Tom Van Court

FPGA Acceleration of Rigid Molecule Interactions

Modeling of molecule interactions often uses rigid models and correlation techniques, either in early screening passes or as steps within more complex models. Even rigid models are time-consuming when applied to large models at 10 3 - 10 5 different three-axis rotations. This paper presents an FPGA structure for performing the correlations efficiently using a systolic array for 3-D correlation and an addressing technique for low-overhead rotation of a 3-D voxel models around three axes. We find a 200 × speedup in our FPGA implementation compared to the standard transform-based method.

Elements of High-Performance Reconfigurable Computing

Abstract Numerous application areas, including bioinformatics and computational biology (BCB), demand increasing amounts of processing capability. In many cases, the computation cores and data types are suited to field‐programmable gate arrays (FPGAs). The challenge is identifying those design techniques that can extract high performance from the FPGA fabric while allowing efficient development of production‐worthy program codes. After brief introductions to high‐performance reconfigurable computing (HPRC) systems and some applications for which they are well suited, we present a dozen such techniques together with examples of their use in our own research in BCB. Each technique, if ignored in a naive implementation, would have cost at least a factor 2 in performance, with most saving a factor of 10 or more. We follow this by comparing HPRC with an alternative accelerator technology, the use of graphics processors for general‐purpose computing (GPGPU). We conclude with a discussion of some implications for future HPRC development tools.