Re: namd-cuda-intel vs. namd-intel

From: Axel Kohlmeyer (
Date: Tue May 12 2009 - 06:24:04 CDT

On Tue, 2009-05-12 at 01:32 -0400, Roman Petrenko wrote:
> Dear developers,
> we compared simulations of intel compiled namd2.7b1 programs with cuda
> disabled and enabled options. NVT simulation of 30-residue peptide in
> water box with PME and SMD was used. The observed speedup of namd with
> GPU is just 4 times. Is it due incompleteness of cuda-namd project or
> we did something wrong?


the one thing that you did wrong for certain is not to provide any
information about what hardware you are running on, what
compilers/flags/libs you are using and most importantly access to your
input, so that somebody can validate it. in general, it would be
preferred to use one of the example inputs provided on the namd
homepage, which people may already have some reference data for.

there are CUDA capable GPUs out there, e.g. GeForce 8400 GS, that
have very little speedup to offer compared to a GeForce GTX 285
or a Tesla C1060.


Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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