[gmx-users] Parallel FFTW performance

Bing Kim abinitiomd at hotmail.com
Mon Oct 27 00:37:01 CET 2003

Thanks for the response.
But, I cannot understand quite well what you explained.
Do you mean that I have to use, for example, 4096x64x1 instread of 64x64x64?
This gives improved speed up but overall speed up compared to 64x64x64 is 
I am sorry. Can you explain again?

Bing Kim

>From: Dean Johnson <dtj at uberh4x0r.org>
>Reply-To: gmx-users at gromacs.org
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Parallel FFTW performance
>Date: 26 Oct 2003 16:18:27 -0600
>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 
> > 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.
>	-Dean
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