Synthesis of FPGA-based accelerators implementing recursive algorithms

Doutoramento em Engenharia InformáticaO desenvolvimento de sistemas computacionais é um processo complexo, com múltiplas etapas, que requer uma análise profunda do problema, levando em consideração as limitações e os requisitos aplicáveis. Tal tarefa envolve a exploração de técnicas alternativas e de algoritmos computacionais para optimizar o sistema e satisfazer os requisitos estabelecidos. Neste contexto, uma das mais importantes etapas é a análise e implementação de algoritmos computacionais. Enormes avanços tecnológicos no âmbito das FPGAs (Field-Programmable Gate Arrays) tornaram possível o desenvolvimento de sistemas de engenharia extremamente complexos. Contudo, o número de transístores disponíveis por chip está a crescer mais rapidamente do que a capacidade que temos para desenvolver sistemas que tirem proveito desse crescimento. Esta limitação já bem conhecida, antes de se revelar com FPGAs, já se verificava com ASICs (Application-Specific Integrated Circuits) e tem vindo a aumentar continuamente. O desenvolvimento de sistemas com base em FPGAs de alta capacidade envolve uma grande variedade de ferramentas, incluindo métodos para a implementação eficiente de algoritmos computacionais. Esta tese pretende proporcionar uma contribuição nesta área, tirando partido da reutilização, do aumento do nível de abstracção e de especificações algorítmicas mais automatizadas e claras. Mais especificamente, é apresentado um estudo que foi levado a cabo no sentido de obter critérios relativos à implementação em hardware de algoritmos recursivos versus iterativos. Depois de serem apresentadas algumas das estratégias para implementar recursividade em hardware mais significativas, descreve-se, em pormenor, um conjunto de algoritmos para resolver problemas de pesquisa combinatória (considerados enquanto exemplos de aplicação). Versões recursivas e iterativas destes algoritmos foram implementados e testados em FPGA. Com base nos resultados obtidos, é feita uma cuidada análise comparativa. Novas ferramentas e técnicas de investigação que foram desenvolvidas no âmbito desta tese são também discutidas e demonstradas.Design of computational systems is a complex multistage process which requires a deep analysis of the problem, taking into account relevant limitations and constraints as well as software/hardware co-design. Such task involves exploring competitive techniques and computational algorithms, enabling the system to be optimized while satisfying given requirements. In this context, one of the most important stages is analysis and implementation of computational algorithms. Tremendous progress in the scope of FPGA (Field-Programmable Gate Array) technology has made it possible to design very complicated engineering systems. However, the number of available transistors grows faster than the ability to meaningfully design with them. This situation is a well known design productivity gap, which was inherited by FPGA from ASIC (Application-Specific Integrated Circuit) and which is increasing continuously. Developing engineering systems on the basis of high capacity FPGAs involves a wide variety of design tools, including methods for efficient implementation of computational algorithms. The thesis is intended to provide a contribution in this area by aiming at reuse, high level abstraction, automation, and clearness of algorithmic specifications. More specifically, it presents research studies which have been carried out in order to obtain criteria regarding implementation of recursive vs. iterative algorithms in hardware. After describing some of the most relevant strategies for implementing recursion in hardware, a selection of algorithms for solving combinatorial search problems (considered as application examples) are also described in detail. Iterative and recursive versions of these algorithms have been implemented and tested in FPGA. Taking into consideration the results obtained, a careful comparative analysis is given. New research-oriented tools and techniques for hardware design which have been developed in the scope of this thesis are also discussed and demonstrated

Applications of reprogrammability in algorithm acceleration

This doctoral thesis consists of an introductory part and eight appended publications, which deal with hardware-based reprogrammability in algorithm acceleration with a specific emphasis on the possibilities offered by modern large-scale Field Programmable Gate Arrays (FPGAs) in computationally demanding applications. The historical evolution of both the theoretical and technological paths culminating in the introduction of reprogrammable logic devices is first outlined. This is followed by defining the commonly used terms in the thesis. The reprogrammable logic market is surveyed, and the architectural structures and the technological reasonings behind them are described in detail. As reprogrammable logic lies between Application Specific Integrated Circuits (ASICs) and general-purpose microprocessors in the implementation spectrum of electronics systems, special attention has been paid to differentiate these three implementation approaches. This has been done to emphasize, that reprogrammable logic offers much more than just a low-volume replacement for ASICs. Design systems for reprogrammable logic are investigated, as the learning curve associated with them is the main hurdle for software-oriented designers for using reprogrammable logic devices. The theoretically important topic of partial reprogrammability is described in detail, but it is concluded, that the practical problems in designing viable development platforms for partially reprogrammable systems will hinder its wide-spread adoption. The main technical, design-oriented, and economic applicability factors of reprogrammable logic are laid out. The main advantages of reprogrammable logic are their suitability for fine-grained bit-level parallelizable computing with a short time-to-market and low upfront costs. It is also concluded, that the main opportunities for reprogrammable logic lie in the potential of high-level design systems, and the ever-growing ASIC design gap. On the other hand, most power-conscious mass-market portable products do not seem to offer major new market potential for reprogrammable logic. The appended publications are examined and compared to contemporaneous research at other research institutions. The conclusion is that for relatively wide classes of well-defined computation problems, reprogrammable logic offers a more efficient solution than a software-centered approach, with a much shorter production cycle than is the case with ASICs.reviewe

FPGA Implementation of Blob Recognition

Real-time embedded vision systems can be used in a wide range of applications and therefore the demand has been increasing for them. In this thesis, an FPGA-based embedded vision system capable of recognizing objects in real time is presented. The proposed system architecture consists of multiple Intellectual Properties (IPs), which are used as a set of complex instructions by an integrated 32-bit CPU Microblaze. Each IP is tailored specifically to meet the needs of the application and at the same time to consume the minimum FPGA logic resources. Integrating both hardware and software on a single FPGA chip, this system can achieve the real-time performance of full VGA video processing at 32 frames per second (fps). In addition, this work comes up with a new method called Dual Connected Component Labelling (DCCL) suitable for FPGA implementation

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

Optimising and evaluating designs for reconfigurable hardware

Growing demand for computational performance, and the rising cost for chip design and manufacturing make reconfigurable hardware increasingly attractive for digital system implementation. Reconfigurable hardware, such as field-programmable gate arrays (FPGAs), can deliver performance through parallelism while also providing flexibility to enable application builders to reconfigure them. However, reconfigurable systems, particularly those involving run-time reconfiguration, are often developed in an ad-hoc manner. Such an approach usually results in low designer productivity and can lead to inefficient designs. This thesis covers three main achievements that address this situation. The first achievement is a model that captures design parameters of reconfigurable hardware and performance parameters of a given application domain. This model supports optimisations for several design metrics such as performance, area, and power consumption. The second achievement is a technique that enhances the relocatability of bitstreams for reconfigurable devices, taking into account heterogeneous resources. This method increases the flexibility of modules represented by these bitstreams while reducing configuration storage size and design compilation time. The third achievement is a technique to characterise the power consumption of FPGAs in different activity modes. This technique includes the evaluation of standby power and dedicated low-power modes, which are crucial in meeting the requirements for battery-based mobile devices

A hardware-software codesign framework for cellular computing

Until recently, the ever-increasing demand of computing power has been met on one hand by increasing the operating frequency of processors and on the other hand by designing architectures capable of exploiting parallelism at the instruction level through hardware mechanisms such as super-scalar execution. However, both these approaches seem to have reached a plateau, mainly due to issues related to design complexity and cost-effectiveness. To face the stabilization of performance of single-threaded processors, the current trend in processor design seems to favor a switch to coarser-grain parallelization, typically at the thread level. In other words, high computational power is achieved not only by a single, very fast and very complex processor, but through the parallel operation of several processors, each executing a different thread. Extrapolating this trend to take into account the vast amount of on-chip hardware resources that will be available in the next few decades (either through further shrinkage of silicon fabrication processes or by the introduction of molecular-scale devices), together with the predicted features of such devices (e.g., the impossibility of global synchronization or higher failure rates), it seems reasonable to foretell that current design techniques will not be able to cope with the requirements of next-generation electronic devices and that novel design tools and programming methods will have to be devised. A tempting source of inspiration to solve the problems implied by a massively parallel organization and inherently error-prone substrates is biology. In fact, living beings possess characteristics, such as robustness to damage and self-organization, which were shown in previous research as interesting to be implemented in hardware. For instance, it was possible to realize relatively simple systems, such as a self-repairing watch. Overall, these bio-inspired approaches seem very promising but their interest for a wider audience is problematic because their heavily hardware-oriented designs lack some of the flexibility achievable with a general purpose processor. In the context of this thesis, we will introduce a processor-grade processing element at the heart of a bio-inspired hardware system. This processor, based on a single-instruction, features some key properties that allow it to maintain the versatility required by the implementation of bio-inspired mechanisms and to realize general computation. We will also demonstrate that the flexibility of such a processor enables it to be evolved so it can be tailored to different types of applications. In the second half of this thesis, we will analyze how the implementation of a large number of these processors can be used on a hardware platform to explore various bio-inspired mechanisms. Based on an extensible platform of many FPGAs, configured as a networked structure of processors, the hardware part of this computing framework is backed by an open library of software components that provides primitives for efficient inter-processor communication and distributed computation. We will show that this dual software–hardware approach allows a very quick exploration of different ways to solve computational problems using bio-inspired techniques. In addition, we also show that the flexibility of our approach allows it to exploit replication as a solution to issues that concern standard embedded applications

Kommunikation und Bildverarbeitung in der Automation

In diesem Open-Access-Tagungsband sind die besten Beiträge des 9. Jahreskolloquiums "Kommunikation in der Automation" (KommA 2018) und des 6. Jahreskolloquiums "Bildverarbeitung in der Automation" (BVAu 2018) enthalten. Die Kolloquien fanden am 20. und 21. November 2018 in der SmartFactoryOWL, einer gemeinsamen Einrichtung des Fraunhofer IOSB-INA und der Technischen Hochschule Ostwestfalen-Lippe statt. Die vorgestellten neuesten Forschungsergebnisse auf den Gebieten der industriellen Kommunikationstechnik und Bildverarbeitung erweitern den aktuellen Stand der Forschung und Technik. Die in den Beiträgen enthaltenen anschaulichen Beispiele aus dem Bereich der Automation setzen die Ergebnisse in den direkten Anwendungsbezug