An energy‐aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures. (27th July 2015)

• Record Type: Journal Article
• Authors: Rucci, Enzo; García, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto‐Matías, Manuel
• Is Part Of: Concurrency and computation. Volume 27:Number 18(2015:Dec.)
• Page Start: 5517
• Page End: 5537
• Publication Date: 2015-07-27
• Subjects: Bioinformatics -- Smith–Waterman -- HPC -- Intel Xeon Phi -- heterogeneous computing -- power consumption; Parallel processing (Electronic computers) -- Periodicals; Parallel computers -- Periodicals; 004.35
• DOI: 10.1002/cpe.3598
• Languages: English
• ISSNs: 1532-0626

Abstract

Summary: Alignment is essential in many areas such as biological, chemical and criminal forensics. The well‐known Smith–Waterman (SW) algorithm is able to retrieve the optimal local alignment with quadratic time and space complexity. There are several implementations that take advantage of computing parallelization, such as manycores, FPGAs or GPUs, in order to reduce the alignment effort. In this research, we adapt, develop and tune the SW algorithm named SWIMM on a heterogeneous platform based on Intel's Xeon and Xeon Phi coprocessor. SWIMM is a free tool available in a public git repository https://github.com/enzorucci/SWIMM . We efficiently exploit data and thread‐level parallelism, reaching up to 380 GCUPS on heterogeneous architecture, 350 GCUPS for the isolated Xeon and 50 GCUPS on Xeon Phi. Despite the heterogeneous implementation obtaining the best performance, it is also the most energy‐demanding. In fact, we also present a trade‐off analysis between performance and power consumption. The greenest configuration is based on an isolated multicore system that exploits AVX2 instruction set architecture reaching 1.5 GCUPS/Watts. Copyright © 2015 John Wiley & Sons, Ltd.