Parallel Smith Waterman with Unified Parallel C on Sun T1 processor

The machine used was a Sun T2000. The algorithm is a traditional smith waterman parallelized through a wave-front mechanism. In order to improve cache utilization the matrix was transposed to allow for more "horizontal" accesses (lessens cache line sharing). Alpha defines data distribution, workload distribution is a quotient of Alpha and Beta. This work was done by myself and Mohammad Bakhouya (bakhouya@gmail.com).