Performance Optimization of a Molecular Dynamics Code Based on Computational Caching
Xiaolin Cao · Computer Engineering and Science · 2009
The codes of molecular dynamics always run in a low performance manner,and achieve only several percents of the peak performance on modern supercomputers. In this paper,we optimize the program PMD3D on the Shenteng 6800 supercomputer. By performance analysis,we obtain that the dependence of the long-latency operations heavily influences the parallel efficiency of instructions. Based on the analysis,we optimize the codes,cache the amount irregular computations,and compute them vectorially. We achieve 32.3% of the peak performance and 4×speedups on the Itanium 2 processor. Finally,we test the program on the Shenteng 6800 with 256 CPUs in 64 nodes,and achieve 27% of the peak performance 1.3TFlops.