Analysis and Performance Results of a Molecular Modeling Application on Merrimac

Mattan Erez, Jung Ho Ahn, Ankit Garg, William J. Dally, and Eric Darve

in Proceedings of the SC'04 Conference, Novemeber 2004, Pittsburgh, Pennsylvania, USA

Abstract:

The Merrimac supercomputer uses stream processors and a high-radix network to achieve high performance at low cost and low power. The stream architecture matches the capabilities of modern semiconductor technology with compute-intensive parallel applications. We present a detailed case study of porting the GROMACS molecular-dynamics force calculation to Merrimac. The characteristics of the architecture which stress locality, parallelism, and decoupling of memory operations and computation, allow for high performance of compiler optimized code. The rich set of hardware memory operations and the ample computation bandwidth of the Merrimac processor present a wide range of algorithmic trade-offs and optimizations which may be generalized to several scientific computing domains. We use a cycle-accurate hardware simulator to analyze the performance bottlenecks of the various implementations and to measure application run-time. A comparison with the highly optimized GROMACS code, tuned for an Intel Pentium 4, confirms Merrimac's potential to deliver high performance.

Paper:

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BibTeX:

@conference{ref:streammd,    author = {Mattan Erez and {Jung Ho} Ahn and Ankit Garg and William J. Dally and Eric Darve},
   title = {{Analysis and Performance Results of a Molecular Modeling Application on Merrimac}},
   booktitle = {{SC}'04},
   year = {2004},
   address = {Pittsburgh, Pennsylvaniva},
   month = {November}
}