From: Aron Broom (broomsday_at_gmail.com)
Date: Sat Sep 14 2013 - 20:19:23 CDT
I would just make sure that if you're considering the second GPU card
option you make sure your motherboard would allow the second card without
reducing the bandwidth to each card. That is, have two full PCI 3 x16
speed slots available.
On Sat, Sep 14, 2013 at 7:59 PM, Neeraj Agrawal <neer1980_at_gmail.com> wrote:
> Hello,
>
> I recently performed few benchmark NAMD runs on a workstation (Dual 8-core
> Xeon E5-2687W, 3.1 GHz with one Nvidia Tesla K20C GPU). Below are the
> results:
>
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> System Size: 85,000 atoms
>
> number of CPU only CPU + K20c Speed-up
> processors (days/ns) (days/ns) from GPU
>
> 4 1.19 0.21 5.7
> 8 0.62 0.18 3.4
> 16 0.33 0.21 1.6
> 32 0.29 0.23 1.3
>
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> System Size: 6300 atoms
>
> number of CPU only CPU + K20c Speed-up
> processors (days/ns) (days/ns) from GPU
>
> 4 0.086 0.087 1.0
> 8 0.05 0.02 2.5
> 16 0.029 0.02 1.5
> 32 0.032 0.017 1.9
>
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> In all these simulations, outputEnergy is written every 100th frame and
> cutoff is set to 12 A. The results of CPU only NAMd were obtained by using
> Linux-x86_64 (version 2.9) and results of CPU+GPU were obtained by using
> Linux-x86_64-multicore-CUDA (version 2.9)
>
> Since, in the future, I will be simulating solvated proteins with around
> 50K-70K atoms (in total), would it be reasonable to conclude the following
> based on the above benchmark results:
>
> 1. The biggest advantage of GPU is seen when one GPU is used per 8 cores.
>
> 2. It might be advantageous to add one more GPU to this workstation so
> that I can run two NAMD simulations (each on 8 procs + 1 GPU)
> simultaneously ?
>
> 3. For a system with <80k atoms, hyper-threading can deteriorate the
> performance.
>
> Thank you,
>
> Neeraj
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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