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.
