Performance analysis and improvement of parallel molecular dynamics algorithm based on OpenMP
Sun Shi-xin · Journal of Computer Applications · 2012
To enhance the computing speed of the molecular dynamics simulations on the shared memory servers,the performance of parallel molecular dynamics program based on Open Multi-Processing(OpenMP) approach with the critical section method was analyzed and improved.After testing performance on a multi-core server,as well as the calculations of speedup and parallel efficiency,an optimized triangle method was developed.In this method,stationary atom sets were assigned to threads respectively,and the number of atoms increased stepwise,which made the threads arrive at critical sections at different time.The triangle method can efficiently halve the idle time in critical sections and therefore can significantly enhance the parallel performance.