FPGA acceleration of DNA sequence alignment: design analysis and optimization

Existing FPGA accelerators for short read mapping often fail to utilize the complete biological information in sequencing data for simple hardware design, leading to missed or incorrect alignment. In this work, we propose a runtime reconfigurable alignment pipeline that considers all information in sequencing data for the biologically accurate acceleration of short read mapping. We focus our efforts on accelerating two string matching techniques: FM-index and the Smith-Waterman algorithm with the affine-gap model which are commonly used in short read mapping. We further optimize the FPGA hardware using a design analyzer and merger to improve alignment performance. The contributions of this work are as follows. 1. We accelerate the exact-match and mismatch alignment by leveraging the FM-index technique. We optimize memory access by compressing the data structure and interleaving the access with multiple short reads. The FM-index hardware also considers complete information in the read data to maximize accuracy. 2. We propose a seed-and-extend model to accelerate alignment with indels. The FM-index hardware is extended to support the seeding stage while a Smith-Waterman implementation with the affine-gap model is developed on FPGA for the extension stage. This model can improve the efficiency of indel alignment with comparable accuracy versus state-of-the-art software. 3. We present an approach for merging multiple FPGA designs into a single hardware design, so that multiple place-and-route tasks can be replaced by a single task to speed up functional evaluation of designs. We first experiment with this approach to demonstrate its feasibility for different designs. Then we apply this approach to optimize one of the proposed FPGA aligners for better alignment performance.Open Acces

LLVM-based and scalable MPEG-RVC decoder

WOSInternational audienceMPEG reconfigurable video coding (RVC) is a new platform-independent specification methodology chosen by the MPEG community for describing coding standards. This methodology aims at producing abstract decoder models (ADMs) of MPEG decoders as programs described in a dataflow language namely "RVC-CAL Actor Language" (RVC-CAL). RVC-CAL naturally expresses potential parallelism between tasks of an application, which makes an ADM description suitable for implementation to a wide variety of platforms, from uniprocessor systems to FPGAs. MPEG RVC eases the development process of decoders by building decoders at a library-component level instead of using monolithic algorithms, and by providing a library of coding tools standardized in MPEG. This paper presents new mechanisms based on the low level virtual machine that allow the conception of a decoder able to dynamically instantiate several RVC decoder descriptions. This decoder, unlike static decoders generated by RVC tools, keeps de facto the features of an RVC description namely portability, scalability and reconfigurability

Baseband analog front-end and digital back-end for reconfigurable multi-standard terminals

Multimedia applications are driving wireless network operators to add high-speed data services such as Edge (E-GPRS), WCDMA (UMTS) and WLAN (IEEE 802.11a,b,g) to the existing GSM network. This creates the need for multi-mode cellular handsets that support a wide range of communication standards, each with a different RF frequency, signal bandwidth, modulation scheme etc. This in turn generates several design challenges for the analog and digital building blocks of the physical layer. In addition to the above-mentioned protocols, mobile devices often include Bluetooth, GPS, FM-radio and TV services that can work concurrently with data and voice communication. Multi-mode, multi-band, and multi-standard mobile terminals must satisfy all these different requirements. Sharing and/or switching transceiver building blocks in these handsets is mandatory in order to extend battery life and/or reduce cost. Only adaptive circuits that are able to reconfigure themselves within the handover time can meet the design requirements of a single receiver or transmitter covering all the different standards while ensuring seamless inter-interoperability. This paper presents analog and digital base-band circuits that are able to support GSM (with Edge), WCDMA (UMTS), WLAN and Bluetooth using reconfigurable building blocks. The blocks can trade off power consumption for performance on the fly, depending on the standard to be supported and the required QoS (Quality of Service) leve

Compiling and optimizing spreadsheets for FPGA and multicore execution

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007."September 2007."Includes bibliographical references (p. 102-104).A major barrier to developing systems on multicore and FPGA chips is an easy-to-use development environment. This thesis presents the RhoZeta spreadsheet compiler and Catalyst optimization system for programming multiprocessors and FPGAs. Any spreadsheet frontend may be extended to work with RhoZeta's multiple interpreters and behavioral abstraction mechanisms. RhoZeta synchronizes a variety of cell interpreters acting on a global memory space. RhoZeta can also compile a group of cells to multithreaded C or Verilog. The result is an easy-to-use interface for programming multicore microprocessors and FPGAs. A spreadsheet environment presents parallelism and locality issues of modem hardware directly to the user and allows for a simple global memory synchronization model. Catalyst is a spreadsheet graph rewriting system based on performing behaviorally invariant guarded atomic actions while a system is being interpreted by RhoZeta. A number of optimization macros were developed to perform speculation, resource sharing and propagation of static assignments through a circuit. Parallelization of a 64-bit serial leading-zero-counter is demonstrated with Catalyst. Fault tolerance macros were also developed in Catalyst to protect against dynamic faults and to offset costs associated with testing semiconductors for static defects. A model for partitioning, placing and profiling spreadsheet execution in a heterogeneous hardware environment is also discussed. The RhoZeta system has been used to design several multithreaded and FPGA applications including a RISC emulator and a MIDI controlled modular synthesizer.by Amir Hirsch.M.Eng

Speed-up run-time reconfiguration implementation on FPGAs

International audienceReconfigurable computing is certainly one of the most important emerging research topics over the last few years, in the field of digital processing architectures. The introduction of run-time reconfiguration (RTR) on FPGAs requires appropriate design flows and methodologies to fully exploit this new functionality. For that purpose we present an automatic design generation methodology for heterogeneous architectures based on Network on Chip (NoC) and FPGAs that eases and speed-up RTR implementation. We focus on how to take into account specificities of partially reconfigurable components during the design generation steps. This method automatically generates designs for both fixed and partially reconfigurable parts of a FPGA with automaticmanagement of the reconfiguration process. Furthermore this automatic design generation enables reconfiguration pre-fetching techniques to minimize reconfiguration latency and buffer merging techniques to minimize memory requirements of the generated design. This concept has been applied to different wireless access schemes, based on a combination of OFDM and CDMA techniques. The implementation example illustrates the benefits of the proposed design methodology