PBB

Abstract

Bioinformatics applications are widely used in life science and medicine industry where the demand on high performance computing system is increasing rapidly. It is very important to understand the characteristics of bioinformatics applications for both end-users and computer system designers. With the advent of mutlticore processors, it is also critical to know how well can multicore processors speedup bioinformatics applications. Although some bioinformatics benchmarks have been proposed, they cover limited application domains and most of them are serial codes. As a result, the analysis based on these benchmarks needs further examination with broader range of bioinformatics applications and it is indispensable to have a parallel bioinformatics benchmark set for shared memory multi-processors. This paper presents PBB, a Parallel Bioinformatics Benchmark suite for shared memory processors. The benchmark suite is a collection of seven bioinformatics applications, which covers seven most important bioinformatics domains, such as sequence alignment, phylogenetic analysis, gene regulatory network learning, single nucleotide polymorphisms study and protein structure prediction. All of the applications have been parallelized with OpenMP except the NCBI BLAST , which was parallelized with the Pthread library. We characterize the PBB on a real system and compare it with SPEC CPU2000 INT and FP. The results confirm and disprove some previous conclusion on bioinformatics workloads. Especially we disprove the claim in previous literature that ”floating point operations are negligible”. Performance results on several shared memory multiprocessors with PBB are also presented and analyzed. Six out of seven PBB applications show satisfactory speedup up to 16 threads. HyperThreading techniques could provide modest speed up on PBB. Overall, the results of characterization and analysis of PBB suggest that multi-core processors could be used to support parallel bioinformatics workloads Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. ATIP 3rd China HPC Workshop , November 11, 2007, Reno, NV Copyright 2007 ACM ISBN 978-1-59593-903-6/11/07...$5.00 effectively.