From Physics Model to Results: An Optimizing Framework for Cross-Architecture Code Generation

Starting from a high-level problem description in terms of partial differential equations using abstract tensor notation, the Chemora framework discretizes, optimizes, and generates complete high performance codes for a wide range of compute architectures. Chemora extends the capabilities of Cactus, facilitating the usage of large-scale CPU/GPU systems in an efficient manner for complex applications, without low-level code tuning. Chemora achieves parallelism through MPI and multi-threading, combining OpenMP and CUDA. Optimizations include high-level code transformations, efficient loop traversal strategies, dynamically selected data and instruction cache usage strategies, and JIT compilation of GPU code tailored to the problem characteristics. The discretization is based on higher-order finite differences on multi-block domains. Chemora's capabilities are demonstrated by simulations of black hole collisions. This problem provides an acid test of the framework, as the Einstein equations contain hundreds of variables and thousands of terms.Comment: 18 pages, 4 figures, accepted for publication in Scientific Programmin

Massively parallel simulations of binary black holes with Dendro-GR

We present results from the new Dendro-GR code. These include simulations of binary black hole mergers for mass ratios up to q=16. Dendro-GR uses Wavelet Adaptive Multi-Resolution (WAMR) to generate an unstructured grid adapted to the spacetime geometry together with an octree based data structure. We demonstrate good scaling, improved convergence properties and efficient use of computational resources. We validate the code with comparisons to LazEv

The Peano software---parallel, automaton-based, dynamically adaptive grid traversals

We discuss the design decisions, design alternatives, and rationale behind the third generation of Peano, a framework for dynamically adaptive Cartesian meshes derived from spacetrees. Peano ties the mesh traversal to the mesh storage and supports only one element-wise traversal order resulting from space-filling curves. The user is not free to choose a traversal order herself. The traversal can exploit regular grid subregions and shared memory as well as distributed memory systems with almost no modifications to a serial application code. We formalize the software design by means of two interacting automata—one automaton for the multiscale grid traversal and one for the application-specific algorithmic steps. This yields a callback-based programming paradigm. We further sketch the supported application types and the two data storage schemes realized before we detail high-performance computing aspects and lessons learned. Special emphasis is put on observations regarding the used programming idioms and algorithmic concepts. This transforms our report from a “one way to implement things” code description into a generic discussion and summary of some alternatives, rationale, and design decisions to be made for any tree-based adaptive mesh refinement software

Parallel computing 2011, ParCo 2011: book of abstracts

This book contains the abstracts of the presentations at the conference Parallel Computing 2011, 30 August - 2 September 2011, Ghent, Belgiu

TweeProfiles4: a weighted multidimensional stream clustering algorithm

O aparecimento das redes sociais abriu aos utilizadores a possibilidade de facilmente partilharem as suas ideias a respeito de diferentes temas, o que constitui uma fonte de informação enriquecedora para diversos campos. As plataformas de microblogging sofreram um grande crescimento e de forma constante nos últimos anos. O Twitter é o site de microblogging mais popular, tornando-se uma fonte de dados interessante para extração de conhecimento. Um dos principais desafios na análise de dados provenientes de redes sociais é o seu fluxo, o que dificulta a aplicação de processos tradicionais de data mining. Neste sentido, a extração de conhecimento sobre fluxos de dados tem recebido um foco significativo recentemente. O TweeProfiles é a uma ferramenta de data mining para análise e visualização de dados do Twitter sobre quatro dimensões: espacial (a localização geográfica do tweet), temporal (a data de publicação do tweet), de conteúdo (o texto do tweet) e social (o grafo dos relacionamentos). Este é um projeto em desenvolvimento que ainda possui muitos aspetos que podem ser melhorados. Uma das recentes melhorias inclui a substituição do algoritmo de clustering original, o qual não suportava o fluxo contínuo dos dados, por um método de streaming. O objetivo desta dissertação passa pela continuação do desenvolvimento do TweeProfiles. Em primeiro lugar, será proposto um novo algoritmo de clustering para fluxos de dados com o objetivo de melhorar o existente. Para esse efeito será desenvolvido um algoritmo incremental com suporte para fluxos de dados multi-dimensionais. Esta abordagem deve permitir ao utilizador alterar dinamicamente a importância relativa de cada dimensão do processo de clustering. Adicionalmente, a avaliação empírica dos resultados será alvo de melhoramento através da identificação e implementação de medidas adequadas de avaliação dos padrões extraídos. O estudo empírico será realizado através de tweets georreferenciados obtidos pelo SocialBus.The emergence of social media made it possible for users to easily share their thoughts on different topics, which constitutes a rich source of information for many fields. Microblogging platforms experienced a large and steady growth over the last few years. Twitter is the most popular microblogging site, making it an interesting source of data for pattern extraction. One of the main challenges of analyzing social media data is its continuous nature, which makes it hard to use traditional data mining. Therefore, mining stream data has also received a lot of attention recently.TweeProfiles is a data mining tool for analyzing and visualizing Twitter data over four dimensions: spatial (the location of the tweet), temporal (the timestamp of the tweet), content (the text of the tweet) and social (relationship graph). This is an ongoing project which still has many aspects that can be improved. For instance, it was recently improved by replacing the original clustering algorithm which could not handle the continuous flow of data with a streaming method. The goal of this dissertation is to continue the development of TweeProfiles. First, the stream clustering process will be improved by proposing a new algorithm. This will be achieved by developing an incremental algorithm with support for multi-dimensional streaming data. Moreover, it should make it possible for the user to dynamically change the relative importance of each dimension in the clustering. Additionally, the empirical evaluation of the results will also be improved.Suitable measures to evaluate the extracted patterns will be identified and implemented. An empirical study will be done using data consisting of georeferenced tweets from SocialBus

HPCCP/CAS Workshop Proceedings 1998

This publication is a collection of extended abstracts of presentations given at the HPCCP/CAS (High Performance Computing and Communications Program/Computational Aerosciences Project) Workshop held on August 24-26, 1998, at NASA Ames Research Center, Moffett Field, California. The objective of the Workshop was to bring together the aerospace high performance computing community, consisting of airframe and propulsion companies, independent software vendors, university researchers, and government scientists and engineers. The Workshop was sponsored by the HPCCP Office at NASA Ames Research Center. The Workshop consisted of over 40 presentations, including an overview of NASA's High Performance Computing and Communications Program and the Computational Aerosciences Project; ten sessions of papers representative of the high performance computing research conducted within the Program by the aerospace industry, academia, NASA, and other government laboratories; two panel sessions; and a special presentation by Mr. James Bailey

A Survey on the Evolution of Stream Processing Systems

Stream processing has been an active research field for more than 20 years, but it is now witnessing its prime time due to recent successful efforts by the research community and numerous worldwide open-source communities. This survey provides a comprehensive overview of fundamental aspects of stream processing systems and their evolution in the functional areas of out-of-order data management, state management, fault tolerance, high availability, load management, elasticity, and reconfiguration. We review noteworthy past research findings, outline the similarities and differences between early ('00-'10) and modern ('11-'18) streaming systems, and discuss recent trends and open problems.Comment: 34 pages, 15 figures, 5 table

Hypersonic flows around complex geometries with adaptive mesh refinement and immersed boundary method

This thesis develops and validates a computational fluid dynamics numerical method for hypersonic flows; and uses it to conduct two novel investigations. The numerical method involves a novel combination of structured adaptive mesh refinement, ghost-point immersed boundary and artificial dissipation shock-stable Euler flux discretisation. The method is high-order, low dissipation and stable up to Mach numbers $M \lesssim 30$ with stationary or moving complex geometries; it is shown to be suitable for direct numerical simulations of laminar and turbulent flows. The method's performance is assessed through various test cases. Firstly, heat transfer to proximal cylinders in hypersonic flow is investigated to improve understanding of destructive atmospheric entries of meteors, satellites and spacecraft components. Binary bodies and clusters with five bodies are considered. With binary proximal bodies, the heat load and peak heat transfer are augmented for either or both proximal bodies by $+20\%$ to $-90\%$ of an isolated body. Whereas with five bodies, the cluster-averaged heat load varied between $+20\%$ to $-60\%$ of an isolated body. Generally, clusters which are thin in the direction perpendicular to free-stream velocity and long in the direction parallel to the free-stream velocity have their heat load reduced. In contrast, clusters which are thick and thin in directions perpendicular and parallel to the free-stream velocity feel an increased heat load. Secondly, hypersonic ablation patterns are investigated. Ablation patterns form on spacecraft thermal protection systems and meteor surfaces, where their development and interactions with the boundary layer are poorly understood. Initially, a simple subliming sphere case without solid conduction in hypersonic laminar flow is used to validate the numerical method. Where the surface recession is artificially sped-up via the wall Damk\"{o}hler number without introducing significant errors in the shape change. Then, a case with transitional inflow over a backward facing step with a subliming boundary is devised. Differential ablation is observed to generate surface roughness and add vorticity to the boundary layer. A maximum surface recession of $\sim 0.8\times$ and a maximum surface fluctuation of $\sim 0.2\times$ the inflow boundary layer thickness were generated over two flow times.Open Acces