high performance computing on graphics processing units: hgpu.org

The Intel Xeon Phi coprocessor is a new choice for the high performance computing industry and it needs to be tested. In this thesis, we compared the difference in performance between the Xeon Phi and the GPU. The Smith-Waterman algorithm is a widely used algorithm for solving the sequence alignment problem. We implemented two versions of parallel Smith-Waterman algorithm for the Xeon Phi and GPU. Inspired by CUDA stream which enables concurrent kernel execution on Nvidia’s GPUs, we propose a socket based mechanism to enable concurrent task execution on the Xeon Phi. We then compared our socket implementation with Intel’s offload mode and with an Nvidia GPU. The results showed that our socket implementation performs better than the offload mode but is still not as good as the GPU.