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Abstract.
We developed a multithreaded parallel implementation of a sequence alignment algorithm that is able to align whole genomes with reliable output and reasonable cost. This paper presents a performance evaluation of the whole genome comparison tool called ATGC – Another Tool for Genome Comparison, on a Hyper-Threading multiprocessor. We use our application to determine the system scalability for this particular type of sequence comparison algorithm and the improvement due to Hyper-Threading technology. The experimental results show that despite of placing a great demand on the memory system, the multithreaded code generated by Intel compiler yields to a 3.3 absolute speedup on a quad-processor machine, with parallelization guided by OpenMP pragmas. Additionally, a relatively high 1st level cache miss rate of 7-8% and a lack of memory bandwidth prevent logical processors with hyper-threading technology enabled from achieving further improvement.
This work was partially supported by NSF and DOE: NSF through the NGS program, grant 0103723; DOE grant DE-FC02-01ER25503.
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References
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Authors and Affiliations
Department of Electrical and Computer Engineering, University of Delaware, DE, 19716, Newark, USA
Juan del Cuvillo & Guang R. Gao
Intel Compiler Laboratory, SSG/EPG, Intel Corporation, 3600 Juliette Lane, CA, 95052, Santa Clara, USA
Xinmin Tian & Milind Girkar
- Juan del Cuvillo
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- Xinmin Tian
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- Guang R. Gao
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- Milind Girkar
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Editors and Affiliations
Department of Computer Science, University of California (UCI), 3019 Donald Bren Hall, 92697-3435, Irvine, CA, USA
Alex Veidenbaum
Department of Information and Computer Science, Faculty of Science, Nara women’s University, Kitauoyanishi-machi, Nara-city, 630-8506, Nara, Japan
Kazuki Joe
Keio University, Hiyoshi, Kohoku, Yokohama, 223–8522, Kanagawa, Japan
Hideharu Amano
Tokyo University of Technology, 1404-1 Katakura, Hachioji, 192-0982, Tokyo, Japan
Hideo Aiso
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del Cuvillo, J., Tian, X., Gao, G.R., Girkar, M. (2003). Performance Study of a Whole Genome Comparison Tool on a Hyper-Threading Multiprocessor. In: Veidenbaum, A., Joe, K., Amano, H., Aiso, H. (eds) High Performance Computing. ISHPC 2003. Lecture Notes in Computer Science, vol 2858. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39707-6_40
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