Lecture Notes in Computer Science 4917

Drug Design Issues on the Cell BE
Harald Servat 1 , Cecilia González-Alvarez 2 , Xavier Aguilar 1 ,
Daniel Cabrera-Benitez 2 , and Daniel Jiménez-González 2
1 Barcelona Supercomputing Center
2 Universitat Politècnica de Catalunya
Jordi Girona 1-3, Campus Nord-UPC, Modul C6, E-08034 Barcelona
harald.servat@bsc.es xavier.aguilar@bsc.es,
cecilia,dcabrera,djimenez@ac.upc.es
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.
1 Introduction
Protein-protein docking algorithms predict the structure alignment between two
or more proteins to form a complex, without the need of experimental measurements
at the laboratory. The computational cost of those algorithms is high
due to the large number of aspects to consider. There are three main types of
docking: flexible docking, rigid-body docking, and their combination. In this paper
we focus on the rigid-body docking, that consideres that the geometries of
the proteins are not modified when forming the complex. Rigid-body docking is
inadequate when there are several conformational changes during the complex
formation, but it is a very good baseline for flexible protein docking algorithms.
In particular, we focus on the fine- and coarse-grain parallelization of the
Fourier Transform Docking (FTDock) application [14,20] on a Cell processor.
We present experiment results using MPI, OpenMP, function offloading, and
vectorization. Note however that we do not intend to propose the fastest version
of the FTDock on a Cell BE blade. Our main objective is to show the performance
impact of different implementation and parallelization decisions that one
can take when porting code to a Cell BE blade.
P. Stenström et al. (Eds.): HiPEAC 2008, LNCS 4917, pp. 176–190, 2008.
c○ Springer-Verlag Berlin Heidelberg 2008