AW: NAMD CUDA performance

From: Norman Geist (
Date: Wed Sep 11 2013 - 01:53:54 CDT

Can you show us your namd script and your parallel namd call please?


Norman Geist.


Von: [] Im Auftrag
von Aron Broom
Gesendet: Dienstag, 10. September 2013 21:30
An: Vlastimil Zma
Betreff: Re: namd-l: NAMD CUDA performance


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:


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

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

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

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