Performance evaluation of a workstation cluster, TMC CM-5, and Intel Paragon/XP using a parallel homology analysis program
✍ Scribed by Satoko Sakata; Umpei Nagashima; Mitsuhisa Sato; Satoshi Sekiguchi; Haruo Hosoya
- Book ID
- 104304507
- Publisher
- Elsevier Science
- Year
- 1997
- Tongue
- English
- Weight
- 972 KB
- Volume
- 22
- Category
- Article
- ISSN
- 0167-8191
No coin nor oath required. For personal study only.
✦ Synopsis
In the homology analysis, required memory size and computing time proportionally increase with the square of the number of amino acids in protein. In order to expand the limit of size and to carry out analysis effectively, we parallelized for homology analysis program adopting the wavefront method with tiling. The performance of a workstation cluster, CM5, and Paragon was compared by using our program.
For performance evaluation of these machines, we have made a model of our parallel homology analysis computation. Using the model, we can understand the characteristics of these machines with respect to our program.
Execution time estimated by the execution model is in good agreement with the observation. The averaged error of the estimation to the observation on a workstation cluster, CM5, and Paragon are 0.1%. 5%, and 2%. Almost linear speed-up has been observed from 1PU to 2OPUs on them. The ratio of the performance of Paragon, CM5, and the workstation cluster is 1 : 0.38 : 0.22. This ratio is constant to the variety of the size of problem and the number of processors.