A. James Clark School of Engineering

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Author: search.filters.author.Albayraktaroglu, Kursad

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    BioBench: A Benchmark Suite of Bioinformatics Applications
    (2005-03) Albayraktaroglu, Kursad; Jaleel, Aamer; Wu, Xue; Franklin, Manoj; Jacob, Bruce; Tseng, Chau-Wen; Yeung, Donald
    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.
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    Characterizing and Accelerating Bioinformatics Workloads on Modern Microarchitectures
    (2007-04-25) Albayraktaroglu, Kursad; Franklin, Manoj; Electrical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Bioinformatics, the use of computer techniques to analyze biological data, has been a particularly active research field in the last two decades. Advances in this field have contributed to the collection of enormous amounts of data, and the sheer amount of available data has started to overtake the processing capability possible with current computer systems. Clearly, computer architects need to have a better understanding of how bioinformatics applications work and what kind of architectural techniques could be used to accelerate these important scientific workloads on future processors. In this dissertation, we develop a bioinformatic benchmark suite and provide a detailed characterization of these applications in common use today from a computer architect's point of view. We analyze a wide range of detailed execution characteristics including instruction mix, IPC measurements, L1 and L2 cache misses on a real architecture; and proceed to analyze the workloads' memory access characteristics. We then concentrate on accelerating a particularly computationally intensive bioinformatics workload on the novel Cell Broadband Engine multiprocessor architecture. The HMMER workload is used for protein profile searching using hidden Markov models, and most of its execution time is spent running the Viterbi algorithm. We parallelize and partition the HMMER application to implement it on the Cell Broadband Engine. In order to run the Viterbi algorithm on the 256KB local stores of the Cell BE synergistic processing units (SPEs), we present a method to develop a fast SIMD implementation of the Viterbi algorithm that reduces the storage requirements significantly. Our HMMER implementation for the Cell BE architecture, Cell-HMMER, exploits the multiple levels of parallelism inherent in this application, and can run protein profile searches up to 27.98 times faster than a modern dual-core x86 microprocessor.