Re: [gmx-users] GROMACS & Speed

[Omololu Akin-Ojo]

Thanks, David. i appreciate your response.

o.

David van der Spoel <[EMAIL PROTECTED]> wrote:

Omololu Akin-Ojo wrote:
> Hi,
>
> i use GROMACS & i like it because it is so fast. But, i would like to
> know if GROMACS "cut corners" ? Otherwise, why is it is so fast?
> if you have a fortran compiler on an Opteron box, GROMACS does not use
> the assembly loops. Right? So, why is it blazingly fast?
>
> o.

gromacs does not cut corners...
Most important we do not compute stuff that we know will give zero as a
result anyway, this gives 20-30% compared to other codes.
Single precision is a factor of two faster than double, assembly is a
factor of two faster than C/Fortran, and finally our innerloops are
completely unrolled, this probably also gives a factor of 1.5.
So if you multiply it all you have a significant factor (even in double
precision).


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--
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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