Locality and parallelism optimization for dynamic programming algorithm in bioinformatics
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
An experimental study of optimizing bioinformatics applications
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
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The exponential growth in the amount of genomic information has spurred growing interest in large scale analysis of genetic data. Bioinformatics applications represent the increasingly important workloads. However, very few results on the behavior of these applications running on the state-of-the-art microprocessor and systems have been published. This paper proposes a suite of widely used bioinformatics applications and studies the execution characteristics of these benchmarks on a representative architecture - the Intel Pentium 4. To understand the impacts and implications of bioinformatics workloads on the microprocessor designs, we contrast the characteristics of bioinformatics workloads and the widely used SPEC 2000 integer benchmarks. The proposed bioinformatics benchmark suite as well as the input datasets can be downloaded from the following website: http://www.ideal.ece.ufl.edu/BioInfoMark.