A configurable vector processor for accelerating speech coding algorithms

The growing demand for voice-over-packer (VoIP) services and multimedia-rich applications has made increasingly important the efficient, real-time implementation of low-bit rates speech coders on embedded VLSI platforms. Such speech coders are designed to substantially reduce the bandwidth requirements thus enabling dense multichannel gateways in small form factor. This however comes at a high computational cost which mandates the use of very high performance embedded processors. This thesis investigates the potential acceleration of two major ITU-T speech coding algorithms, namely G.729A and G.723.1, through their efficient implementation on a configurable extensible vector embedded CPU architecture. New scalar and vector ISAs were introduced which resulted in up to 80% reduction in the dynamic instruction count of both workloads. These instructions were subsequently encapsulated into a parametric, hybrid SISD (scalar processor)–SIMD (vector) processor. This work presents the research and implementation of the vector datapath of this vector coprocessor which is tightly-coupled to a Sparc-V8 compliant CPU, the optimization and simulation methodologies employed and the use of Electronic System Level (ESL) techniques to rapidly design SIMD datapaths

System software techniques to enhance reliability of modern platforms

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STATISTICAL MACHINE LEARNING BASED MODELING FRAMEWORK FOR DESIGN SPACE EXPLORATION AND RUN-TIME CROSS-STACK ENERGY OPTIMIZATION FOR MANY-CORE PROCESSORS

The complexity of many-core processors continues to grow as a larger number of heterogeneous cores are integrated on a single chip. Such systems-on-chip contains computing structures ranging from complex out-of-order cores, simple in-order cores, digital signal processors (DSPs), graphic processing units (GPUs), application specific processors, hardware accelerators, I/O subsystems, network-on-chip interconnects, and large caches arranged in complex hierarchies. While the industry focus is on putting higher number of cores on a single chip, the key challenge is to optimally architect these many-core processors such that performance, energy and area constraints are satisfied. The traditional approach to processor design through extensive cycle accurate simulations are ill-suited for designing many-core processors due to the large microarchitecture design space that must be explored. Additionally it is hard to optimize such complex processors and the applications that run on them statically at design time such that performance and energy constraints are met under dynamically changing operating conditions. The dissertation establishes statistical machine learning based modeling framework that enables the efficient design and operation of many-core processors that meets performance, energy and area constraints. We apply the proposed framework to rapidly design the microarchitecture of a many-core processor for multimedia, computer graphics rendering, finance, and data mining applications derived from the Parsec benchmark. We further demonstrate the application of the framework in the joint run-time adaptation of both the application and microarchitecture such that energy availability constraints are met

Overcoming the Intuition Wall: Measurement and Analysis in Computer Architecture

These are exciting times for computer architecture research. Today there is significant demand to improve the performance and energy-efficiency of emerging, transformative applications which are being hammered out by the hundreds for new computing platforms and usage models. This booming growth of applications and the variety of programming languages used to create them is challenging our ability as architects to rapidly and rigorously characterize these applications. Concurrently, hardware has become more complex with the emergence of accelerators, multicore systems, and heterogeneity caused by further divergence between processor market segments. No one architect can now understand all the complexities of many systems and reason about the full impact of changes or new applications. To that end, this dissertation presents four case studies in quantitative methods. Each case study attacks a different application and proposes a new measurement or analytical technique. In each case study we find at least one surprising or unintuitive result which would likely not have been found without the application of our method

High-Order Epistasis Detection in High Performance Computing Systems

Programa Oficial de Doutoramento en Investigación en Tecnoloxías da Información. 524V01[Resumo] Nos últimos anos, os estudos de asociación do xenoma completo (Genome-Wide Association Studies, GWAS) están a gañar moita popularidade de cara a buscar unha explicación xenética á presenza ou ausencia de certas enfermidades nos humanos.Hai un consenso nestes estudos sobre a existencia de interaccións xenéticas que condicionan a expresión de enfermidades complexas, un fenómeno coñecido como epistasia. Esta tese céntrase no estudo deste fenómeno empregando a computación de altas prestacións (High-Performance Computing, HPC) e dende a súa perspectiva estadística: a desviación da expresión dun fenotipo como a suma dos efectos individuais de múltiples variantes xenéticas. Con este obxectivo desenvolvemos unha primeira ferramenta, chamada MPI3SNP, que identifica interaccións de tres variantes a partir dun conxunto de datos de entrada. MPI3SNP implementa unha busca exhaustiva empregando un test de asociación baseado na Información Mutua, e explota os recursos de clústeres de CPUs ou GPUs para acelerar a busca. Coa axuda desta ferramenta avaliamos o estado da arte da detección de epistasia a través dun estudo que compara o rendemento de vintesete ferramentas. A conclusión máis importante desta comparativa é a incapacidade dos métodos non exhaustivos de atopar interacción ante a ausencia de efectos marxinais (pequenos efectos de asociación das variantes individuais que participan na epistasia). Por isto, esta tese continuou centrándose na optimización da busca exhaustiva de epistasia. Por unha parte, mellorouse a eficiencia do test de asociación a través dunha implantación vectorial do mesmo. Por outro lado, creouse un algoritmo distribuído que implementa unha busca exhaustiva capaz de atopar epistasia de calquera orden. Estes dous fitos lógranse en Fiuncho, unha ferramenta que integra toda a investigación realizada, obtendo un rendemento en clústeres de CPUs que supera a todas as súas alternativas no estado da arte. Adicionalmente, desenvolveuse unha libraría para simular escenarios biolóxicos con epistasia chamada Toxo. Esta libraría permite a simulación de epistasia seguindo modelos de interacción xenética existentes para orde alto.[Resumen] En los últimos años, los estudios de asociación del genoma completo (Genome- Wide Association Studies, GWAS) están ganando mucha popularidad de cara a buscar una explicación genética a la presencia o ausencia de ciertas enfermedades en los seres humanos. Existe un consenso entre estos estudios acerca de que muchas enfermedades complejas presentan interacciones entre los diferentes genes que intervienen en su expresión, un fenómeno conocido como epistasia. Esta tesis se centra en el estudio de este fenómeno empleando la computación de altas prestaciones (High-Performance Computing, HPC) y desde su perspectiva estadística: la desviación de la expresión de un fenotipo como suma de los efectos de múltiples variantes genéticas. Para ello se ha desarrollado una primera herramienta, MPI3SNP, que identifica interacciones de tres variantes a partir de un conjunto de datos de entrada. MPI3SNP implementa una búsqueda exhaustiva empleando un test de asociación basado en la Información Mutua, y explota los recursos de clústeres de CPUs o GPUs para acelerar la búsqueda. Con la ayuda de esta herramienta, hemos evaluado el estado del arte de la detección de epistasia a través de un estudio que compara el rendimiento de veintisiete herramientas. La conclusión más importante de esta comparativa es la incapacidad de los métodos no exhaustivos de localizar interacciones ante la ausencia de efectos marginales (pequeños efectos de asociación de variantes individuales pertenecientes a una relación epistática). Por ello, esta tesis continuó centrándose en la optimización de la búsqueda exhaustiva. Por un lado, se mejoró la eficiencia del test de asociación a través de una implementación vectorial del mismo. Por otra parte, se diseñó un algoritmo distribuido que implementa una búsqueda exhaustiva capaz de encontrar relaciones epistáticas de cualquier tamaño. Estos dos hitos se logran en Fiuncho, una herramienta que integra toda la investigación realizada, obteniendo un rendimiento en clústeres de CPUs que supera a todas sus alternativas del estado del arte. A mayores, también se ha desarrollado una librería para simular escenarios biológicos con epistasia llamada Toxo. Esta librería permite la simulación de epistasia siguiendomodelos de interacción existentes para orden alto.[Abstract] In recent years, Genome-Wide Association Studies (GWAS) have become more and more popular with the intent of finding a genetic explanation for the presence or absence of particular diseases in human studies. There is consensus about the presence of genetic interactions during the expression of complex diseases, a phenomenon called epistasis. This thesis focuses on the study of this phenomenon, employingHigh- Performance Computing (HPC) for this purpose and from a statistical definition of the problem: the deviation of the expression of a phenotype from the addition of the individual contributions of genetic variants. For this purpose, we first developedMPI3SNP, a programthat identifies interactions of three variants froman input dataset. MPI3SNP implements an exhaustive search of epistasis using an association test based on the Mutual Information and exploits the resources of clusters of CPUs or GPUs to speed up the search. Then, we evaluated the state-of-the-art methods with the help of MPI3SNP in a study that compares the performance of twenty-seven tools. The most important conclusion of this study is the inability of non-exhaustive approaches to locate epistasis in the absence of marginal effects (small association effects of individual variants that partake in an epistasis interaction). For this reason, this thesis continued focusing on the optimization of the exhaustive search. First, we improved the efficiency of the association test through a vector implementation of this procedure. Then, we developed a distributed algorithm capable of locating epistasis interactions of any order. These two milestones were achieved in Fiuncho, a program that incorporates all the research carried out, obtaining the best performance in CPU clusters out of all the alternatives of the state-of-the-art. In addition, we also developed a library to simulate particular scenarios with epistasis called Toxo. This library allows for the simulation of epistasis that follows existing interaction models for high-order interactions

Characterizing and Accelerating Bioinformatics Workloads on Modern Microarchitectures

Bioinformatics, the use of computer techniques to analyze biological data, has been a particularly active research field in the last two decades. Advances in this field have contributed to the collection of enormous amounts of data, and the sheer amount of available data has started to overtake the processing capability possible with current computer systems. Clearly, computer architects need to have a better understanding of how bioinformatics applications work and what kind of architectural techniques could be used to accelerate these important scientific workloads on future processors. In this dissertation, we develop a bioinformatic benchmark suite and provide a detailed characterization of these applications in common use today from a computer architect's point of view. We analyze a wide range of detailed execution characteristics including instruction mix, IPC measurements, L1 and L2 cache misses on a real architecture; and proceed to analyze the workloads' memory access characteristics. We then concentrate on accelerating a particularly computationally intensive bioinformatics workload on the novel Cell Broadband Engine multiprocessor architecture. The HMMER workload is used for protein profile searching using hidden Markov models, and most of its execution time is spent running the Viterbi algorithm. We parallelize and partition the HMMER application to implement it on the Cell Broadband Engine. In order to run the Viterbi algorithm on the 256KB local stores of the Cell BE synergistic processing units (SPEs), we present a method to develop a fast SIMD implementation of the Viterbi algorithm that reduces the storage requirements significantly. Our HMMER implementation for the Cell BE architecture, Cell-HMMER, exploits the multiple levels of parallelism inherent in this application, and can run protein profile searches up to 27.98 times faster than a modern dual-core x86 microprocessor