Design and application of reconfigurable circuits and systems

Open Acces

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

statistical framework for dimensionality reduction implementation in fpgas

Abstract-Dimensionality reduction or feature extraction has been widely used in applications that require a set of data to be represented by a small set of variables. A linear projection is often chosen due to its computational attractiveness. The calculation of the linear basis that best explains the data is usually addressed using the Karhunen-Loeve Transform (KLT). Moreover, for applications where real-time performance and flexibility to accommodate new data are required, the linear projection is implemented in FPGAs due to their fine-grain parallelism and reconfigurability properties. Currently, the optimization of such a design in terms of area usage is considered as a separate problem to the basis calculation. In this paper, we propose a novel approach that couples the calculation of the linear projection basis and the area optimization problems under a probabilistic Bayesian framework. The power of the proposed framework is based on the flexibility to insert information regarding the implementation requirements of the linear basis by assigning a proper prior distribution. Results using real-life examples demonstrate the effectiveness of our approach

A Methodology to Design Pipelined Simulated Annealing Kernel Accelerators on Space-Borne Field-Programmable Gate Arrays

Increased levels of science objectives expected from spacecraft systems necessitate the ability to carry out fast on-board autonomous mission planning and scheduling. Heterogeneous radiation-hardened Field Programmable Gate Arrays (FPGAs) with embedded multiplier and memory modules are well suited to support the acceleration of scheduling algorithms. A methodology to design circuits specifically to accelerate Simulated Annealing Kernels (SAKs) in event scheduling algorithms is shown. The main contribution of this thesis is the low complexity scoring calculation used for the heuristic mapping algorithm used to balance resource allocation across a coarse-grained pipelined data-path. The methodology was exercised over various kernels with different cost functions and problem sizes. These test cases were benchedmarked for execution time, resource usage, power, and energy on a Xilinx Virtex 4 LX QR 200 FPGA and a BAE RAD 750 microprocessor