Hi Ross:
thank you for such kind comments.
Probably it also would be nice if you have more comments on the
coming Amber workshop in Europe. Probably we may also meet in that
event. ;-)
best
Albert
On 07/05/2012 06:28 PM, Ross Walker wrote:
> Hi Albert,
>
>> it seems that for general biology system size (60K), most MD tools
>> are with efficiency around 20 ns/day.... I thought that some could much
>> faster.....
> No that's pretty normal and when you actually do apples to apples
> comparisons there tends not to be that much difference between the various
> codes. Note for a 60K atom system a single GTX580 will likely get you around
> 20 to 25ns/day, you can probably get to 30 or so with a GTX680 and maybe 35
> with multiple GPUs. So no need to spend millions on massive supercomputers.
> ;-)
>
> I'd be wary of marketing type benchmarks which is what you often see touted
> around. If you are seeing things going much much faster than 20ns/day then
> likely they are cheating somehow, using hacks like H-mass repartitioning to
> get artificially long time steps, or using very short cutoffs, or extremely
> coarse FFT grids or being extremely lax on the precision of the math
> involved etc. Essentially when looking at any benchmarks you need to look
> very carefully at what the exact simulation parameters used were and use
> your experience with MD to determine whether they are reasonable or not.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Thu Jul 05 2012 - 10:00:03 PDT
