Drug design issues on the cell BE

Authors:
Harald Servat;Cecilia González-Alvarez;Xavier Aguilar;Daniel Cabrera-Benitez;Daniel Jiménez-González
Affiliations:
Barcelona Supercomputing Center, Barcelona;Universitat Politècnica de Catalunya;Barcelona Supercomputing Center, Barcelona;Universitat Politècnica de Catalunya;Universitat Politècnica de Catalunya
Venue:
HiPEAC'08 Proceedings of the 3rd international conference on High performance embedded architectures and compilers
Year:
2008

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Abstract

Structure alignment prediction between proteins (protein docking) is crucial for drug design, and a challenging problem for bioinformatics, pharmaceutics, and current and future processors due to it is a very time consuming process. Here, we analyze a well known protein docking application in the Bioinformatic field, Fourier Transform Docking (FTDock), on a 3.2GHz Cell Broadband Engine (BE) processor. FTDock is a geometry complementary approximation of the protein docking problem, and baseline of several protein docking algorithms currently used. In particular, we measure the performance impact of reducing, tuning and overlapping memory accesses, and the efficiency of different parallelization strategies (SIMD, MPI, OpenMP, etc.) on porting that biomedical application to the Cell BE. Results show the potential of the Cell BE processor for drug design applications, but also that there are important memory and computer architecture aspects that should be considered.