Reconfigurable acceleration of Recurrent Neural Networks

Recurrent Neural Networks (RNNs) have been successful in a wide range of applications involving temporal sequences such as natural language processing, speech recognition and video analysis. However, RNNs often require a significant amount of memory and computational resources. In addition, the recurrent nature and data dependencies in RNN computations can lead to system stall, resulting in low throughput and high latency. This work describes novel parallel hardware architectures for accelerating RNN inference using Field-Programmable Gate Array (FPGA) technology, which considers the data dependencies and high computational costs of RNNs. The first contribution of this thesis is a latency-hiding architecture that utilizes column-wise matrix-vector multiplication instead of the conventional row-wise operation to eliminate data dependencies and improve the throughput of RNN inference designs. This architecture is further enhanced by a configurable checkerboard tiling strategy which allows large dimensions of weight matrices, while supporting element-based parallelism and vector-based parallelism. The presented reconfigurable RNN designs show significant speedup over CPU, GPU, and other FPGA designs. The second contribution of this thesis is a weight reuse approach for large RNN models with weights stored in off-chip memory, running with a batch size of one. A novel blocking-batching strategy is proposed to optimize the throughput of large RNN designs on FPGAs by reusing the RNN weights. Performance analysis is also introduced to enable FPGA designs to achieve the best trade-off between area, power consumption and performance. Promising power efficiency improvement has been achieved in addition to speeding up over CPU and GPU designs. The third contribution of this thesis is a low latency design for RNNs based on a partially-folded hardware architecture. It also introduces a technique that balances initiation interval of multi-layer RNN inferences to increase hardware efficiency and throughput while reducing latency. The approach is evaluated on a variety of applications, including gravitational wave detection and Bayesian RNN-based ECG anomaly detection. To facilitate the use of this approach, we open source an RNN template which enables the generation of low-latency FPGA designs with efficient resource utilization using high-level synthesis tools.Open Acces

Optimising algorithm and hardware for deep neural networks on FPGAs

This thesis proposes novel algorithm and hardware optimisation approaches to accelerate Deep Neural Networks (DNNs), including both Convolutional Neural Networks (CNNs) and Bayesian Neural Networks (BayesNNs). The first contribution of this thesis is to propose an adaptable and reconfigurable hardware design to accelerate CNNs. By analysing the computational patterns of different CNNs, a unified hardware architecture is proposed for both 2-Dimension and 3-Dimension CNNs. The accelerator is also designed with runtime adaptability, which adopts different parallelism strategies for different convolutional layers at runtime. The second contribution of this thesis is to propose a novel neural network architecture and hardware design co-optimisation approach, which improves the performance of CNNs at both algorithm and hardware levels. Our proposed three-phase co-design framework decouples network training from design space exploration, which significantly reduces the time-cost of the co-optimisation process. The third contribution of this thesis is to propose an algorithmic and hardware co-optimisation framework for accelerating BayesNNs. At the algorithmic level, three categories of structured sparsity are explored to reduce the computational complexity of BayesNNs. At the hardware level, we propose a novel hardware architecture with the aim of exploiting the structured sparsity for BayesNNs. Both algorithmic and hardware optimisations are jointly applied to push the performance limit.Open Acces

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPU-days to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists

dReDBox: Materializing a full-stack rack-scale system prototype of a next-generation disaggregated datacenter

Current datacenters are based on server machines, whose mainboard and hardware components form the baseline, monolithic building block that the rest of the system software, middleware and application stack are built upon. This leads to the following limitations: (a) resource proportionality of a multi-tray system is bounded by the basic building block (mainboard), (b) resource allocation to processes or virtual machines (VMs) is bounded by the available resources within the boundary of the mainboard, leading to spare resource fragmentation and inefficiencies, and (c) upgrades must be applied to each and every server even when only a specific component needs to be upgraded. The dRedBox project (Disaggregated Recursive Datacentre-in-a-Box) addresses the above limitations, and proposes the next generation, low-power, across form-factor datacenters, departing from the paradigm of the mainboard-as-a-unit and enabling the creation of function-block-as-a-unit. Hardware-level disaggregation and software-defined wiring of resources is supported by a full-fledged Type-1 hypervisor that can execute commodity virtual machines, which communicate over a low-latency and high-throughput software-defined optical network. To evaluate its novel approach, dRedBox will demonstrate application execution in the domains of network functions virtualization, infrastructure analytics, and real-time video surveillance.This work has been supported in part by EU H2020 ICTproject dRedBox, contract #687632.Peer ReviewedPostprint (author's final draft

Run-time reconfigurable acceleration for genetic programming fitness evaluation in trading strategies

Genetic programming can be used to identify complex patterns in financial markets which may lead to more advanced trading strategies. However, the computationally intensive nature of genetic programming makes it difficult to apply to real world problems, particularly in real-time constrained scenarios. In this work we propose the use of Field Programmable Gate Array technology to accelerate the fitness evaluation step, one of the most computationally demanding operations in genetic programming. We propose to develop a fully-pipelined, mixed precision design using run-time reconfiguration to accelerate fitness evaluation. We show that run-time reconfiguration can reduce resource consumption by a factor of 2 compared to previous solutions on certain configurations. The proposed design is up to 22 times faster than an optimised, multithreaded software implementation while achieving comparable financial returns

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