As I understand it, Blue Matter is a very stripped down laboratory
code, so I think the scaling is the only large virtue that one would
want to acquire.
At 02:06 AM 4/7/2007, you wrote:
Eric Jakobsson wrote:
Not a direct response but a thought: Wouldn't it be wonderful to
have a code that combined the best qualities of Gromacs and Blue
Matter? Is it possible to assemble a group or community of people to do that?
Erik L. has been in touch with IBM about their 3D FFT routines, but
apparently they pointed out that there is already another FFTW based
library that is even better, so we'll be trying that. Apart from
that, I do not know too much about Blue matter. The IBM website
boasts about scaling, which looks great indeed, but it doesn't say
anything about absolute performance (ns/day), which may be in the
papers of course.
We are currently in the process of writing up a paper on the
absolute performance of the gromacs development version, and even if
GROMACS doesn't reach the same absolute performance as Blue matter
(which it may!) it gives a lot more bang for the buck in terms of
hardware costs.
But to further the discussion: is there anything else in Blue matter
that would be interesting to have implemented into GROMACS?
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 Fax 217 244 9757
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