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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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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DOI: https://doi.org/10.1007/978-3-540-39707-6_40
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