[gmx-developers] FLOP accounting in Gromacs 4.6

[Berk Hess]

Hi,

Every time we get such a question, our return question is: why are you 
asking?
Any application should only care about application performance and not 
about any other measure, such as flops.

The flop rate will depend very much on the algorithm, as well as on the 
hardware.
On Sandy/Ivy Bridge, the Verlet PME kernels reach around 50% of peak, 
even more with GMX_NBNXN_SIMD_4XN set:
http://www.sciencedirect.com/science/article/pii/S0010465513001975
The FFT probably also get around 50% of peak. But all other code is far 
less flop intensive. The total I get is around 30% of peak.
But you can crank this up by shifting work from PME mesh to pair 
interactions, using GMX_NBNXN_SIMD_4XN, etc.
RF will get lower flop rates, but higher ns/day, etc.

So flop numbers are meaningless for most purposes.
I think there are only two useful cases: analyzing algorithm performance 
(but combined with other measures) and convincing people when they can't 
be convinced that flops are a useless measure. In the latter case we 
should make sure to maximize the flops by optimizing the settings for 
that purpose.
But I think the flop count is still reasonably accurate (+-10%). Flops 
in communication should be negligible.

Cheers,

Berk

On 09/16/2013 10:10 AM, Carsten Kutzner wrote:
> Hi,
>
> can I use the Mega-Flops accounting at the end of the md.log file to
> calculate how much of the theoretical peak performance of a processor
> Gromacs is using? I understand that Flops used in communication are
> not counted, so the accounting will give me a lower estimate.
>
> At what percentage of the theoretical peak performance will Gromacs 4.6
> typically run using the Verlet kernels and PME (let's say we have a
> big MD system)?
>
> Do I have to divide the reported Flops by two when running single precision?
>
> Thanks,
>    Carsten
>
>