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 it is demonstrated 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, a new parallel implementation was developed that exploited the multiple levels of parallelism present in the Blue Gene/C cellular architecture. Both analytical and simulation studies were performed of the behavior of this application when executed on a very large number of threads. As a result, it is demonstrated that this class of applications can execute efficiently on a large cellular machine.