[gmx-users] Compile Gromacs for Blue Gene/L
lindahl at cbr.su.se
Tue Apr 10 12:45:35 CEST 2007
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
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.
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 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
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>> gmx-users mailing list gmx-users at gromacs.org
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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
> Senior Research Scientist, National Center for Supercomputing
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
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