BioBench: A Benchmark Suite of Bioinformatics Applications

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Albayraktaroglu, Kursad
Jaleel, Aamer
Wu, Xue
Franklin, Manoj
Jacob, Bruce
Tseng, Chau-Wen
Yeung, Donald
"BioBench: A benchmark suite of bioinformatics applications." Kursad Albayraktaroglu, Aamer Jaleel, Xue Wu, Manoj Franklin, Bruce Jacob, Chau-Wen Tseng, and Donald Yeung. Proc. 2005 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS 2005), pp. 2-9. Austin TX, March 2005.
Recent advances in bioinformatics and the significant increase in computational power available to researchers have made it possible to make better use of the vast amounts of genetic data that has been collected over the last two decades. As the uses of genetic data expand to include drug discovery and development of gene-based therapies, bioinformatics is destined to take its place in the forefront of scientific computing application domains. Despite the clear importance of this field, common bioinformatics applications and their implication on microarchitectural design have received scant attention from the computer architecture community so far. The availability of a common set of bioinformatics benchmarks could be the first step to motivate further research in this crucial area. To this end, this paper presents BioBench, a benchmark suite that represents a diverse set of bioinformatics applications. The first version of BioBench includes applications from different application domains, with a particular emphasis on mature genomics applications. The applications in the benchmark are described briefly, and basic execution characteristics obtained on a real processor are presented. Compared to SPEC INT and SPEC FP benchmarks, applications in BioBench display a higher percentage of load/store instructions, almost negligible floating point operation content, and higher IPC than either SPEC INT and SPEC FP applications. Our evaluation suggests that bioinformatics applications have distinctly different characteristics from the applications in both of the mentioned SPEC suites; and our findings indicate that bioinformatics workloads can benefit from architectural improvements to memory bandwidth and techniques that exploit their high levels of ILP. The entire BioBench suite and accompanying reference data will be made freely available to researchers.