[gmx-users] improving cluster performance

[Anton Feenstra]

David van der Spoel wrote:
> 
> You won't need to rebuild anything, just select the right driver for
> your network (at the OS level). Please send some comparisons to the
> mailing list.
> 
> I will soon have the possibility to test an optimized MPI for Gigabit
> ethernet. This may speed up things considerably, but it is a commercial
> package.

Alternatively, you might try out M-VIA in combination with MVICH.
M-VIA is a networking layer that has lower latency than TCP/IP, 
and MVICH is an MPI-CH based MPI implementation that uses M-VIA for 
its communication. The documentation states that a threefold decrease
in latency can be reached, but to my knowledge no-one has yet tried
it out for Gromacs. Also, only a limited number of netwerk cards
are supported by M-VIA.

M-VIA homepage: http://www.nersc.gov/research/FTG/via/
MVICH homepage: http://www.nersc.gov/research/FTG/mvich/

In theory, it should be as simple as compling M-VIA against your kernel
source, compile MVICH against the M-VIA libraries and compile Gromacs
(and fftw) against MVICH (in stead of MPICH or LAM-MPI).


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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