Intel 11 compilers

From: Xavier Deupi (
Date: Fri Jul 10 2009 - 08:52:58 CDT

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?



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

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