PBB: A Parallel Bioinformatics Benchmark Suite

PBB is a parallel bioinformatics benchmark suite which contains seven representative programs covering several most important fields in Bioinformatics. These benchmark programs have been parallelized using either OpenMP or Pthread. Since most of the original programs are not parallelized, we did the parallelization ourselves.

We perform experiments on several different systems in order to achieve better understanding of the programs. The characterization of the programs confirms the assumption that the bioinformatics programs have high percentage of load/store instructions , but also controdicts with a former conclusion that these programs contain negligible floating-point instructions.

We also examined the speedup of the programs on different systems. Most of the programs show satisfactory speedup up to 16 processors.

The entire benchmark suite can be downloaded from: benchmark download

Here is our paper and presentation published in 3rd ATIP: paper ppt