Synthesis, structure and power of systolic computations

AbstractA variety of problems related to systolic architectures, systems, models and computations are discussed. The emphases are on theoretical problems of a broader interest. Main motivations and interesting/important applications are also presented. The first part is devoted to problems related to synthesis, transformations and simulations of systolic systems and architectures. In the second part, the power and structure of tree and linear array computations are studied in detail. The goal is to survey main research directions, problems, methods and techniques in not too formal a way

Nonacceptability criteria and closure properties for the class of languages accepted by binary systolic tree automata

AbstractIn this paper a contribution is given to the solution of the problem of finding an inductive characterization of the class of languages accepted by binary systolic tree automata, L(BSTA), in terms of the closure of a class of languages with respect to certain operations. It is shown that L(BSTA) is closed with respect to some new operations: selective concatenation, restricted concatenation and restricted iteration. The known nonclosure of L(BSTA) with respect to classical language operations, like concatenation and Kleene iteration is proved here by using a new nonacceptability criterion

Parallelization of dynamic programming recurrences in computational biology

The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained parallelism in dynamic programming kernels using field-programmable gate arrays: FPGAs). We advocate a high-level synthesis approach, using the recurrence equation abstraction to represent dynamic programming and polyhedral analysis to exploit parallelism. We suggest a novel technique within the polyhedral model to optimize for throughput by pipelining independent computations on an array. This design technique improves on the state of the art, which builds latency-optimal arrays. We also suggest a method to dynamically switch between a family of designs using FPGA reconfiguration to achieve a significant performance boost. We have used polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four Xilinx Virtex 4 FPGAs outperforms 198 3 GHz Intel Core 2 Duo processors. Furthermore, our design running on a single FPGA is an order of magnitude faster than competing implementations on similar-generation FPGAs and graphics processors. Our work is a step toward the goal of automated synthesis of hardware accelerators for dynamic programming algorithms