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

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Mon Mar 5 23:19:05 CET 2012

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

and inserted:
     cutoff-scheme = verlet

then, generated a new tpr,
     "Set rlist to 1.37 nm, buffer size 0.17 nm"

     c:\> mdrun -nt 1 -nb gpu -v

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

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).

If I got some more time, I'll test the build against CUDA 4.0,
according to Szilárds hint (possible performance drop in 4.1).

I'm really impressed.

Thanks & regards


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