Reconfigurable computing for large-scale graph traversal algorithms

This thesis proposes a reconfigurable computing approach for supporting parallel processing in large-scale graph traversal algorithms. Our approach is based on a reconfigurable hardware architecture which exploits the capabilities of both FPGAs (Field-Programmable Gate Arrays) and a multi-bank parallel memory subsystem. The proposed methodology to accelerate graph traversal algorithms has been applied to three case studies, revealing that application-specific hardware customisations can benefit performance. A summary of our four contributions is as follows. First, a reconfigurable computing approach to accelerate large-scale graph traversal algorithms. We propose a reconfigurable hardware architecture which decouples computation and communication while keeping multiple memory requests in flight at any given time, taking advantage of the high bandwidth of multi-bank memory subsystems. Second, a demonstration of the effectiveness of our approach through two case studies: the breadth-first search algorithm, and a graphlet counting algorithm from bioinformatics. Both case studies involve graph traversal, but each of them adopts a different graph data representation. Third, a method for using on-chip memory resources in FPGAs to reduce off-chip memory accesses for accelerating graph traversal algorithms, through a case-study of the All-Pairs Shortest-Paths algorithm. This case study has been applied to process human brain network data. Fourth, an evaluation of an approach based on instruction-set extension for FPGA design against many-core GPUs (Graphics Processing Units), based on a set of benchmarks with different memory access characteristics. It is shown that while GPUs excel at streaming applications, the proposed approach can outperform GPUs in applications with poor locality characteristics, such as graph traversal problems.Open Acces

High performance graph analysis on parallel architectures

PhD ThesisOver the last decade pharmacology has been developing computational methods to enhance drug development and testing. A computational method called network pharmacology uses graph analysis tools to determine protein target sets that can lead on better targeted drugs for diseases as Cancer. One promising area of network-based pharmacology is the detection of protein groups that can produce better e ects if they are targeted together by drugs. However, the e cient prediction of such protein combinations is still a bottleneck in the area of computational biology. The computational burden of the algorithms used by such protein prediction strategies to characterise the importance of such proteins consists an additional challenge for the eld of network pharmacology. Such computationally expensive graph algorithms as the all pairs shortest path (APSP) computation can a ect the overall drug discovery process as needed network analysis results cannot be given on time. An ideal solution for these highly intensive computations could be the use of super-computing. However, graph algorithms have datadriven computation dictated by the structure of the graph and this can lead to low compute capacity utilisation with execution times dominated by memory latency. Therefore, this thesis seeks optimised solutions for the real-world graph problems of critical node detection and e ectiveness characterisation emerged from the collaboration with a pioneer company in the eld of network pharmacology as part of a Knowledge Transfer Partnership (KTP) / Secondment (KTS). In particular, we examine how genetic algorithms could bene t the prediction of protein complexes where their removal could produce a more e ective 'druggable' impact. Furthermore, we investigate how the problem of all pairs shortest path (APSP) computation can be bene ted by the use of emerging parallel hardware architectures as GPU- and FPGA- desktop-based accelerators. In particular, we address the problem of critical node detection with the development of a heuristic search method. It is based on a genetic algorithm that computes optimised node combinations where their removal causes greater impact than common impact analysis strategies. Furthermore, we design a general pattern for parallel network analysis on multi-core architectures that considers graph's embedded properties. It is a divide and conquer approach that decomposes a graph into smaller subgraphs based on its strongly connected components and computes the all pairs shortest paths concurrently on GPU. Furthermore, we use linear algebra to design an APSP approach based on the BFS algorithm. We use algebraic expressions to transform the problem of path computation to multiple independent matrix-vector multiplications that are executed concurrently on FPGA. Finally, we analyse how the optimised solutions of perturbation analysis and parallel graph processing provided in this thesis will impact the drug discovery process.This research was part of a Knowledge Transfer Partnership (KTP) and Knowledge Transfer Secondment (KTS) between e-therapeutics PLC and Newcastle University. It was supported as a collaborative project by e-therapeutics PLC and Technology Strategy boar

An FPGA based approach for Černý conjecture falsification

A synchronizing sequence for an automaton is a special input sequence that sends all states of the automaton to the same state. J. Černý conjectured that the length of the shortest synchronizing sequence of an automaton with n states cannot be greater than (n-1)2, which is known today as the Černý conjecture. This half-a-century old conjecture is still open and it is considered to be the most long-standing open problem in the combinatorial theory of finite state automata. One research line that has been pursued in the literature is to check if the conjecture holds for a fixed number of states n, by considering all automata with n states and checking if any of these automata falsifies the conjecture. This is a computationally intensive task, even for automata up to a dozen of states and only two input symbols. To accelerate the search parallel computation approaches using multicore CPUs have been tried before. In this thesis, we study the use of FPGAs to accelerate the search for an automaton falsifying the Černý conjecture. We present a design to calculate iii the minimum length synchronizing sequence of a finite state automaton. The proposed design is implemented with the parallel computing capability of hardware designs while optimizing the time performance

High level compilation for gate reconfigurable architectures

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.Includes bibliographical references (p. 205-215).A continuing exponential increase in the number of programmable elements is turning management of gate-reconfigurable architectures as "glue logic" into an intractable problem; it is past time to raise this abstraction level. The physical hardware in gate-reconfigurable architectures is all low level - individual wires, bit-level functions, and single bit registers - hence one should look to the fetch-decode-execute machinery of traditional computers for higher level abstractions. Ordinary computers have machine-level architectural mechanisms that interpret instructions - instructions that are generated by a high-level compiler. Efficiently moving up to the next abstraction level requires leveraging these mechanisms without introducing the overhead of machine-level interpretation. In this dissertation, I solve this fundamental problem by specializing architectural mechanisms with respect to input programs. This solution is the key to efficient compilation of high-level programs to gate reconfigurable architectures. My approach to specialization includes several novel techniques. I develop, with others, extensive bitwidth analyses that apply to registers, pointers, and arrays. I use pointer analysis and memory disambiguation to target devices with blocks of embedded memory. My approach to memory parallelization generates a spatial hierarchy that enables easier-to-synthesize logic state machines with smaller circuits and no long wires.(cont.) My space-time scheduling approach integrates the techniques of high-level synthesis with the static routing concepts developed for single-chip multiprocessors. Using DeepC, a prototype compiler demonstrating my thesis, I compile a new benchmark suite to Xilinx Virtex FPGAs. Resulting performance is comparable to a custom MIPS processor, with smaller area (40 percent on average), higher evaluation speeds (2.4x), and lower energy (18x) and energy-delay (45x). Specialization of advanced mechanisms results in additional speedup, scaling with hardware area, at the expense of power. For comparison, I also target IBM's standard cell SA-27E process and the RAW microprocessor. Results include sensitivity analysis to the different mechanisms specialized and a grand comparison between alternate targets.by Jonathan William Babb.Ph.D

Design and Programming Methods for Reconfigurable Multi-Core Architectures using a Network-on-Chip-Centric Approach

A current trend in the semiconductor industry is the use of Multi-Processor Systems-on-Chip (MPSoCs) for a wide variety of applications such as image processing, automotive, multimedia, and robotic systems. Most applications gain performance advantages by executing parallel tasks on multiple processors due to the inherent parallelism. Moreover, heterogeneous structures provide high performance/energy efficiency, since application-specific processing elements (PEs) can be exploited. The increasing number of heterogeneous PEs leads to challenging communication requirements. To overcome this challenge, Networks-on-Chip (NoCs) have emerged as scalable on-chip interconnect. Nevertheless, NoCs have to deal with many design parameters such as virtual channels, routing algorithms and buffering techniques to fulfill the system requirements. This thesis highly contributes to the state-of-the-art of FPGA-based MPSoCs and NoCs. In the following, the three major contributions are introduced. As a first major contribution, a novel router concept is presented that efficiently utilizes communication times by performing sequences of arithmetic operations on the data that is transferred. The internal input buffers of the routers are exchanged with processing units that are capable of executing operations. Two different architectures of such processing units are presented. The first architecture provides multiply and accumulate operations which are often used in signal processing applications. The second architecture introduced as Application-Specific Instruction Set Routers (ASIRs) contains a processing unit capable of executing any operation and hence, it is not limited to multiply and accumulate operations. An internal processing core located in ASIRs can be developed in C/C++ using high-level synthesis. The second major contribution comprises application and performance explorations of the novel router concept. Models that approximate the achievable speedup and the end-to-end latency of ASIRs are derived and discussed to show the benefits in terms of performance. Furthermore, two applications using an ASIR-based MPSoC are implemented and evaluated on a Xilinx Zynq SoC. The first application is an image processing algorithm consisting of a Sobel filter, an RGB-to-Grayscale conversion, and a threshold operation. The second application is a system that helps visually impaired people by navigating them through unknown indoor environments. A Light Detection and Ranging (LIDAR) sensor scans the environment, while Inertial Measurement Units (IMUs) measure the orientation of the user to generate an audio signal that makes the distance as well as the orientation of obstacles audible. This application consists of multiple parallel tasks that are mapped to an ASIR-based MPSoC. Both applications show the performance advantages of ASIRs compared to a conventional NoC-based MPSoC. Furthermore, dynamic partial reconfiguration in terms of relocation and security aspects are investigated. The third major contribution refers to development and programming methodologies of NoC-based MPSoCs. A software-defined approach is presented that combines the design and programming of heterogeneous MPSoCs. In addition, a Kahn-Process-Network (KPN) –based model is designed to describe parallel applications for MPSoCs using ASIRs. The KPN-based model is extended to support not only the mapping of tasks to NoC-based MPSoCs but also the mapping to ASIR-based MPSoCs. A static mapping methodology is presented that assigns tasks to ASIRs and processors for a given KPN-model. The impact of external hardware components such as sensors, actuators and accelerators connected to the processors is also discussed which makes the approach of high interest for embedded systems

Feasibility Study of High-Level Synthesis : Implementation of a Real-Time HEVC Intra Encoder on FPGA

High-Level Synthesis (HLS) on automatisoitu suunnitteluprosessi, joka pyrkii parantamaan tuottavuutta perinteisiin suunnittelumenetelmiin verrattuna, nostamalla suunnittelun abstraktiota rekisterisiirtotasolta (RTL) käyttäytymistasolle. Erilaisia kaupallisia HLS-työkaluja on ollut markkinoilla aina 1990-luvulta lähtien, mutta vasta äskettäin ne ovat alkaneet saada hyväksyntää teollisuudessa sekä akateemisessa maailmassa. Hidas käyttöönottoaste on johtunut pääasiassa huonommasta tulosten laadusta (QoR) kuin mitä on ollut mahdollista tavanomaisilla laitteistokuvauskielillä (HDL). Uusimmat HLS-työkalusukupolvet ovat kuitenkin kaventaneet QoR-aukkoa huomattavasti. Tämä väitöskirja tutkii HLS:n soveltuvuutta videokoodekkien kehittämiseen. Se esittelee useita HLS-toteutuksia High Efficiency Video Coding (HEVC) -koodaukselle, joka on keskeinen mahdollistava tekniikka lukuisille nykyaikaisille mediasovelluksille. HEVC kaksinkertaistaa koodaustehokkuuden edeltäjäänsä Advanced Video Coding (AVC) -standardiin verrattuna, saavuttaen silti saman subjektiivisen visuaalisen laadun. Tämä tyypillisesti saavutetaan huomattavalla laskennallisella lisäkustannuksella. Siksi reaaliaikainen HEVC vaatii automatisoituja suunnittelumenetelmiä, joita voidaan käyttää rautatoteutus- (HW ) ja varmennustyön minimoimiseen. Tässä väitöskirjassa ehdotetaan HLS:n käyttöä koko enkooderin suunnitteluprosessissa. Dataintensiivisistä koodaustyökaluista, kuten intra-ennustus ja diskreetit muunnokset, myös enemmän kontrollia vaativiin kokonaisuuksiin, kuten entropiakoodaukseen. Avoimen lähdekoodin Kvazaar HEVC -enkooderin C-lähdekoodia hyödynnetään tässä työssä referenssinä HLS-suunnittelulle sekä toteutuksen varmentamisessa. Suorituskykytulokset saadaan ja raportoidaan ohjelmoitavalla porttimatriisilla (FPGA). Tämän väitöskirjan tärkein tuotos on HEVC intra enkooderin prototyyppi. Prototyyppi koostuu Nokia AirFrame Cloud Server palvelimesta, varustettuna kahdella 2.4 GHz:n 14-ytiminen Intel Xeon prosessorilla, sekä kahdesta Intel Arria 10 GX FPGA kiihdytinkortista, jotka voidaan kytkeä serveriin käyttäen joko peripheral component interconnect express (PCIe) liitäntää tai 40 gigabitin Ethernettiä. Prototyyppijärjestelmä saavuttaa reaaliaikaisen 4K enkoodausnopeuden, jopa 120 kuvaa sekunnissa. Lisäksi järjestelmän suorituskykyä on helppo skaalata paremmaksi lisäämällä järjestelmään käytännössä minkä tahansa määrän verkkoon kytkettäviä FPGA-kortteja. Monimutkaisen HEVC:n tehokas mallinnus ja sen monipuolisten ominaisuuksien mukauttaminen reaaliaikaiselle HW HEVC enkooderille ei ole triviaali tehtävä, koska HW-toteutukset ovat perinteisesti erittäin aikaa vieviä. Tämä väitöskirja osoittaa, että HLS:n avulla pystytään nopeuttamaan kehitysaikaa, tarjoamaan ennen näkemätöntä suunnittelun skaalautuvuutta, ja silti osoittamaan kilpailukykyisiä QoR-arvoja ja absoluuttista suorituskykyä verrattuna olemassa oleviin toteutuksiin.High-Level Synthesis (HLS) is an automated design process that seeks to improve productivity over traditional design methods by increasing design abstraction from register transfer level (RTL) to behavioural level. Various commercial HLS tools have been available on the market since the 1990s, but only recently they have started to gain adoption across industry and academia. The slow adoption rate has mainly stemmed from lower quality of results (QoR) than obtained with conventional hardware description languages (HDLs). However, the latest HLS tool generations have substantially narrowed the QoR gap. This thesis studies the feasibility of HLS in video codec development. It introduces several HLS implementations for High Efficiency Video Coding (HEVC) , that is the key enabling technology for numerous modern media applications. HEVC doubles the coding efficiency over its predecessor Advanced Video Coding (AVC) standard for the same subjective visual quality, but typically at the cost of considerably higher computational complexity. Therefore, real-time HEVC calls for automated design methodologies that can be used to minimize the HW implementation and verification effort. This thesis proposes to use HLS throughout the whole encoder design process. From data-intensive coding tools, like intra prediction and discrete transforms, to more control-oriented tools, such as entropy coding. The C source code of the open-source Kvazaar HEVC encoder serves as a design entry point for the HLS flow, and it is also utilized in design verification. The performance results are gathered with and reported for field programmable gate array (FPGA) . The main contribution of this thesis is an HEVC intra encoder prototype that is built on a Nokia AirFrame Cloud Server equipped with 2.4 GHz dual 14-core Intel Xeon processors and two Intel Arria 10 GX FPGA Development Kits, that can be connected to the server via peripheral component interconnect express (PCIe) generation 3 or 40 Gigabit Ethernet. The proof-of-concept system achieves real-time. 4K coding speed up to 120 fps, which can be further scaled up by adding practically any number of network-connected FPGA cards. Overcoming the complexity of HEVC and customizing its rich features for a real-time HEVC encoder implementation on hardware is not a trivial task, as hardware development has traditionally turned out to be very time-consuming. This thesis shows that HLS is able to boost the development time, provide previously unseen design scalability, and still result in competitive performance and QoR over state-of-the-art hardware implementations

Security of Ubiquitous Computing Systems

The chapters in this open access book arise out of the EU Cost Action project Cryptacus, the objective of which was to improve and adapt existent cryptanalysis methodologies and tools to the ubiquitous computing framework. The cryptanalysis implemented lies along four axes: cryptographic models, cryptanalysis of building blocks, hardware and software security engineering, and security assessment of real-world systems. The authors are top-class researchers in security and cryptography, and the contributions are of value to researchers and practitioners in these domains. This book is open access under a CC BY license

Security of Ubiquitous Computing Systems

The chapters in this open access book arise out of the EU Cost Action project Cryptacus, the objective of which was to improve and adapt existent cryptanalysis methodologies and tools to the ubiquitous computing framework. The cryptanalysis implemented lies along four axes: cryptographic models, cryptanalysis of building blocks, hardware and software security engineering, and security assessment of real-world systems. The authors are top-class researchers in security and cryptography, and the contributions are of value to researchers and practitioners in these domains. This book is open access under a CC BY license