State of the art Smith-Waterman implementations for Cell BE
Michael Farrar, None
29 September 2008
The CBESW is not the only Smith-Waterman implementation for the Cell Broadband Engine (Cell BE). The Cell BE, developed by Sony, Toshiba and IBM, is found in Sony’s PlayStation 3 (PS3). The speed reported for the CBESW on the PS3 is ~3.6 GCUPS with the ability to handle sequences less than 900 residues in length.
One of the first ports of the Smith-Waterman algorithm to the Cell BE was done by IBM[1]. The port was of Erik Lindhal’s Altivec code found in SSEARCH. This Wozniak implementation is able to handle sequences of 2000 residues in length with speeds of ~4.2 GCUPS.
Another recent paper[2] describes an Alpern implementation running on a PS3. This paper reports speeds approaching 9 GCUPS while able to handle sequences of 3000 residues in length. For optimal performance, the sequence database first needs to be sorted by sequence length.
The last paper[3] describes the port of the Striped Smith-Waterman to the Cell BE. This port achieves speeds of 12 GCUPS on a PS3 and is able to handle sequences of 32,000 residues.
[1] Sachdeva, V., Kistler, M., Speight, E. and Tzeng, T. K. (2007) Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications. In Proceedings of the 21st IEEE International Parallel and Distributed processing Symposium: Long Beach, California, March 26-30, 2007.
[2] Rudnicki, W. R., Jankowski, A., Modzelewski, A., Piotrowski, A., Zadrozny, A. (2008) Efficient implementation of the Smith Waterman algorithm on Cell processor. In Bioinformatics 2008 Conference: Warsaw, Poland, April 24-27, 2008.
State of the art Smith-Waterman implementations for Cell BE
29 September 2008
The CBESW is not the only Smith-Waterman implementation for the Cell Broadband Engine (Cell BE). The Cell BE, developed by Sony, Toshiba and IBM, is found in Sony’s PlayStation 3 (PS3). The speed reported for the CBESW on the PS3 is ~3.6 GCUPS with the ability to handle sequences less than 900 residues in length.
One of the first ports of the Smith-Waterman algorithm to the Cell BE was done by IBM[1]. The port was of Erik Lindhal’s Altivec code found in SSEARCH. This Wozniak implementation is able to handle sequences of 2000 residues in length with speeds of ~4.2 GCUPS.
Another recent paper[2] describes an Alpern implementation running on a PS3. This paper reports speeds approaching 9 GCUPS while able to handle sequences of 3000 residues in length. For optimal performance, the sequence database first needs to be sorted by sequence length.
The last paper[3] describes the port of the Striped Smith-Waterman to the Cell BE. This port achieves speeds of 12 GCUPS on a PS3 and is able to handle sequences of 32,000 residues.
[1] Sachdeva, V., Kistler, M., Speight, E. and Tzeng, T. K. (2007) Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications. In Proceedings of the 21st IEEE International Parallel and Distributed processing Symposium: Long Beach, California, March 26-30, 2007.
http://www.hicomb.org/HiCOMB2007/proceedings.html. Accessed 2008 Sep 18.
[2] Rudnicki, W. R., Jankowski, A., Modzelewski, A., Piotrowski, A., Zadrozny, A. (2008) Efficient implementation of the Smith Waterman algorithm on Cell processor. In Bioinformatics 2008 Conference: Warsaw, Poland, April 24-27, 2008.
https://bioinformatics2008.icm.edu.pl/web/guest/abstracts. Accessed 2008 Sep 18.
[3] Farrar, M. S. (2008) Optimizing Smith-Waterman for the Cell Broadband Engine.
http://farrar.michael.googlepages.com/smith-watermanfortheibmcellbe. Accessed 2008 Sep 18.
Competing interests
Author of "Optimizing Smith-Waterman for the Cell Broadband Engine."