoma de Barcelona
> Bellaterra, 08193 (Barcelona)
> Catalunya, EU
>
>
>
>
--
Dr 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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