Research of asynchronous algorithm for molecular dynamics task on the PDCS “Buran” models
Лев Соломонович Ходош, A. V. Klimov, N. N. Levchenko, A.S. Okunev, D.N. Zmejev · 2016
Molecular dynamics (MD) task scales poorly due to the global barriers used to maintain neighbour lists. The paper presents the asynchronous algorithm for MD task simulation free from this drawback. The experiments with MD on various models of parallel dataflow computing system (PDCS) “Buran ” also presented. Synchronization in this algorithm relies solely on the local interactions between the cores responsible for nearby areas. The paper describes a series of experiments with MD task on cycle-accurate and behaviour block-register models as well as on PDCS emulator (on cluster) which allow to re-assessing capabilities of the created computing system. Scalability for the tasks with equal size on PDCS will be by one-two orders higher than on the traditional systems. Furthermore, the research has shown the possibility to create the simple version of basic algorithm, from which can be derived the more efficient completely asynchronous algorithm based on counting of the transmitted particles.