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).> > > Sponsored Link> > Try Netflix today! With plans starting at only $5.99 a month what are > you waiting for? > > > > > > ___> gmx-users mailing listgmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED]> Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- 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, Swedenphone: 46 18 471 4205  fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php 


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Re: [gmx-users] GROMACS & Speed

[David van der Spoel]

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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[gmx-users] GROMACS & Speed

[Omololu Akin-Ojo]

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. 


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