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ISHPC
2003
Springer

Performance Study of a Whole Genome Comparison Tool on a Hyper-Threading Multiprocessor

11 years 6 months ago
Performance Study of a Whole Genome Comparison Tool on a Hyper-Threading Multiprocessor
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 hyperthreading technology enabled from achieving further improvement.
Juan del Cuvillo, Xinmin Tian, Guang R. Gao, Milin
Added 07 Jul 2010
Updated 07 Jul 2010
Type Conference
Year 2003
Where ISHPC
Authors Juan del Cuvillo, Xinmin Tian, Guang R. Gao, Milind Girkar
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