[gmx-developers] Re: GROMACS 4.6 pre-release: new algorithms, parallelization schemes, & GPU acceleration

[Szilárd Páll]

On Mon, Mar 5, 2012 at 11:19 PM, Mirco Wahab
<mirco.wahab at chemie.tu-freiberg.de> wrote:
> Am 05.03.2012 22:42, schrieb Berk Hess:
>
>> All you need to add to make the gpu work, if you compiled with gpu
>> support is:
>> to your mdp file:
>> cutoff-scheme = verlet
>
>
> OK, lets see. I removed (from mdp) completely
>    vdw_type
>    coulombtype

You didn't need to remove those.

> and *VOILA*, I can't believe this, it *does* work
> - Win7/x64
> - Cuda4.1
> - VS2010/SP1
> - fftw3f
> - gsl/gslcblas
> - libxml2

Why would it not work :)

> A first test set of ~ 1 million particles (most MARTINI W,
> ~10,000 lipids) will run on a i7/920/(@3GHz) at about 11.5 GFlops
> with "*-nt 8*" (15.9 ns/day). On a stock GT-550 in the same
> machine (*-nt 1 -nb gpu*), it reaches  14.4 GFlops (23.5 ns/day).

A few things that can improve performance:
- increase nstcalcenergy, e.g. to 100;
- try increasing nstlist, 20-30 is generally the best.

Cheers,
--
Szilárd


> Thanks & regards
>
> M.
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