Re: NAMD CUDA performance

From: Aron Broom (
Date: Tue Sep 10 2013 - 14:30:26 CDT

I would suspect the bottleneck is memory bandwidth, since the GPUs must
communicate with the CPU and adding more GPUs doesn't help this. I see you
already mentioned a motherboard upgrade, but are you now using PCI 3x for
the 690?

I would recommend testing some MD code that is entirely on the GPU and see
if you get the kind of difference between the 590 and the 690 that you were
expecting (AMBER or OpenMM).

Regardless, it may in the end still be that the best use of both GPUs
within the 690 or 590 is to run multiple simulations (maybe in replica
exchange if you want to help a particular simulation explore faster, but
still have limited communication between GPUs).


On Tue, Sep 10, 2013 at 8:59 AM, Vlastimil Zma <> wrote:

> Hi,
> 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
> simulations).
> 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
> size.
> 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
> experiment.
> If needed I can provide more details about my experiments with NAMD
> performance.
> Vlastik Z

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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