NAMD CUDA performance

From: Vlastimil Zíma (
Date: Tue Sep 10 2013 - 07:59:41 CDT


I'm somewhat troubled with the performance of the NAMD, when run on CUDA.
We have two graphic cards GTX 590 and GTX 690, but it seems that GTX690
produces only minimal performance benefit.

Using both GPU cores of the GTX690 produces only about 8 % performance
benefit, which is not a lot. Neither the upgrade of CPU+motherboard
produced expected benefit in CUDA simulations (as compared to CPU only

I can not tell what is the occupation of the GPU's as nvidia does not
provide any reasonable tool to investigate this on linux, but it seems that
GPU's are underoccupied. Also I have not noticed a dependency on system

Is there any way to tell what is the bottleneck of the performance? I did
found a note about charm projections, but it seems like a long term

If needed I can provide more details about my experiments with NAMD

Vlastik Z

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