Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Sun Apr 01 2012 - 03:41:08 CDT

.. which is even more interesting given that when we moved from the
Linux-x86_64-CUDA executable to 2.9's Linux-x86_64-multicore-CUDA we saw
speed-ups of the order of ~40%. For a tiny system (7400 atoms) on a
single node based on AMD FX-8150 + GTX 570 the Linux-x86_64-multicore-CUDA
executable is 45% faster than the 'CVS-2012-02-26 for Linux-x86_64-CUDA'.
Hmmm ....

On Sat, 31 Mar 2012, Thomas Albers wrote:

> Hello!
>
> We have a cluster consisting of 8 AMD Phenom II x4 computers with GTX
> 460 video card linked with SDR Infiniband, and we find that the CUDA
> version of NAMD 2.9b2 scales worse than NAMD 2.8 and runs slower. I
> did compile the program myself since UIUC offers only the
> Linux-x86_64-ibverbs-smp-CUDA binary for download, not the
> Linux-x86_64-ibverbs-CUDA version that would be suitable for us.
>
> Some timing results, all with the F1ATPase benchmark:
> NAMD 2.9b2 Linux-x86_64-ibverbs, 32 cores: 0.160 s/step
> NAMD 2.8 Linux-x86_64-ibverbs, 32 cores: 0.160 s/step
> NAMD 2.9.b2, compiled w/ gcc 4.5.3, 32 cores: 0.160 s/step
>
> (One node:)
> NAMD 2.9b2 Linux-x86_64-multicore-CUDA, 4 cores: 0.238 s/step
> NAMD 2.8 Linux-x86_64-ibverbs-CUDA, 4 cores: 0.231 s/step
> NAMD 2.9b2, compiled w/ gcc 4.5.3, 4 cores: 0.251 s/step
>
> NAMD 2.9b2, compiled w/ gcc 4.5.3, 4 cores: 0.251 s/step
> NAMD 2.9b2, compiled w/ gcc 4.5.3, 8 cores: 0.173 s/step
> NAMD 2.9b2, compiled w/ gcc 4.5.3, 16 cores: 0.104 s/step
> NAMD 2.9b2, compiled w/ gcc 4.5.3, 32 cores: 0.065 s/step
> NAMD 2.8 Linux-x86_64-ibverbs-CUDA, 32 cores: 0.039 s/step
>
> What is interesting is that timing results on one node are comparable
> between versions, and that the non-CUDA version also does not seem to
> be affected. It's only the CUDA version of NAMD 2.9 that shows this
> odd scaling behavior. What is going on?
>
> Thomas
>

-- 
            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

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