Hi Eric,
I think you'll be _very_ happy with Gromacs4, or the current CVS
version if you want to test that :-)
One problem is that "relative scaling" is a rather pointless measure,
since it will be better the slower the code is on a single CPU (less
time spent in communication). Our parallelization goal is rather been
to get the highest possible absolute performance on any given number
of nodes.
From what I've seen, I still think Blue Matter might show better
relative scaling when you use several thousand of nodes for small
systems, but Gromacs4 will beat that absolute performance using a
(significantly) smaller number of nodes.
Cheers,
Erik
On Apr 8, 2007, at 11:19 PM, Eric Jakobsson wrote:
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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