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

A framework for automatically generating optimized digital designs from C-language loops

Reconfigurable computing has the potential for providing significant performance increases to a number of computing applications. However, realizing these benefits requires digital design experience and knowledge of hardware description languages (HDLs). While a number of tools have focused on translation of high-level languages (HLLs) to HDLs, the tools do not always create optimized digital designs that are competitive with hand-coded solutions. This work describes an automatic optimization in the C-to-HDL transformation that reorganizes operations between pipeline stages in order to reduce critical path lengths. The effects of this optimization are examined on the MD5, SHA-1, and Smith-Waterman algorithms. Results show that the optimization results in performance gains of 13%-37% and that the automatically-generated implementations perform comparably to hand-coded implementations

A framework for automatically generating optimized digital designs from C-language loops

Reconfigurable computing has the potential for providing significant performance increases to a number of computing applications. However, realizing these benefits requires digital design experience and knowledge of hardware description languages (HDLs). While a number of tools have focused on translation of high-level languages (HLLs) to HDLs, the tools do not always create optimized digital designs that are competitive with hand-coded solutions. This work describes an automatic optimization in the C-to-HDL transformation that reorganizes operations between pipeline stages in order to reduce critical path lengths. The effects of this optimization are examined on the MD5, SHA-1, and Smith-Waterman algorithms. Results show that the optimization results in performance gains of 13%-37% and that the automatically-generated implementations perform comparably to hand-coded implementations

Study of OpenCL processing models for FPGA device

In our study, we present the results of the implementation of SHA-512 algorithm in FPGA. The distinguished element of our work is that we conducted the work using OpenCL for FPGA which is a relatively new development method for reconfigurable logic. We examine the loop unrolling; as the OpenCL performance optimisation method, and compare the efficiency of the different kernel implementation types: NDRange, Single-Work Item, and SIMD kernels. In conclusions, we compare metrics of the created FPGA accelerator to the corresponding GPGPU solutions. Also, our paper is accompanied by the source code repository to allow the reader to follow and extend our survey

Transformations of High-Level Synthesis Codes for High-Performance Computing

Specialized hardware architectures promise a major step in performance and energy efficiency over the traditional load/store devices currently employed in large scale computing systems. The adoption of high-level synthesis (HLS) from languages such as C/C++ and OpenCL has greatly increased programmer productivity when designing for such platforms. While this has enabled a wider audience to target specialized hardware, the optimization principles known from traditional software design are no longer sufficient to implement high-performance codes. Fast and efficient codes for reconfigurable platforms are thus still challenging to design. To alleviate this, we present a set of optimizing transformations for HLS, targeting scalable and efficient architectures for high-performance computing (HPC) applications. Our work provides a toolbox for developers, where we systematically identify classes of transformations, the characteristics of their effect on the HLS code and the resulting hardware (e.g., increases data reuse or resource consumption), and the objectives that each transformation can target (e.g., resolve interface contention, or increase parallelism). We show how these can be used to efficiently exploit pipelining, on-chip distributed fast memory, and on-chip streaming dataflow, allowing for massively parallel architectures. To quantify the effect of our transformations, we use them to optimize a set of throughput-oriented FPGA kernels, demonstrating that our enhancements are sufficient to scale up parallelism within the hardware constraints. With the transformations covered, we hope to establish a common framework for performance engineers, compiler developers, and hardware developers, to tap into the performance potential offered by specialized hardware architectures using HLS