Pairwise alignments on the cell processor

ABSTRACT

We are evaluating the performance of bioinformatics applications on the CBE recently developed at IBM. The characteristics of pairwise alignment, critical to bioinformatics applications, makes it uniquely suitable for the Cell processor. We have implemented two different strategies for pairwise alignment on Cell. We analyze the bottlenecks for each strategy, a diagonal approach which uses the vector processing capabilities of the SPE and a row wise approach in which cells are dependant and has expensive branches. Despite the presence of branches, the row-wise approach outperforms a 2.4 Ghz Opteron by almost 5X, the diagonal approach spending a majority of time looking up the alignment matrix.Also, due to the commonality of all-to-all pairwise comparisons in bioinformatics codes, we have implemented a framework for these computations on the Cell with minimum load imbalance and minimal PPU intervention. We evaluate the performance of popular bioinformatics codes Clustalw and HMMER using such a framework, in which the workload is shared among the PPU and the SPUs.

INDEX TERMS

Primary Classification:
  C. Computer Systems Organization
  C.5 COMPUTER SYSTEM IMPLEMENTATION
      C.5.1 Large and Medium ("Mainframe") Computers
          Subjects: Super (very large) computers

Additional Classification:
  C. Computer Systems Organization
  C.1 PROCESSOR ARCHITECTURES
      C.1.2 Multiple Data Stream Architectures (Multiprocessors)
          Subjects: Array and vector processors
      C.1.4 Parallel Architectures

General Terms:
Design