Abstract: The Partitioned Global Address Space (PGAS) programming
paradigm offers ease-of-use in expressing parallelism
through a global shared address space while emphasizing performance
by providing locality awareness through the partitioning of
this address space. Therefore, the interest in PGAS programming
languages is growing and many new languages have emerged and
are becoming ubiquitously available on nearly all modern parallel
architectures. Recently, new parallel machines with multiple cores
are designed for targeting high performance applications. Most of the
efforts have gone into benchmarking but there are a few examples of
real high performance applications running on multicore machines.
In this paper, we present and evaluate a parallelization technique
for implementing a local DNA sequence alignment algorithm using
a PGAS based language, UPC (Unified Parallel C) on a chip
multithreading architecture, the UltraSPARC T1.