Modeling dynamic load balancing in molecular dynamics to achieve scalable parallel execution [chapter]

Lars Nyland, Jan Prins, Ru Huai Yun, Jan Hermans, Hye-Chung Kum, Lei Wang
1998 Lecture Notes in Computer Science  
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
more » ... und 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.
doi:10.1007/bfb0018552 fatcat:evotkoeo4zccdi7ui7nam5kspe