[gmx-users] Compile Gromacs for Blue Gene/L

Eric Jakobsson jake at ncsa.uiuc.edu
Sun Apr 8 23:19:58 CEST 2007

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
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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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