Molecular Dynamics On 670 on the new cards become twice as fast

On the new 670 card molecular mechanics is twice faster than was on the cards of five hundredth series. Thanks NVIDIA team.
(This was tested on Abalone program http://www.biomolecular-modeling.com/Abalone/index.html).

I expect that this is due to a decrease in memory latency, which in turn is associated with an increase in memory frequency. My expectation is that the latency decreased by 2-3 times.
Is this true?

Is the problem almost completely compute-bound?

Or perhaps you have a lot of atomic operations ? According to the whitepaper on GK104 there was a 3x atomic performance improvement, which I guess would be closely related to the latency improvements that you mention.

Yes, there are atomic operations. But I do not think they eat more than 20-30% of the speed.
There must be something else.

Yet, what about the latency. Do I understand correctly that it improved in the 600th cards?

Sorry for my English. What mean the phrase “compute-bound”?

Well if for example your application has a high bandwidth utilization we would consider it to be bandwidth-bound, ie the bandwidth of the card is the bottleneck of your application.

Now if your problem has a very high arithmetic intensity ( ex many addition and multiplications on the same data element => high FLOP / byte ratio ) we might say that it is compute-bound. If this is the case your performance increase would make sense since the GTX670 has roughly 2x the theoretical performance of the GTX570.

Hope I’m making sense :)

Thank you.

No, the problem is not in the long-term calculations. Conversely card mostly unloaded.

It basically waits for a response from the global memory, accessed by the virtually non-regular.

It would be more quantitative if you can use your algorithm in the roofline model.

What is “roofline model”?

Samuel Williams, Andrew Waterman, David Patterson
Roofline: an insightful visual performance model for multicore architectures
Communications of the ACM, Volume 52, Issue 4, April 2009, pp. 65-76