[gmx-users] Parallel FFTW performance

Dean Johnson dtj at uberh4x0r.org
Sun Oct 26 23:19:00 CET 2003

On Sun, 2003-10-26 at 15:45, Bing Kim wrote:
> Hi All!
> I am sorry this question is not for Gromacs exactly but for FFTW.
> But this question would raise on Gramacs too.
> I recently installed FFTW-2.1.5 which can use MPI.
> It was compiled with gcc-3.3.2 and mpich-
> When I ran a benchmark test program, rfftw_mpi_test, which is located in 
> fftw-2.1.5/mpi,
> I found that its performace is worse in dual cpus than single cpu.
> Basically, communication cost should be zero in SMP machine.. that I 
> expected.
> So.. I wonder if gromacs use rfftw_mpi, how it can get speed up in multiple 
> processors.
> Please help me understand this thing.

That is also our experience, not just with Gromacs/FFTW, but also with
Amber7. We solve that by running two 16x1 models concurrently. The cost
of 8x2 is only a little more than 16x1.



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