DocumentCode :
3359878
Title :
HMMer-Cell: High Performance Protein Profile Searching on the Cell/B.E. Processor
Author :
Lu, Jizhu ; Perrone, Michael ; Albayraktaroglu, Kursad ; Franklin, Manoj
Author_Institution :
T. J. Watson Res. Center, IBM, Yorktown Heights, NY
fYear :
2008
fDate :
20-22 April 2008
Firstpage :
223
Lastpage :
232
Abstract :
This paper presents HMMer-Cell, an implementation of the computationally intensive bioinformatics application HMMER on the Cell/B.E. multiprocessor architecture. The core of the HMMER workload is the Plan7 Viterbi algorithm, which has a memory requirement of O(N*M) where N is the length of the HMM and M is the length of the input sequence length. The main challenge in implementing the Plan7 Viterbi algorithm on the novel Cell/B.E. multiprocessor is the limited local storage space of the Cell/B.E. SPEs (synergistic processing element). We describe our approach to modifying the Viterbi algorithm to reduce the space complexity from 0(M*N) to O(N). We then proceed to discuss design considerations such as task parallelization and code partitioning, in addition to other optimizations we used to implement HMMer-Cell. We demonstrate near-linear speedup when processing relatively larger HMM profiles; and compare our results to those obtained on commodity x86 processors.
Keywords :
biology computing; cellular biophysics; computational complexity; multiprocessing systems; Cell/B.E. multiprocessor architecture; HMMer-Cell; Plan7 Viterbi algorithm; code partitioning; commodity x86 processor; computationally intensive bioinformatics; memory requirement; protein; space complexity; synergistic processing element; task parallelization; Bioinformatics; Computer applications; Computer architecture; Educational institutions; Engines; Hidden Markov models; Microprocessors; Proteins; Sequences; Viterbi algorithm;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Performance Analysis of Systems and software, 2008. ISPASS 2008. IEEE International Symposium on
Conference_Location :
Austin, TX
Print_ISBN :
978-1-4244-2232-6
Electronic_ISBN :
978-1-4244-2233-3
Type :
conf
DOI :
10.1109/ISPASS.2008.4510754
Filename :
4510754
Link To Document :
بازگشت