To achieve scalable parallel performance in Molecular Dynamics Simulation, we have modeled and implemented several dynamic spatial domain decomposition algorithms. The modeling is based upon Valiant's Bulk Synchronous Parallel architecture model (BSP), which describes supersteps of computation, communication, and synchronization. We have developed prototypes that estimate the differing costs of several spatial decomposition algorithms using the BSP model. Our parallel MD implementation is not bound to the limitations of the BSP model, allowing us to extend the spatial decomposition algorithm. For an initial decomposition, we use one of the successful decomposition strategies from the BSP study, and then subsequently use performance data to adjust the decomposition, dynamically improving the load balance. We report our results here.
Nyland, L., Prins, J., Yun, R. H., Hermans, J., Kum, H. C., & Wang, L. (1998). Modeling dynamic load balancing in molecular dynamics to achieve scalable parallel execution. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 1457 LNCS, pp. 356–365). Springer Verlag. https://doi.org/10.1007/bfb0018552