Topology-Aware Parallel Molecular Dynamics Simulation Algorithm

We have developed the topology-aware parallel molecular dynamics (TAPMD) algorithm, in which the processors are rearranged automatically according to resource topology so as to minimize the cost required for the simulation. It is demonstrated that TAPMD can reduce the communication time to less than half compared to the time in the worst case on a distributed PC clusters. This improvement is expected to be more significant when the communication time is dominating over the total wall-clock time and when the resource topology consists of more types of the clusters. Additional tests involving several clusters having different types of connections as well as different types of processors are under progress