Demonstrating the scalability of a molecular dynamics application on a Petaflop computer

ABSTRACT

The IBM Blue Gene project has endeavored into the development of a cellular architecture computer with millions of concurrent threads of execution. One of the major challenges of this project is demonstrating that applications can successfully exploit this massive amount of parallelism. Starting from the sequential version of a well known molecular dynamics code, we developed a new application that exploits the multiple levels of parallelism in the Blue Gene cellular architecture. We perform both analytical and simulation studies of the behavior of this application when executed on a very large number of threads. As a result, we demonstrate that this class of applications can execute efficiently on a large cellular machine.

REFERENCES

• 1: M. P. Allen , D. J. Tildesley, Computer simulation of liquids, Clarendon Press, New York, NY, 1988
• 2: The Blue Gene project. http://www.research.ibm.com/bluegene.
• 3: B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. Charmm: A program for macromolecular energy minimization, and dynamics calculations. J. Comput. Chem., 4:187-217, 1983.
• 4: P. Ewald. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys., 64:253-287, 1921.
• 5: Y. Kang, M. Huang, S.-M. Yoo, Z. Ge, D. Keen, V. Lam, P. Pattnaik, and J. Torrellas. FlexRAM: Toward an advanced intelligent memory system. In International Conference on Computer Design (ICCD), October 1999.
• 6: P. B. Moore. CM3D CMM MD Code. http://www.cmm.upenn.edu/~moore/code/code.html.
• 7: D. Patterson, T. Anderson, N. Cardwell, R. Fromm, K. Keeton, C. Kozyrakis, R. Thomas, and K. Yelick. A case for intelligent RAM: IRAM. In Proceedings of IEEE Micro, April 1997.
• 8: Steve Plimpton, Fast parallel algorithms for short-range molecular dynamics, Journal of Computational Physics, v.117 n.1, p.1-19, March 1, 1995 [doi>10.1006/jcph.1995.1039]
• 9: L. R. Scolnick, A. M. Clements, J. Liao, L. Crenshaw, M. Hellberg, J. May, T. R. Dean, and D. W. Christianson. Novel binding mode of hydroxamate inhibitors to human carbonic anhydrase II. J. Am. Chem. Soc., 119:850-851, 1997.
• 10: T. Sterling et al. Hybrid technology multithreaded. http://htmt.jpl.nasa.gov.
• 11: Valerie E. Taylor , Rick L. Stevens , Kathryn E. Arnold, Parallel molecular dynamics: implications for massively parallel machines, Journal of Parallel and Distributed Computing, v.45 n.2, p.166-175, Sept. 15, 1997 [doi>10.1006/jpdc.1997.1370]
• 12: J. Torrellas, L. Yang, and A.-T. Nguyen. Toward a cost-effective DSM organization that exploits processor-memory integration. In Sixth International Symposium on High-Performance Computer Architecture, January 2000.
• 13: M. E. Tuckerman and B. J. Berne. Molecular dynamics in systems with multiple time scales. J. Comp. Chem., 95:8362-8364, May 1992.
• 14: M. E. Tuckerman, B. J. Berne, and G. J. Martyna. Reversible multiple time scale molecular dynamics. J. Chem. Phys.,, 97:1990-2001, 1992.
• 15: L. Verlet. Computer experiments on classical fluids. I. thermodynamical properties of Lennard-Jones molecules. Phys. Rev., 159:98-103, 1967.

INDEX TERMS

Primary Classification:
  G. Mathematics of Computing
  G.1 NUMERICAL ANALYSIS

Additional Classification:
  J. Computer Applications

General Terms:
Design, Performance

Keywords:
Blue Gene, cellular architecture, massively parallel computing, molecular dynamics, performance evaluation