Accelerating pairwise statistical significance estimation using NUMA machine
Yuhong Zhang, Fan Zhou, Jianping Gou, Hua Xiao, Zhiguang Qin, Ankit Kumar Agrawal · Journal of Computer Information Systems · 2012
Pairwise statistical significance (PSS) has been found as a promising alternative to database statistical significance for homology detection. However, the estimation of PSS is both computationally and data intensive, which poses a big challenge on performance and scalability in terms of distributed computations. In this work, we develop the parallel accelerator for the estimation of PSS using NonUniform Memory Acess (NUMA) machine, which is implemented in C++ using OpenMP, MPI and hybrid paradig-ms, respectively. Through distributing the computation kernels of the estimation of PSS procedure across multiple cores, we achieve up to 22:65× speedup using 24 CPU cores compared to sequential implementation.