[gmx-developers] GROMACS optimization for IBM Cell processor

[Giovanni Lovato]

Il giorno 19/giu/09, alle ore 11:01, Maik Nijhuis ha scritto:

> On Wed, Jun 17, 2009 at 10:05:30PM +0200, Giovanni Lovato wrote:
>> Hi all,
>> at the University of Verona (Italy) we are starting to work on the
>> porting of MD algorithms to the IBM Cell processor. Before descending
>> into the code, is there already any sort of contribution/fork/ 
>> patches/
>> hints or anything else related to GROMACS optimization for Cell?
>
> You can take a look at the following papers:
>
> http://www.cs.unc.edu/~olivier/pdsec07.pdf
>
> http://www.ncbi.nlm.nih.gov/pubmed/18615421
>
> http://www.hicomb.org/papers/HICOMB2007-02.pdf
>
> I have ported non-bonded kernels 010 and 112 to the SPEs in the Cell
> processor. My implementation supports any number of particles and uses
> the existing neighborlist. Since I'm storing the particle data
> (positions/forces) in main memory, I'm facing a memory bottleneck, and
> the speedup of these kernels is only 2 and 5, respectively, relative  
> to
> the speed of the corresponding PPE altivec kernel (single-threaded).

Thank you Maik, you gave me useful informations!
  Is your work under an open-source license? Maybe we can collaborate  
on the porting of GROMACS on Cell! Now I'm trying to understand the  
flow of runtime execution in the sources, then I'll look for pieces of  
code suitable for SPE parallelization.

Giovanni
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