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Reconfigurable computing architectures are gaining popularity as a replacement for general-purpose architectures for many high performance embedded applications. These machines support parallel computation and direct the data from the producers of an intermediate result to the consumers over custom pathways. The Wormhole Run-time Reconfigurable (RTR) computing architecture is a concept developed at Virginia Tech to address the weaknesses of contemporary FPGAs for configurable computing. The Stallion chip is a full-custom configurable computing "FPGA"-like integrated circuit with a coarse grained nature. Based on the result of the first generation device, the Colt chip, the Stallion chip is a follow-up configurable computing chip. This thesis focuses on the VLSI layout implementation of the Stallion chip. Effort has been made to explain many facts and advantages of the Wormhole Configurable Computing Machine (CCM). Design techniques, strategies, circuit characterization, performance estimation, and ways to solve problems when using CAD layout design tools are illustrated. / Master of Science

Este trabalho apresenta a implementação de um roteador global de circuitos integrados capaz de tratar os problemas de roteamento atuais, utilizando como referência para avaliação os circuitos de benchmark publicados durante as competições de roteamento global realizadas no ACM International Symposium on Physical Design 2007 e 2008. O roteador global desenvolvido utiliza como ferramenta principal a técnica de ripup and reroute associada às técnicas de roteamento monotônico e maze routing, ambas com grande histórico de uso nas ferramentas acadêmicas descritas também neste trabalho. O desenvolvimento da ferramenta também possui características diferenciadas e únicas, com um novo método de ordenamento das redes durante a fase de rip-up and reroute. Para a geração dos resultados foram definidas duas versões diferentes da ferramenta, sendo estas duas versões analisadas com duas diferentes técnicas de construção das árvores de roteamento, gerando no total quatro configurações da ferramenta. Como decisão de projeto, a versão principal utilizada no desenvolvimento e discussão dos resultados é a versão que prioriza a qualidade do roteamento, utilizando MSTs para construção das árvores de roteamento. Os resultados mostram que o roteador global desenvolvido é capaz de gerar resultados com boa qualidade mesmo sem fazer uso de técnicas de identificação de áreas de congestionamento, sem otimizações pós-roteamento e sem nenhuma forma de ajuste (tuning) para os diferentes circuitos de benchmark, apesar de ainda ter tempo de execução acima dos apresentados por outras ferramentas acadêmicas. O foco durante o processo de desenvolvimento e implementação da ferramenta foram os circuitos mais recentes, entretanto a ferramenta obteve ótimos resultados também para os circuitos publicados no ISPD 1998, gerando soluções com qualidade similar ou melhor que as reportadas na literatura. A diferença dos resultados deste trabalho em relação aos melhores resultados dos roteadores globais com código disponível, para circuitos 3D lançados no ISPD 2008 é de, em média, 1,78%1 na métrica de comprimento de fio sem considerar o custo das vias e de 15,56% considerando o custo da via como uma unidade de comprimento de fio (ISPD 2008), para a versão voltada a qualidade de roteamento. Já para a versão da ferramenta que busca a convergência o mais rápido possível a diferença foi de 3,39% e 16,32%, respectivamente. As maiores diferenças são encontradas nos circuitos mais difíceis de gerar uma solução sem violações. Isso mostra como as técnicas de identificação de região podem contribuir tanto para uma convergência mais rápida quanto para evitar que fios passem por rotas desnecessárias durante a fase de negociação. Na métrica que avalia as vias como custo de uma unidade de comprimento, os resultados obtidos apresentam em média 18,67% maior comprimento de fio que os melhores resultados da literatura, sendo que dois circuitos com solução sem violações2 apresentam resultado com violações utilizando a ferramenta desenvolvida neste trabalho. / This work describes the implementation of an integrated circuit global router capable of handling the current routing problems, using as a reference the evaluation of benchmark circuits from the two global routing contests held in ISPD 2007 and 2008. The developed global router uses rip-up and reroute as the main technique associated with monotonic and maze routing techniques, both with large history of use in academic tools, also described in this work. The tool also has distinctive and unique characteristics, with a new method of net ordering during the rip-up and reroute stage. In order to generate the results were defined two different versions of the tool analyzed with two different techniques of routing tree construction, generating a total of four configurations. As a design decision, the major version used in the development and discussion of results is the version that prioritizes the routing quality, using MSTs for tree construction. The results show that the global router developed is able to generate good results even without making use of techniques to identify congestion areas, without post-routing optimizations and without any form of tuning for the different benchmark circuits, despite having run time above other academic tools. The focus during the development and implementation of the tool were the newer circuits, however the tool also obtained excellent results for the circuits released in ISPD 1998, generating solutions with similar quality or better than those reported in the literature. The difference in the results of this work over the best results generated with the available code global routers for 3D circuits released in ISPD 2008 is, on average, 2.53% in wirelength metric without considering the cost of vias and 18.34% considering the cost of the vias as one wirelength unit (ISPD 2008), for the best routing quality version. As for the version of the tool that seeks convergence as soon as possible the difference was 3.82% and 17.03%, respectively. The largest differences were found in the most difficult circuits to generate a solution without violations. This shows how the techniques of congested region identification can contribute to both a faster convergence and to avoid unnecessary wire detours during the negotiation phase. In the metric that evaluates the cost of vias as one wirelength unit, the results show an average of 22.5% greater wirelength than the best results found in literature. Also, the developed global router was unable to find a violation free solution for two circuits that are known to have a violation free solution3.

Mathematical and statistical modeling of biological systems is a desired goal for many years. Many biochemical models are often evaluated using a deterministic approach, which uses differential equations to describe the chemical interactions. However, such an approach is inaccurate for small species populations as it neglects the discrete representation of population values, presents the possibility of negative populations, and does not represent the stochastic nature of biochemical systems. The Stochastic Simulation Algorithm (SSA) developed by Gillespie is able to properly account for these inherent noise fluctuations. Due to the stochastic nature of the Monte Carlo simulations, large numbers of simulations must be run in order to get accurate statistics for the species populations and reactions. However, the algorithm tends to be computationally heavy and leads to long simulation runtimes for large systems. Therefore, this thesis explores implementing the SSA on a Field Programmable Gate Array (FPGA) to improve performance. Employing the Field programmable Gate Arrays exploits the parallelism present in the SSA, providing speedup over the software implementations that execute sequentially. In contrast to prior work that requires re-construction and re-synthesis of the design to simulate a new biochemical system, this work explores the use of reconfigurable hardware in implementing a generic biochemical simulator.