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

David van der Spoel spoel at xray.bmc.uu.se
Sat Apr 7 09:06:17 CEST 2007

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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