[gmx-developers] Gromacs FFT

Roland Schulz roland at utk.edu
Tue Dec 9 21:24:20 CET 2008

Hi Kent,

usually FFT is not a bottleneck for MD when run on one or a few processors.
You can increase the FFT load slightly by using a small cut-off (rcoulomb in
the mdp file) and a fine grid (fourierspacing in mdp). Typical one uses a
minimum of rcoloumb 0.8 and fourierspacing of 1.1. But you could decrease
fourierspacing further to see the effect on the FFT time.

FFT becomes the mayor bottleneck for parallel runs on more than a few
hundred CPUs. I did some work on parallel FFT on Jaguar and Kraken. Let me
know in case you are also interested in parallel FFT. Is it correct that the
ACML only supports serial FFT so far? Do you plan to add an parallel FFT or
an extension as for the linear algegra routines with AMD ScaLAPACK?


On Tue, Dec 9, 2008 at 2:40 PM, Knox, Kent <Kent.Knox at amd.com> wrote:

> Hi all,
> I'm interested in gromacs to find out how it uses FFT's.  I've
> downloaded the latest tarballs from the website
> Gromacs-4.0.2.tar.gz
> Gmxtest-3.3.3.tgz
> Gmxbench-3.0.tar.gz
> built everything single-threaded single-precision, grabbed a profile of
> the d.lzm benchmark, which I understand is the only included bench that
> uses FFT's.
> After Oprofiling the resulting executables, I am only finding about 2%
> of the time is spent in fft's.
> CPU: AMD64 family10, speed 2300 MHz (estimated)
> Counted CPU_CLK_UNHALTED events (Cycles outside of halt state) with a
> unit mask of 0x00 (No unit mask) count 100000
>  samples|      %|
> ------------------
>  11992213 41.3899 mdrun
>  6312771 21.7879 libmd.so.5.0.0
>  5121677 17.6770 libgmx.so.5.0.0
>  3659315 12.6298 no-vmlinux
>  1201312  4.1462 libm-2.4.so
>   620405  2.1413 libfftw3f.so.3.2.2
>    43580  0.1504 oprofiled
>    20128  0.0695 libc-2.4.so
> Does this sound typical?  Are FFT's not a bottleneck?  Maybe there are
> better workloads available that stress FFT computation?
> For disclosure, I do not know much about Molecular Dynamics, but am
> interested in interesting and useful workloads that stress math
> computation.
> Thanks in advance for any of your time.
> Kent Knox
> Member of Technical Staff; AMD ACML
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ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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