[gmx-users] [Fwd: [FFTW-announce] FFTW 3.2 is released]
ckutzne at gwdg.de
Mon Nov 17 11:30:42 CET 2008
On Nov 16, 2008, at 12:47 PM, Mark Abraham wrote:
> Apologies to people receiving this from the FFTW list too, but it
> should be of interest to a large slice of people using GROMACS. In
> particular, the improvements for SIMD and size of multiples of 5/10
> should be of value for lots of people.
> Does anyone (Carsten?) have an off-the-cuff opinion on whether the
> latter means that FFT grids with dimensions that are multiples of 5
> might now be more desirable? How might that affect PME load-splitting?
I fear that the performance gain in mdrun due to a faster FFT will not
be too large - of course that
depends on how 'bad' the performance was before for multiples of 5.
The reason is that a significant
amount of the time used for transforming to and from reciprocal space
is actually communication
time: MPI transposes of the FFT data, while the calculation itself is
not so time consuming for a
normal-sized MD system. Since these transposes are done in Gromacs
anyway, the only thing that
could be faster with the new FFTW library is the calculation itself -
which should not make a big
difference in the overall mdrun performance. But why not compare the
old and new FFTW performance
with a test MD system? I would choose zero PME nodes for that test,
just to be shure that a
possible FFTW performance gain does not get hidden behind a PME/PP
> -------- Original Message --------
> Subject: [FFTW-announce] FFTW 3.2 is released
> Date: Sat, 15 Nov 2008 22:01:44 -0500 (EST)
> From: Steven G. Johnson <stevenj at ab-initio.mit.edu>
> Reply-To: Steven G. Johnson <stevenj at alum.mit.edu>
> To: fftw-announce at fftw.org
> Dear FFTW users,
> The official release of FFTW 3.2 is now available from the FFTW home
> This release does *not* contain the experimental MPI transfroms from
> 3.2alpha; as those routines are still in alpha, they have been moved
> to FFTW
> 3.3alpha1 (also available from the FFTW web page).
> Compared to version 3.1.3 of FFTW, highlights of the FFTW 3.2
> release include:
> * Significantly faster r2c/c2r transforms, especially on machines
> (e.g. x86) with SIMD instruction.
> * Performance improvements for sizes with factors of 5 and 10.
> * Rewritten threading support for improved performance.
> * Support for the Cell processor, donated by IBM Research; see
> README.Cell and the Cell section of the manual.
> * Support for MIPS paired-single SIMD instructions, donated by
> The complete release notes can be found in the NEWS and ChangeLog
> files of the
> release, and at:
> Specific changes compared to FFTW 3.2alpha3 are listed below.
> Steven G. Johnson and Matteo Frigo
> FFTW 3.2 changes from 3.2alpha3
> * Worked around apparent glibc bug that leads to rare hangs when
> * Fixed segfault due to unaligned access in certain obscure problems
> that use SSE and multiple threads.
> * MPI transforms not included, as they are still in alpha; the alpha
> versions of the MPI transforms have been moved to FFTW 3.3alpha1.
> FFTW-announce mailing list
> FFTW-announce at fftw.org
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
ckutzne at gwdg.de
More information about the gromacs.org_gmx-users