TY - GEN
T1 - Preliminary analysis of the cell BE processor limitations for sequence alignment applications
AU - Isaza, Sebastian
AU - Sánchez, Friman
AU - Gaydadjiev, Georgi
AU - Ramirez, Alex
AU - Valero, Mateo
PY - 2008
Y1 - 2008
N2 - The fast growth of bioinformatics field has attracted the attention of computer scientists in the last few years. At the same time the increasing database sizes require greater efforts to improve the computational performance. From a computer architecture point of view, we intend to investigate how bioinformatics applications can benefit from future multi-core processors. In this paper we present a preliminary study of the Cell BE processor limitations when executing two representative sequence alignment applications (Ssearch and ClustalW). The inherent large parallelism of the targeted algorithms makes them ideal for architectures supporting multiple dimensions of parallelism (TLP and DLP). However, in the case of Cell BE we identified several architectural limitations that need a careful study and quantification.
AB - The fast growth of bioinformatics field has attracted the attention of computer scientists in the last few years. At the same time the increasing database sizes require greater efforts to improve the computational performance. From a computer architecture point of view, we intend to investigate how bioinformatics applications can benefit from future multi-core processors. In this paper we present a preliminary study of the Cell BE processor limitations when executing two representative sequence alignment applications (Ssearch and ClustalW). The inherent large parallelism of the targeted algorithms makes them ideal for architectures supporting multiple dimensions of parallelism (TLP and DLP). However, in the case of Cell BE we identified several architectural limitations that need a careful study and quantification.
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U2 - 10.1007/978-3-540-70550-5_7
DO - 10.1007/978-3-540-70550-5_7
M3 - Conference contribution
AN - SCOPUS:50649101481
SN - 354070549X
SN - 9783540705499
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 53
EP - 64
BT - Embedded Computer Systems
T2 - 8th International Workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2008
Y2 - 21 July 2008 through 24 July 2008
ER -