Showing papers in "Scientific Programming in 2012"
TL;DR: This paper developed Isorropia as a Trilinos package, which supports most of Zoltan's features via a matrix-based interface, and serves as a platform for additional matrix algorithms.
Abstract: Partitioning and load balancing are important problems in scientific computing that can be modeled as combinatorial problems using graphs or hypergraphs. The Zoltan toolkit was developed primarily for partitioning and load balancing to support dynamic parallel applications, but has expanded to support other problems in combinatorial scientific computing, including matrix ordering and graph coloring. Zoltan is based on abstract user interfaces and uses callback functions. To simplify the use and integration of Zoltan with other matrix-based frameworks, such as the ones in Trilinos, we developed Isorropia as a Trilinos package, which supports most of Zoltan's features via a matrix-based interface. In addition to providing an easy-to-use matrix-based interface to Zoltan, Isorropia also serves as a platform for additional matrix algorithms. In this paper, we give an overview of the Zoltan and Isorropia toolkits, their design, capabilities and use. We also show how Zoltan and Isorropia enable large-scale, parallel scientific simulations, and describe current and future development in the next-generation package Zoltan2.
101 citations
TL;DR: Together, Amesos2 and Belos form a complete suite of sparse linear solvers, which favors algorithms that solve higher-level problems, such as multiple simultaneous linear systems and sequences of related linear systems, faster than standard algorithms.
Abstract: Solvers for large sparse linear systems come in two categories: direct and iterative. Amesos2, a package in the Trilinos software project, provides direct methods, and Belos, another Trilinos package, provides iterative methods. Amesos2 offers a common interface to many different sparse matrix factorization codes, and can handle any implementation of sparse matrices and vectors, via an easy-to-extend C++ traits interface. It can also factor matrices whose entries have arbitrary “Scalar” type, enabling extended-precision and mixed-precision algorithms. Belos includes many different iterative methods for solving large sparse linear systems and least-squares problems. Unlike competing iterative solver libraries, Belos completely decouples the algorithms from the implementations of the underlying linear algebra objects. This lets Belos exploit the latest hardware without changes to the code. Belos favors algorithms that solve higher-level problems, such as multiple simultaneous linear systems and sequences of related linear systems, faster than standard algorithms. The package also supports extended-precision and mixed-precision algorithms. Together, Amesos2 and Belos form a complete suite of sparse linear solvers.
90 citations
Journal Article•
TL;DR: This work develops a large stereo dataset with ground truth disparity maps using highly realistic computer graphic techniques and applies some of the most common stereo matching techniques to this dataset to confirm that the highly realistic CG stereo images remain as challenging as real-world stereo images.
Abstract: Stereo matching is one of the most active research areas in computer vision. While a large number of algorithms for stereo correspondence have been developed, research in some branches of the field has been constrained due to the few number of stereo datasets with ground truth disparity maps available. Having available a large dataset of stereo images with ground truth disparity maps would boost the research on new stereo matching methods, for example, methods based on machine learning. In this work we develop a large stereo dataset with ground truth disparity maps using highly realistic computer graphic techniques. We also apply some of the most common stereo matching techniques to our dataset to confirm that our highly realistic CG stereo images remain as challenging as real-world stereo images. This dataset will also be of great use for camera tracking algorithms, because we provide the exact camera position and rotation in every frame.
63 citations
TL;DR: This paper focuses on some of the most notable changes to the Trilinos project in the last few years.
Abstract: Since An Overview of the Trilinos Project [ACM Trans. Math. Softw. 313 2005, 397--423] was published in 2005, Trilinos has grown significantly. It now supports the development of a broad collection of libraries for scalable computational science and engineering applications, and a full-featured software infrastructure for rigorous lean/agile software engineering. This growth has created significant opportunities and challenges. This paper focuses on some of the most notable changes to the Trilinos project in the last few years.At the time of the writing of this article, the current release version of Trilinos was 10.12.2.
54 citations
TL;DR: This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms.
Abstract: An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering.
46 citations
TL;DR: The Kokkos Array programming model provides library-based approach to implement computational kernels that are performance-portable to CPU-multicore and GPGPU accelerator devices.
Abstract: Large, complex scientific and engineering application code have a significant investment in computational kernels to implement their mathematical models. Porting these computational kernels to the collection of modern manycore accelerator devices is a major challenge in that these devices have diverse programming models, application programming interfaces APIs, and performance requirements. The Kokkos Array programming model provides library-based approach to implement computational kernels that are performance-portable to CPU-multicore and GPGPU accelerator devices. This programming model is based upon three fundamental concepts: 1 manycore compute devices each with its own memory space, 2 data parallel kernels and 3 multidimensional arrays. Kernel execution performance is, especially for NVIDIA® devices, extremely dependent on data access patterns. Optimal data access pattern can be different for different manycore devices --potentially leading to different implementations of computational kernels specialized for different devices. The Kokkos Array programming model supports performance-portable kernels by 1 separating data access patterns from computational kernels through a multidimensional array API and 2 introduce device-specific data access mappings when a kernel is compiled. An implementation of Kokkos Array is available through Trilinos [Trilinos website, http://trilinos.sandia.gov/, August 2011].
44 citations
TL;DR: Tpetra, a Trilinos package for parallel linear algebra primitives implementing the Petra object model is presented, based on generic programming via C++ templated types and template metaprogramming.
Abstract: We present Tpetra, a Trilinos package for parallel linear algebra primitives implementing the Petra object model. We describe Tpetra's design, based on generic programming via C++ templated types and template metaprogramming. We discuss some benefits of this approach in the context of scientific computing, with illustrations consisting of code and notable empirical results.
41 citations
TL;DR: This paper describes the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations PDEs and presents shape optimization and uncertainty quantification results for a 3D PDE application.
Abstract: A template-based generic programming approach was presented in Part I of this series of papers [Sci. Program. 20 2012, 197--219] that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations PDEs. We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application.
33 citations
TL;DR: The mathematical ideas and software design principles incorporated in the Intrepid package are described and representative examples showcasing the use are provided both in the context of numerical PDEs and the more general context of data analysis.
Abstract: Intrepid is a Trilinos package for advanced discretizations of Partial Differential Equations PDEs. The package provides a comprehensive set of tools for local, cell-based construction of a wide range of numerical methods for PDEs. This paper describes the mathematical ideas and software design principles incorporated in the package. We also provide representative examples showcasing the use of Intrepid both in the context of numerical PDEs and the more general context of data analysis.
25 citations
TL;DR: A tool is described which enables to convert the GridSpace application source code into a workflow representation which, in turn, may be used for scheduling, provenance, or visualization.
Abstract: For programming and executing complex applications on grid infrastructures, scientific workflows have been proposed as convenient high-level alternative to solutions based on general-purpose programming languages, APIs and scripts. GridSpace is a collaborative programming and execution environment, which is based on a scripting approach and it extends Ruby language with a high-level API for invoking operations on remote resources. In this paper we describe a tool which enables to convert the GridSpace application source code into a workflow representation which, in turn, may be used for scheduling, provenance, or visualization. We describe how we addressed the issues of analyzing Ruby source code, resolving variable and method dependencies, as well as building workflow representation. The solutions to these problems have been developed and they were evaluated by testing them on complex grid application workflows such as CyberShake, Epigenomics and Montage. Evaluation is enriched by representing typical workflow control flow patterns.
13 citations
TL;DR: This paper provides a brief overview of the production-grade I/O libraries in Trios as well as some of the ongoing research efforts that contribute to the experimental libraries inTrios.
Abstract: Trilinos I/O Support Trios is a new capability area in Trilinos that serves two important roles: 1 it provides and supports I/O libraries used by in-production scientific codes; 2 it provides a research vehicle for the evaluation and distribution of new techniques to improve I/O on advanced platforms. This paper provides a brief overview of the production-grade I/O libraries in Trios as well as some of the ongoing research efforts that contribute to the experimental libraries in Trios.
TL;DR: An overview of design considerations for the MueLu package is given: user interfaces, internal design, data management, usage of modern software constructs, leveraging Trilinos capabilities, linear algebra operations and advanced application.
Abstract: MueLu is a library within the Trilinos software project [An overview of Trilinos, Technical Report SAND2003-2927, Sandia National Laboratories, 2003] and provides a framework for parallel multigrid preconditioning methods for large sparse linear systems. While providing efficient implementations of modern multigrid methods based on smoothed aggregation and energy minimization concepts, MueLu is designed to be customized and extended. This article gives an overview of design considerations for the MueLu package: user interfaces, internal design, data management, usage of modern software constructs, leveraging Trilinos capabilities, linear algebra operations and advanced application.
TL;DR: The architecture of the Sundance problem specification components allow immediate extension of a forward simulator for use in an optimization context, and examples of the use of these components to develop full-space and reduced-space codes for linear and nonlinear PDE-constrained inverse problems are shown.
Abstract: Sundance is a package in the Trilinos suite designed to provide high-level components for the development of high-performance PDE simulators with built-in capabilities for PDE-constrained optimization. We review the implications of PDE-constrained optimization on simulator design requirements, then survey the architecture of the Sundance problem specification components. These components allow immediate extension of a forward simulator for use in an optimization context. We show examples of the use of these components to develop full-space and reduced-space codes for linear and nonlinear PDE-constrained inverse problems.
TL;DR: This work presents the first three-dimensional, partial differential equation solver to be built atop the recently released, open-source ForTrilinos package, and demonstrates the level of effort required to set up a high-order, finite-difference solution on a Cartesian grid.
Abstract: We present the first three-dimensional, partial differential equation solver to be built atop the recently released, open-source ForTrilinos package http://trilinos.sandia.gov/packages/fortrilinos. ForTrilinos currently provides portable, object-oriented Fortran 2003 interfaces to the C++ packages Epetra, AztecOO and Pliris in the Trilinos library and framework [ACM Trans. Math. Softw. 313 2005, 397--423]. Epetra provides distributed matrix and vector storage and basic linear algebra calculations. Pliris provides direct solvers for dense linear systems. AztecOO provides iterative sparse linear solvers. We demonstrate how to build a parallel application that encapsulates the Message Passing Interface MPI without requiring the user to make direct calls to MPI except for startup and shutdown. The presented example demonstrates the level of effort required to set up a high-order, finite-difference solution on a Cartesian grid. The example employs an abstract data type ADT calculus [Sci. Program. 164 2008, 329--339] that empowers programmers to write serial code that lower-level abstractions resolve into distributed-memory, parallel implementations. The ADT calculus uses compilable Fortran constructs that resemble the mathematical formulation of the partial differential equation of interest.
TL;DR: An overview of the central Playa objects from a user's perspective is given, application to a sequence of increasingly complex solver algorithms is shown, and timing results for Playa's overloaded operators and other functions are provided.
Abstract: This paper introduces Playa, a high-level user interface layer for composing algorithms for complex multiphysics problems out of objects from other Trilinos packages. Among other features, Playa provides very high-performance overloaded operators implemented through an expression template mechanism. In this paper, we give an overview of the central Playa objects from a user's perspective, show application to a sequence of increasingly complex solver algorithms, provide timing results for Playa's overloaded operators and other functions, and briefly survey some of the implementation issues involved.
TL;DR: In this paper, the authors analyse a history indigena no contexto da historiografia produzida no Brasil e no estado de Mato Grosso do Sul.
Abstract: Neste artigo o autor analisa a historia indigena no contexto da historiografia produzida no Brasil e no estado de Mato Grosso do Sul Apresenta o surgimento e o desenvolvimento desta tendencia historiografica a partir da decada de 1990 e suas principais caracteristicas no Programa de Pos-Graduacao em Historia (PPGH) da Universidade Federal da Grande Dourados (UFGD) Tambem apresenta discussoes teorico-metodologicas sobre a etno-historia e suas possibilidades de aplicacao para o conhecimento da historia dos povos indigenas na America do Sul
TL;DR: In el noroccidnete amazonico, entre otras, two types of fiestas: an enmascarada dedicada a la cosecha de Bactris gassipaes and otrras frutas, and otra flautas sagradas dedicado a evocar seres extraordinarios as mentioned in this paper.
Abstract: En el noroccidnete amazonico se realizan, entre otras, dos tipos de fiestas: una enmascarada dedicada a la cosecha de Bactris gassipaes y otras frutas, y otra con flautas sagradas dedicada a evocar seres extraordinarios. Ellas, cuando coinciden en un mismo pueblo, se realizan en momentos diferentes. Sin embargo, en el caso de los Piaroas y Wiros de la cuenca del Orinoco, ambas fiestas coinciden entiempo y lugar. En este ensayo vamos a describir los personajes y procedimientos que son parte de la fiesta y a evaluar algunos de los juegos de poder de genero y edad que en ella se expresan. Se trata de una fiesta que consolida alianzas de los shamanes y sus comunidades con los duenos de animales y plantas sometidas a la depredacion piaroa, que institucionaliza la expropiacion por los hombres y la redefinicion hacia lo domestico del poder femenino, y que transforma una sociedad sin grandes jerarquias en su citianeidad en una sociedad altamente jerarquizada mientras dura la fiesta.
TL;DR: Recent, previously unpublished advances in the PyTrilinos package are covered, which takes advantage of the flexibility and ease of use of Python, and the efficiency of the underlying C++, C and Fortran numerical kernels.
Abstract: PyTrilinos is a set of Python interfaces to compiled Trilinos packages. This collection supports serial and parallel dense linear algebra, serial and parallel sparse linear algebra, direct and iterative linear solution techniques, algebraic and multilevel preconditioners, nonlinear solvers and continuation algorithms, eigensolvers and partitioning algorithms. Also included are a variety of related utility functions and classes, including distributed I/O, coloring algorithms and matrix generation. PyTrilinos vector objects are compatible with the popular NumPy Python package. As a Python front end to compiled libraries, PyTrilinos takes advantage of the flexibility and ease of use of Python, and the efficiency of the underlying C++, C and Fortran numerical kernels. This paper covers recent, previously unpublished advances in the PyTrilinos package.
TL;DR: In this paper, the authors present a proposal to understand how identities are situated today relating to the territoritalities experienced in Bolivia and Brazil, since these people are currently split because the division of national states.
Abstract: It is intended to reflect, from the history of the people Chiquitano, originally a set of more than twenty ethnic groups that were aldeadas by Jesuits in the Chiquitos mission, elements of contemporary identity and ethnicity. The proposal presented is to understand how identities are situated today relating to the territoritalities experienced in Bolivia and Brazil, since these people are currently split because the division of national states. The fact that they live in one country or in another causes different experiences and propositions of identity. However, until the 1980s the frontier between the two countries was not yet fully institutionalized, and it was possible a transit to and fro, and this freedom allowed maintenance of social relations and kinship networks. How are the identities currently in territorial diversity and historical? How they configure their territoritalities Chiquitanos in Bolivia and Brazil if the indigenous policies are different? How the self-identifications occur if there are different concepts for "Indians" - here and Bolivia indigenous "peasant" or "pueblos originales"? How the official recognition of ethnicity in Brazil Chiquitanos brought new elements that caused conflicts? These are questions we intend to answer in this paper.
TL;DR: In this article, the authors characterize the common or customary law of indigenous peoples in order to identify the legal pluralism existent in Brazil and characterize the orality and the absence of the state in form of entity.
Abstract: This paper aims to characterize the common or customary law of indigenous peoples in order to identify the legal pluralism existent in Brazil. Whereas each society presents its own social organization; positive law -- written, codified and founded on the state -- is not the only source of law, neither the safest or fairest manner to sort societies. The orality and the absence of the state in form of entity, which characterize customary law, give dynamism to indigenous societies and sort these communities based on the social body’s inherent rules.
TL;DR: In this article, the influence of certain basketball elements on the final result by means of regressive analysis has been analyzed and the correlation link between the observed variables which have been established on the basis of simple linear and partial correlation quotients.
Abstract: Statistical modelling of quantitative evaluation of the influence of certain basketball elements onto the final result by means of regressive analysis has enabled us to come to an answer regarding the quantitative parameters and their influence on the final result. The evaluation of regressive models is extracted on the basis of differentation in the final result and differentation of certain quantitative parameters as insubordinate variables. Depending on the choice of quantitative parameters, their scope and the nature itself (absolute or relative), several different regressive models may be formed. The evaluation of influence of certain parameters on the final result has been extracted on the basis of the obtained regressive models and the correlation link between the observed variables which have been established on the basis of simple linear and partial correlation quotients. Based on the obtained results the following can be concluded: (1) the obtained regressive models are in general statistically very significant ; and (2) the obtained regressive models are statistically significant in relation to the included variables, i.e. the observed parameters. In other words, it means that in both cases there is a significant correlation between subordinate variables (difference in the total number of points) and the sets of insubordinate variables. Presented by the quotient of multiple determination, it means that: (1) for the first regressive model on the basis of apsolute elemenents of basketball, R2 = .905, and for the second model on the basis of relative elements of basketball, R2 =.736.
TL;DR: In this article, the authors interweave the different views on the contemporary Indian art through the testimony of Benilda Vergilio, Kadiweu's Indian, who graduated in Design at Dom Bosco Catholic University.
Abstract: The article aims to interweave the different views on the contemporary Indian art through the testimony of Benilda Vergilio, Kadiweu’s Indian, graduated in Design at Dom Bosco Catholic University. The analysis it takes as backdrop the controversies surrounding the anthropological symbolic approaches that over time have had full control and subjugation in the study of art in the anthropological perspective. In this study, conducted by interview with the artist, it was emphasized the cognitive action of art in native context, showing that it is necessary to discuss the essence and meaning of indigenous art, without leaving aside their own speech.
TL;DR: In this article, a discussao a partir de pesquisa de campo, levantamento bibliografico e fontes primarias acerca de tres ocupacoes mbya contemporâneas, a saber, Petim, Passo Grande e Arroio do Conde.
Abstract: Neste ensaio buscamos sistematizar informacoes de cunho historico e etnografico acerca da presenca mbya na regiao hidrografica do Guaiba (Rio Grande do Sul), levando em conta as relacoes estabelecidas entre indigenas e brancos ao longo do processo de configuracao territorial da Bacia Platina. Para tanto, embasamos a discussao a partir de pesquisa de campo, levantamento bibliografico e fontes primarias acerca de tres ocupacoes mbya contemporâneas, a saber, Petim, Passo Grande e Arroio do Conde. Miramos dois objetivos: 1. reunir informacoes existentes e dispersas em varios documentos a fim de contextualizar ocupacoes guarani na Bacia Hidrografica do Guaiba; 2. ressaltar as circunstâncias atuais de ocupacoes em beiras de estradas sob premissas diacronicas, evidenciando a vida mbya nos teko’a e ensaiando algumas consideracoes a respeito das aliancas circunstanciais acionadas no acesso ao territorio.
TL;DR: In this paper, the authors describe how research training is delivered in teaching programas at TECNologico de Antioquia College in Mexico, where the purpose is to meet the needs from the environment and students.
Abstract: The topic this paper addresses is articulated by two basic aspects: teacher formation and research training.Both make up a unity, since formation at college must be reflected in a professional practice characterized by reflexive, critical, autonomous, logical, and flexible thinking, which allows meeting the needs from the environment and students. This is the purpose for showing how research training is delivered in Teaching Programas at Tecnologico de Antioquia College.Keywords: Formation, research skills, pedagogical model.
TL;DR: In this paper, the authors think over the chiquitano perspective of living, which can be understood as some sort of animism, once it deems that all elements of nature possess souls, to which the Chiquitanos relate.
Abstract: This work thinks over the chiquitano perspective of living, which can be understood as some sort of animism, once it deems that all elements of nature possess souls, to which the Chiquitanos relate. The understanding of the Chiquitanos’ ethnic identity appears in theirs ceremonies and in the relationship of the believers with the Saints and hitchis. There are several rituals – such as curusse, romarias and festas de Santo – able to reveal the Chiquitanos’ ethnic identity and the permanent cultural flow in their traditional territory.
TL;DR: The counter-terrorism act operates as a device for perpetuating the sovereign model in the framework of a governmental model whose aim is the selective administration and security of the population as discussed by the authors.
Abstract: A colonialist logic has marked the historical relationship between Mapuche people and the Chilean State. After the return of democracy, the continuation of private exploitation in disputed territories and the lack of adaptation of State policies to Mapuche worldview, opened the way for organized sectors of this ethnic to radicalize their protest. The reaction of the State to this situation resulted in the implementation of the counter-terrorism act from the beginning of the 21st century. This article seeks to understand this State action based the concepts of "sovereignty" and "governmentality" raised by Foucault. We propose that the counter-terrorism act operates as a device for perpetuating the sovereign model in the framework of a governmental model whose aim is the selective administration and security of the population.
TL;DR: In this article, the authors reflect on the deeds of the mentioned section during its execution and reflect on their own activities in Ceara province throughout 3 years (1859-1961) during the Comissao Cientifica de Exploracao (CCE) project.
Abstract: Brazil should be known and studied by the Brazilians. This idea was the force that justified the constitution of the Comissao Cientifica de Exploracao (CCE), founded by members of the Brazilian Historic and Geographic Institute and supported by the Brazilian imperial government, in order to motivate research on the “young” country. Within this ambitious scientific and political project, ethnographic knowledge and practices were embraced in the deeds assigned to the scientist and poet Goncalves Dias, chief of the section of ethnography and travel narrative, whom should have performed his activities in Ceara province throughout 3 years (1859-1961). To reflect on the deeds of the mentioned section during its execution is the goal of this paper.