Biobench: A benchmark suite of bioinformatics applications

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Biobench: A benchmark suite of bioinformatics applications (2005)

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by Kursad Albayraktaroglu , Aamer Jaleel , Xue Wu , Manoj Franklin , Bruce Jacob , Chau-wen Tseng , Donald Yeung

Venue:	in Proceedings of the International Symposium on Performance Analysis of Systems and Software
Citations:	53 - 4 self

BibTeX

@INPROCEEDINGS{Albayraktaroglu05biobench:a,
    author = {Kursad Albayraktaroglu and Aamer Jaleel and Xue Wu and Manoj Franklin and Bruce Jacob and Chau-wen Tseng and Donald Yeung},
    title = {Biobench: A benchmark suite of bioinformatics applications},
    booktitle = {in Proceedings of the International Symposium on Performance Analysis of Systems and Software},
    year = {2005},
    pages = {2--9}
}

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Abstract

edu 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 †Dept. of Computer Science,

Keyphrases

bioinformatics application benchmark suite spec int crucial area computer architecture community mentioned spec suite gene-based therapy diverse set different application domain common bioinformatics application scant attention spec fp benchmark application domain computer science common set drug discovery genetic data expand edu recent advance mature genomics application load store instruction spec fp application first version bioinformatics benchmark point operation content clear importance computational power real processor first step genetic data microarchitectural design different characteristic vast amount basic execution characteristic significant increase particular emphasis

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