Strategies to hide communication for a classical molecular dynamics proxy application
Issakar Ngatang, Masha Sosonkina · IEEE International Conference on High Performance Computing, Data, and Analytics · 2015
Co-designing applications and computer architectures has become of major importance due to the growing complexity of both applications and architectures and the need to better match application characteristics to the available hardware. Thus, mini-applications, which serve as proxies of large-scale ones by highlighting their most intensive parts and major workflow components, appeared to the co-design, tuning, and adaptation purposes. This paper presents a work on optimizing the communication subsystem of a classical MD proxy (CoMD) application executed on multi-core computing clusters. The research focuses on hiding communication with certain buffer handling operations. In particular, two strategies are presented: one that uses two parallel threads for communication and buffer handling and another that introduces more parallelism by allowing all the available threads to unload the buffers while using two thread to communicate, thereby improving load balancing. The first proposed strategy yields performance gains up to 61% in the communication routines, corresponding to 6% gains in the overall time, while the second strategy achieves, respectively, about 73% and 6.3% improvement.