Memory Access Optimizations for High-Performance Computing

This paper discusses the importance of memory access optimizations which are shown to be highly effective on the MasPar architecture. The study is based on two MasPar machines, a 16K-processor MP-1 and a 4K-processor MP-2. A software pipelining technique overlaps memory accesses with computation and/or communication. Another optimization, called the register window technique reduces the number of loads in a loop. These techniques are evaluated using three parallel matrix multiplication algorithms on both the MasPar machines. The matrix multiplication study shows that for a highly computation intensive problem, reducing the interprocessor communication can become a secondary issue compared to memory access optimization. Also, it is shown that memory access optimizations can play a more important role than the choice of a superior parallel algorithm. Keywords: load/store architecture, memory accesses, matrix multiplication, parallel programming

Investigation into the wafer-scale integration of fine-grain parallel processing computer systems

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.This thesis investigates the potential of wafer-scale integration (WSI) for the implementation of low-cost fine-grain parallel processing computer systems. As WSI is a relatively new subject, there was little work on which to base investigations. Indeed, most WSI architectures existed only as untried and sometimes vague proposals. Accordingly, the research strategy approached this problem by identifying a representative WSI structure and architecture on which to base investigations. An analysis of architectural proposals identified associative memory to be general purpose parallel processing component used in a wide range of WSI architectures. Furthermore, this analysis provided a set of WSI-level design requirements to evaluate the sustainability of different architectures as research vehicles. The WSI-ASP (WASP) device, which has a large associative memory as its main component is shown to meet these requirements and hence was chosen as the research vehicle. Consequently, this thesis addresses WSI potential through an in-depth investigation into the feasibility of implementing a large associative memory for the WASP device that meets the demanding technological constraints of WSI. Overall, the thesis concludes that WSI offers significant potential for the implementation of low-cost fine-grain parallel processing computer systems. However, due to the dual constraints of thermal management and the area required for the power distribution network, power density is a major design constraint in WSI. Indeed, it is shown that WSI power densities need to be an order of magnitude lower than VLSI power densities. The thesis demonstrates that for associative memories at least, VLSI designs are unsuited to implementation in WSI. Rather, it is shown that WSI circuits must be closely matched to the operational environment to assure suitable power densities. These circuits are significantly larger than their VLSI equivalents. Nonetheless, the thesis demonstrates that by concentrating on the most power intensive circuits, it is possible to achieve acceptable power densities with only a modest increase in area overheads.SER

Systolic genetic search, a parallel metaheuristic for GPUs

La utilización de unidades de procesamiento gráfico (GPUs) para la resolución de problemas de propósito general ha experimentado un crecimiento vertiginoso en los últimos años, sustentado en su amplia disponibilidad, su bajo costo económico y en contar con una arquitectura inherentemente paralela, así como en la aparición de lenguajes de programación de propósito general que han facilitado el desarrollo de aplicaciones en estas plataformas. En este contexto, el diseño de nuevos algoritmos paralelos que puedan beneficiarse del uso de GPUs es una línea de investigación prometedora e interesante. Las metaheurísticas son algoritmos estocásticos capaces de encontrar soluciones muy precisas (muchas veces óptimas) a problemas de optimización en un tiempo razonable. Sin embargo, como muchos problemas de optimización involucran tareas que exigen grandes recursos computacionales y/o el tamaño de las instancias que se están abordando actualmente se están volviendo muy grandes, incluso las metaheurísticas pueden ser computacionalmente muy costosas. En este escenario, el paralelismo surge como una alternativa exitosa con el fin de acelerar la búsqueda de este tipo de algoritmos. Además de permitir reducir el tiempo de ejecución de los algoritmos, las metaheurísticas paralelas a menudo son capaces de mejorar la calidad de los resultados obtenidos por los algoritmos secuenciales tradicionales.Si bien el uso de GPUs ha representado un dominio inspirador también para la investigación en metaheurísticas paralelas, la mayoría de los trabajos previos tenían como objetivo portar una familia existente de algoritmos a este nuevo tipo de hardware. Como consecuencia, muchas publicaciones están dirigidas a mostrar el ahorro en tiempo de ejecución que se puede lograr al ejecutar los diferentes tipos paralelos de metaheurísticas existentes en GPU. En otras palabras, a pesar de que existe un volumen considerable de trabajo sobre este tópico, se han propuesto pocas ideas novedosas que busquen diseñar nuevos algoritmos y/o modelos de paralelismo que exploten explícitamente el alto grado de paralelismo disponible en las arquitecturas de las GPUs. Esta tesis aborda el diseño de una propuesta innovadora de algoritmo de optimización paralelo denominada Búsqueda Genética Sistólica (SGS), que combina ideas de los campos de metaheurísticas y computación sistólica. SGS, así como la computación sistólica, se inspiran en el mismo fenómeno biológico: la contracción sistólica del corazón que hace posible la circulación de la sangre. En SGS, las soluciones circulan de forma síncrona a través de una grilla (rejilla) de celdas. Cuando dos soluciones se encuentran en una celda se aplican operadores evolutivos adaptados para generar nuevas soluciones que continúan moviéndose a través de la grilla (rejilla). La implementación de esta nueva propuesta saca partido especialmente de las características específicas de las GPUs. Un extenso análisis experimental que considera varios problemas de benchmark clásicos y dos problemas del mundo real del área de Ingeniería de Software, muestra que el nuevo algoritmo propuesto es muy efectivo, encontrando soluciones óptimas o casi óptimas en tiempos de ejecución cortos. Además, los resultados numéricos obtenidos por SGS son competitivos con los resultados del estado del arte para los dos problemas del mundo real en cuestión. Por otro lado, la implementación paralela en GPU de SGS ha logrado un alto rendimiento, obteniendo grandes reducciones de tiempo de ejecución con respecto a la implementación secuencial y mostrando que escala adecuadamente cuando se consideran instancias de tamaño creciente. También se ha realizado un análisis teórico de las capacidades de búsqueda de SGS para comprender cómo algunos aspectos del diseño del algoritmo afectan a sus resultados numéricos. Este análisis arroja luz sobre algunos aspectos del funcionamiento de SGS que pueden utilizarse para mejorar el diseño del algoritmo en futuras variantes

Data decomposition and load balancing for networked data-parallel processing

Graduation date: 199

Proceedings of the Caltech Conference on Very Large Scale Integration, held at the California Institute of Technology 22 - 24 January 1979 ; Organized by the Caltech Computer Science Department and the Caltech Industrial Associates Office

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Index to 1985 NASA Tech Briefs, volume 10, numbers 1-4

Short announcements of new technology derived from the R&D activities of NASA are presented. These briefs emphasize information considered likely to be transferrable across industrial, regional, or disciplinary lines and are issued to encourage commercial application. This index for 1985 Tech Briefs contains abstracts and four indexes: subject, personal author, originating center, and Tech Brief Number. The following areas are covered: electronic components and circuits, electronic systems, physical sciences, materials, life sciences, mechanics, machinery, fabrication technology, and mathematics and information sciences

Biofunctional hydrogels for skeletal muscle constructs

Skeletal muscle tissue damage costs the US government hundreds of billions of dollars annually. Meanwhile, there is great potential to use skeletal muscle as a scalable actuator system, covering wide length scales, frequencies, and force regimes. Hence, the interest in soft robotics and regenerative medicine methods to engineer skeletal muscle has increased in recent years. The challenges to generate a functional muscle strip are typical to those of tissue engineering, where common issues such as cell source, material scaffold, bioreactor method or configuration play key roles. Specifically, it is important to translate the existing body of myogenesis knowledge into engineering muscle constructs by examining the impact of the cell microenvironment on growth, alignment, fusion, and differentiation of skeletal muscle cells. The main motivation behind this thesis was to generate a contractile 3D skeletal muscle construct utilizing organized biochemical and physical cues to guide muscle cell differentiation and maturation. Such a construct is expected to play an important role in medical applications and the development of soft robotics. To do this, 3D, swollen hydrogels were chosen to provide tailorable platforms that support cellular activities to similar extents as native matrices. For this work, we utilized an engineered bio-functionalized poly(ethylene glycol)-(PEG)-hydrogel with maleimide (MAL) cross-linking reaction chemistry that gels rapidly with high reaction efficiency under cytocompatible reaction conditions. PEG alone has been shown to have low protein adsorption, a minimal inflammatory profile, well established chemistry, and a long history of safety in vivo. The PEG-MAL system in particular allows “plug-and-play” design variation, control over polymerization time, and small degradation products. To develop an effective soft biomaterial for the development of an aligned, functional muscle construct, we (i) screened hydrogel properties for differentiation, (ii) recreated alignment of skeletal muscle cells, (iii) determined effective generated force upon action of an external agonist. The impact of this study in generating a controllable force actuator will be significant in the construction of biological machines. Concomitantly, this study will provide a unique regenerative solution for skeletal muscle tissue repair and regeneration.Ph.D