Optimization and Scaling of Multiple Sequence Alignment Software ClustalW on Intel Xeon Phi

This work is aimed to investigate and to improve the performance of multiple sequence alignment software ClustalW on the test platform EURORA at CINECA, for the case study of the influenza virus sequences. The objective is code optimization, porting, scaling and performance evaluation of parallel multiple sequence alignment software ClustalW for Intel Xeon Phi (the MIC architecture). For this purpose a parallel multithreaded optimization including OpenMP has been implemented and verified. The experimental results show that the hybrid parallel implementation utilizing MPI and OpenMP provides considerably better performance than the original code