A load balancing algorithm for Molecular Dynamics simulations

This report describes a prototype load balancing algorithm designed to improve the efficiency of molecular dynamics simulations, specifically those in which the system under study is characterised by large spatial variations in atom density. At root the parallelisation scheme used in the load balancer is similar to the widely used domain decomposition scheme, however each domain is further subdivided into a number of cells. The coordinates of the atoms within cells can be reallocated from processors with a heavy work load to ones with more modest work loads to effect a more even work distribution. The prototype load balancing algorithm is based around a rudimentary MD time stepping loop in which only 2-body interactions are considered and the atom trajectories are non-physical. The intention here was to provide a simple framework on which to develop and test the basic algorithm. The results of performance tests carried out on HECToR are encouraging, with good speed ups observed for a number of simple test systems. The largest test run consisted of some 5 million atoms run on a maximum of 2744 cores. The prototype load balancer code as it stands provides a good basis for understanding how the performance of the algorithm is affected by various operational parameters. However further work is necessary to integrate the algorithm into DL_POLY_4, a long standing, general purpose MD package with a wide user base. This is the ultimate aim of the project and the ultimate test for the load balancing algorithm. If this can be achieved it is hoped that the improved performance conferred by the load balancing will enable users to obtain results in a shorter time frame and to make better use of the resources on which they run their jobs.