Optimizing LeanMD on Blue Gene/L Machine

We have taken leanMD, a molecular dynamics application developed at PPL, and tried to optimize its performance on the Blue Gene architecture. We examined the sequential and parallel performance of leanMD both in terms of execution time and memory usage. We identified the hot spots which restrict sequential performance. To boost parallel performance, we attempted to optimize the calculation of long range electrostatic forces and used topology aware mapping to reduce communication on the Blue Gene torus network. We obtained a significant reduction in the memory usage and a small reduction in the execution time.