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?
Hi,
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
load imbalance.
Carsten
Mark
-------- Original Message --------
Subject: [FFTW-announce] FFTW 3.2 is released
Date: Sat, 15 Nov 2008 22:01:44 -0500 (EST)
From: Steven G. Johnson <[EMAIL PROTECTED]>
Reply-To: Steven G. Johnson <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Dear FFTW users,
The official release of FFTW 3.2 is now available from the FFTW home
page:
http://www.fftw.org/
This release does *not* contain the experimental MPI transfroms from
FFTW
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
Codesourcery.
The complete release notes can be found in the NEWS and ChangeLog
files of the
release, and at:
http://fftw.org/release-notes
Specific changes compared to FFTW 3.2alpha3 are listed below.
Regards,
Steven G. Johnson and Matteo Frigo
FFTW 3.2 changes from 3.2alpha3
* Worked around apparent glibc bug that leads to rare hangs when
freeing
semaphores.
* 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.
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