Demonstrating the Scalability of a Molecular Dynamics Application on a Petaflops Computer

The IBM Blue Gene/C parallel computer aims to demonstrate the feasibility of a cellular architecture computer with millions of concurrent threads of execution. One of the major challenges in this project is showing that applications can successfully scale to this massive amount of parallelism. In this paper we demonstrate that the simulation of protein folding using classical molecular dynamics falls in this category. Starting from the sequential version of a well known molecular dynamics code, we developed a new parallel implementation that exploited the multiple levels of parallelism present in the Blue Gene/C cellular architecture. We performed 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.

[1]  L. Verlet.  Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[2]  Luiz André Barroso,et al.  Piranha: a scalable architecture based on single-chip multiprocessing , 2000, Proceedings of 27th International Symposium on Computer Architecture (IEEE Cat. No.RS00201).

[3]  Allan Snavely,et al.  DATA INTENSIVE VOLUME VISUALIZATION ON THE TERA MTA AND CRAY T � , 1999 .

[4]  Frederic T. Chong,et al.  Active pages: a computation model for intelligent memory , 1998, ISCA.

[5]  Dean M. Tullsen,et al.  Simultaneous multithreading: Maximizing on-chip parallelism , 1995, Proceedings 22nd Annual International Symposium on Computer Architecture.

[6]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[7]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[8]  Jaewook Shin,et al.  Mapping Irregular Applications to DIVA, a PIM-based Data-Intensive Architecture , 1999, ACM/IEEE SC 1999 Conference (SC'99).

[9]  Thomas Sterling,et al.  The Gilgamesh processor-in-memory architecture and its execution model , 2001 .

[10]  Dean M. Tullsen,et al.  Simultaneous multithreading: a platform for next-generation processors , 1997, IEEE Micro.

[11]  Valerie E. Taylor,et al.  Parallel Molecular Dynamics: Implications for Massively Parallel Machines , 1997, J. Parallel Distributed Comput..

[12]  Mark E. Tuckerman,et al.  Reversible multiple time scale molecular dynamics , 1992 .

[13]  Josep Torrellas,et al.  Toward a cost-effective DSM organization that exploits processor-memory integration , 2000, Proceedings Sixth International Symposium on High-Performance Computer Architecture. HPCA-6 (Cat. No.PR00550).

[14]  William J. Dally,et al.  A bandwidth-efficient architecture for media processing , 1998, Proceedings. 31st Annual ACM/IEEE International Symposium on Microarchitecture.

[15]  P.M. Kogge,et al.  Pursuing a petaflop: point designs for 100 TF computers using PIM technologies , 1996, Proceedings of 6th Symposium on the Frontiers of Massively Parallel Computation (Frontiers '96).

[16]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[17]  Larry A. Bergman,et al.  A design analysis of a hybrid technology multithreaded architecture for petaflops scale computation3 , 1999, ICS '99.

[18]  Katherine Yelick,et al.  A Case for Intelligent RAM: IRAM , 1997 .

[19]  P. P. Ewald.  Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .

[20]  David W. Christianson,et al.  Novel Binding Mode of Hydroxamate Inhibitors to Human Carbonic Anhydrase II , 1997 .

[21]  Vivek Sarkar,et al.  Baring It All to Software: Raw Machines , 1997, Computer.

[22]  Ajay K. Royyuru,et al.  Blue Gene: A vision for protein science using a petaflop supercomputer , 2001, IBM Syst. J..