High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools), FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs

High performance computing with FPGAs

Field-programmable gate arrays represent an army of logical units which can be organized in a highly parallel or pipelined fashion to implement an algorithm in hardware. The flexibility of this new medium creates new challenges to find the right processing paradigm which takes into account of the natural constraints of FPGAs: clock frequency, memory footprint and communication bandwidth. In this paper first use of FPGAs as a multiprocessor on a chip or its use as a highly functional coprocessor are compared, and the programming tools for hardware/software codesign are discussed. Next a number of techniques are presented to maximize the parallelism and optimize the data locality in nested loops. This includes unimodular transformations, data locality improving loop transformations and use of smart buffers. Finally, the use of these techniques on a number of examples is demonstrated. The results in the paper and in the literature show that, with the proper programming tool set, FPGAs can speedup computation kernels significantly with respect to traditional processors

An empirical evaluation of High-Level Synthesis languages and tools for database acceleration

High Level Synthesis (HLS) languages and tools are emerging as the most promising technique to make FPGAs more accessible to software developers. Nevertheless, picking the most suitable HLS for a certain class of algorithms depends on requirements such as area and throughput, as well as on programmer experience. In this paper, we explore the different trade-offs present when using a representative set of HLS tools in the context of Database Management Systems (DBMS) acceleration. More specifically, we conduct an empirical analysis of four representative frameworks (Bluespec SystemVerilog, Altera OpenCL, LegUp and Chisel) that we utilize to accelerate commonly-used database algorithms such as sorting, the median operator, and hash joins. Through our implementation experience and empirical results for database acceleration, we conclude that the selection of the most suitable HLS depends on a set of orthogonal characteristics, which we highlight for each HLS framework.Peer ReviewedPostprint (author’s final draft

State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms

Searching biological sequence database is a common and repeated task in bioinformatics and molecular biology. The Smith–Waterman algorithm is the most accurate method for this kind of search. Unfortunately, this algorithm is computationally demanding and the situation gets worse due to the exponential growth of biological data in the last years. For that reason, the scientific community has made great efforts to accelerate Smith–Waterman biological database searches in a wide variety of hardware platforms. We give a survey of the state-of-the-art in Smith–Waterman protein database search, focusing on four hardware architectures: central processing units, graphics processing units, field programmable gate arrays and Xeon Phi coprocessors. After briefly describing each hardware platform, we analyse temporal evolution, contributions, limitations and experimental work and the results of each implementation. Additionally, as energy efficiency is becoming more important every day, we also survey performance/power consumption works. Finally, we give our view on the future of Smith–Waterman protein searches considering next generations of hardware architectures and its upcoming technologies.Instituto de Investigación en InformáticaUniversidad Complutense de Madri

Intelligent systems engineering with reconfigurable computing

Intelligent computing systems comprising microprocessor cores, memory and reconfigurable user-programmable logic represent a promising technology which is well-suited for applications such as digital signal and image processing, cryptography and encryption, etc. These applications employ frequently recursive algorithms which are particularly appropriate when the underlying problem is defined in recursive terms and it is difficult to reformulate it as an iterative procedure. It is known, however, that hardware description languages (such as VHDL) as well as system-level specification languages (such as Handel-C) that are usually employed for specifying the required functionality of reconfigurable systems do not provide a direct support for recursion. In this paper a method allowing recursive algorithms to be easily described in Handel-C and implemented in an FPGA (field-programmable gate array) is proposed. The recursive search algorithm for the knapsack problem is considered as an exampleApplications in Artificial Intelligence - Knowledge EngineeringRed de Universidades con Carreras en Informática (RedUNCI

FPGA design methodology for industrial control systems—a review

This paper reviews the state of the art of fieldprogrammable gate array (FPGA) design methodologies with a focus on industrial control system applications. This paper starts with an overview of FPGA technology development, followed by a presentation of design methodologies, development tools and relevant CAD environments, including the use of portable hardware description languages and system level programming/design tools. They enable a holistic functional approach with the major advantage of setting up a unique modeling and evaluation environment for complete industrial electronics systems. Three main design rules are then presented. These are algorithm refinement, modularity, and systematic search for the best compromise between the control performance and the architectural constraints. An overview of contributions and limits of FPGAs is also given, followed by a short survey of FPGA-based intelligent controllers for modern industrial systems. Finally, two complete and timely case studies are presented to illustrate the benefits of an FPGA implementation when using the proposed system modeling and design methodology. These consist of the direct torque control for induction motor drives and the control of a diesel-driven synchronous stand-alone generator with the help of fuzzy logic