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Compucon HPC for NAMD Print
November 2012

NAMD is a world class software program for molecular dynamic studies created in 1995 and maintained by the University of Illinois.  It is designed for parallel computation to study the interactive behaviour of as many as 100 million molecules.  NAMD stands for “Not Another Molecular Dynamic” program.  See Slide 1.  Nvidia listed NAMD among 8 other well know molecular dynamic programs on its website as in November 2012.  

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NAMD uses the GPU for non-bonded force evaluation only whereas energy evaluation is done on the CPU.   The CUDA code in NAMD is completely self-contained.

We tested NAMD v2.9 with its benchmarking sample in length in our technical service workshop in October 2012 with 4 desktop systems based on X79 and Z77 platforms, and verified the information given on a chart shown on Nvidia website.  The chart shows that one Tesla is equivalent to 4 Quad Core CPU for running STMV with NAMD.  STMV stands for Simulated Test Molecular.  See Slide 2.

In brief, one Tesla GPU is equivalent to 4 Quad Core CPU.  Our tests used Tesla C2075 with 448 cores, Pentium PG630 with 2 cores, Core i3 3220 with 4 Hyper-threads (2 cores), Xeon E3-1230V2 with 8 threads, and Core i7 3930K with 12 threads.  We have been able to confirm that the variations of CPU frequency, cores, and generation have some effect on the NAMD computation process; but the presence of Tesla has a much more significant effect than additional CPU cores or frequency or generation.   We ran NAMD on single precision floating point only and with Non ECC memory.  

The significance of our verification is that a Compucon HPC workstation fitted with a Tesla card can run NAMD like two Dual Xeon servers in terms of time to compute, and a Compucon HPC 4U workstation is equivalent to 8 Dual Xeon servers.  A research scientist can afford to have a Compucon HPC workstation at his desk and this was virtually impossible a year ago.

Like most other parallel processing application programs, NAMD runs on Linux and our tests were based on Ubuntu.  Visualisation of the NAMD process needs a separate program called VMD.  The visualisation we have obtained is simplified. See slide 3.

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