Implementing a parallel molecular dynamics as a parallel application presents some unique load balancing challenges. Non-uniform distribution of atoms in space, along with the need to avoid symmetric redundant computations, produces a highly irregular computational load. Scalability and efficiency considerations produce further irregularity. Also, as the simulation evolves, the movement of atoms causes changes in the load distributions. This paper describes the use of an object-based, measurement-based load balancing strategy for a parallel molecular dynamics application, and its impact on performance.
Kalé, L. V., Bhandarkar, M., & Brunner, R. (1998). Load balancing in parallel molecular dynamics. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 1457 LNCS, pp. 251–261). Springer Verlag. https://doi.org/10.1007/bfb0018544