David A. Bader
IEEE Fellow
AAAS Fellow
College of Computing
Georgia Tech
Atlanta, GA 30332



Evaluating Cell/B.E Software Cache for ClustalW

This paper evaluates the performance of the bioinformatics application ClustalW developed on Cell Broadband Engine(TM) (Cell/B.E.) using a software data cache for SPEs, instead of explicit DMA transfers. The software cache of the SPEs, once it has been configured, provides the capability to access main memory with data-transfer functions that override the need for DMA commands. ClustalW exhibits high spatial locality but little temporal locality. We compare performance of ClustalW with a previous version that uses explicit DMA transfers as a means of communication with the system memory, and provide analysis and results of our comparison.

Publication History

Versions of this paper appeared as:
  1. V. Sachdeva, M. Kistler, and D.A. Bader ``Evaluating Cell/B.E. Software Cache for ClustalW,'' The IEEE International Symposium on Circuits and Systems (ISCAS 2010), Paris, France, May 31 - June 2, 2010.

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Last updated: June 1, 2012


Computational Biology

Parallel Computing