NAMD PERFORMANCE ON NVIDIA K20 GPU

From: Neeraj Agrawal (neer1980_at_gmail.com)
Date: Sat Sep 14 2013 - 18:59:08 CDT

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:

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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

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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

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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

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