Accelerating Binary String Comparisons with a Scalable, Streaming-Based System Architecture Based on FPGAs

Analysis and Comparison of Different Approaches to Implementing a Network-Based Parallel Data Processing Algorithm

It is well known that network-based parallel data processing algorithms are well suited to implementation in reconfigurable hardware recurring to either Field-Programmable Gate Arrays (FPGA) or Programmable Systems-on-Chip (PSoC). The intrinsic parallelism of these devices makes it possible to execute several data-independent network operations in parallel. However, the approaches to designing the respective systems vary significantly with the experience and background of the engineer in charge. In this paper, we analyze and compare the pros and cons of using an embedded processor, high-level synthesis methods, and register-transfer low-level design in terms of design effort, performance, and power consumption for implementing a parallel algorithm to find the two smallest values in a dataset. This problem is easy to formulate, has a number of practical applications (for instance, in low-density parity check decoders), and is very well suited to parallel implementation based on comparator networks.

Proposal of Smith-Waterman algorithm on FPGA to accelerate the forward and backtracking steps

In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume in biological databases and their continuous exponential increase, high-speed data processing is necessary. Therefore, this work proposes a parallel hardware design for the SW algorithm with a systolic array structure to accelerate the forward and backtracking steps. For this purpose, the architecture calculates and stores the paths in the forward stage for pre-organizing the alignment, which reduces the complexity of the backtracking stage. The backtracking starts from the maximum score position in the matrix and generates the optimal SW sequence alignment path. The architecture was validated on Field-Programmable Gate Array (FPGA), and synthesis analyses have shown that the proposed design reaches up to 79.5 Giga Cell Updates per Second (GCPUS).

A Survey of Network-Based Hardware Accelerators

Many practical data-processing algorithms fail to execute efficiently on general-purpose CPUs (Central Processing Units) due to the sequential matter of their operations and memory bandwidth limitations. To achieve desired performance levels, reconfigurable (FPGA (Field-Programmable Gate Array)-based) hardware accelerators are frequently explored that permit the processing units’ architectures to be better adapted to the specific problem/algorithm requirements. In particular, network-based data-processing algorithms are very well suited to implementation in reconfigurable hardware because several data-independent operations can easily and naturally be executed in parallel over as many processing blocks as actually required and technically possible. GPUs (Graphics Processing Units) have also demonstrated good results in this area but they tend to use significantly more power than FPGA, which could be a limiting factor in embedded applications. Moreover, GPUs employ a Single Instruction, Multiple Threads (SIMT) execution model and are therefore optimized to SIMD (Single Instruction, Multiple Data) operations, while in FPGAs fully custom datapaths can be built, eliminating much of the control overhead. This review paper aims to analyze, compare, and discuss different approaches to implementing network-based hardware accelerators in FPGA and programmable SoC (Systems-on-Chip). The performed analysis and the derived recommendations would be useful to hardware designers of future network-based hardware accelerators.

Accelerating Population Count with a Hardware Co-Processor for MicroBlaze

This paper proposes a Field-Programmable Gate Array (FPGA)-based hardware accelerator for assisting the embedded MicroBlaze soft-core processor in calculating population count. The population count is frequently required to be executed in cyber-physical systems and can be applied to large data sets, such as in the case of molecular similarity search in cheminformatics, or assisting with computations performed by binarized neural networks. The MicroBlaze instruction set architecture (ISA) does not support this operation natively, so the count has to be realized as either a sequence of native instructions (in software) or in parallel in a dedicated hardware accelerator. Different hardware accelerator architectures are analyzed and compared to one another and to implementing the population count operation in MicroBlaze. The achieved experimental results with large vector lengths (up to 217) demonstrate that the best hardware accelerator with DMA (Direct Memory Access) is ~31 times faster than the best software version running on MicroBlaze. The proposed architectures are scalable and can easily be adjusted to both smaller and bigger input vector lengths. The entire system was implemented and tested on a Nexys-4 prototyping board containing a low-cost/low-power Artix-7 FPGA.