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

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 vow large number of threads. As a result, we demonstrate that this class of applications can execute efficiently on a large cellular machine.