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IEEE International Conference on E-science Workshops

作者： Jorg Bernsdorf Guntram Berti Bastien Chopard Jan Hegewald Manfred Krafczyk Dinan Wang Eric Lorenz Alfons Hoekstra German Research School for Simulation Sciences RWTH Aachen University Aachen Germany Consulting mathematical methods Berti CMM Bonn Germany Scientific and Parallel Computing Group University of Geneva Geneva Switzerland Institute for Computational Modeling in Civil Engineering Technische Universität Braunschweig Brunswick Germany Meteorological Institute University of Bonn Bonn Germany Section Computational Science University of Amsterdam Amsterdam Netherlands

The understanding of biological processes, e.g. related to cardio-vascular disease and treatment, can significantly be improved by numerical simulation. In this paper, we present an approach for a multiscale simulation environment, applied for the prediction of in-stent re-stenos is. Our focus is on the coupling of distributed, heterogeneous hardware to take into account the different requirements of the coupled sub-systems concerning computing power. For such a concept, which is an extension of the standard multiscale computing approach, we want to apply the term Distributed Multiscale computing.

关键词： computational modeling Couplings Biological system modeling Numerical models Muscles Automata Drugs

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On the error bounds of nonconforming finite elements

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science China Mathematics 2010年第11期53卷 2917-2926页

作者： MAO ShiPeng SHI ZhongCi The State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China

We prove that the error estimates of a large class of nonconforming finite elements are dominated by their approximation errors, which means that the well-known Cea’s lemma is still valid for these nonconforming finite element methods. Furthermore, we derive the error estimates in both energy and L2 norms under the regularity assumption u ∈ H1+s(Ω) with any s > 0. The extensions to other related problems are possible.

关键词： nonconforming finite elements Cea’s lemma error estimates

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Sparse two-sided rank-one updates for nonlinear equations

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science China Mathematics 2010年第11期53卷 2907-2915页

作者： CHENG MingHou & DAI YuHong State Key Laboratory of Scientific and engineering computing, institute of computational Mathematics and Scientific/engineering computing, Academy of Mathematics and Systems science, Chinese Academy of sciences, Beijing 100190, China 1. State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China

The two-sided rank-one (TR1) update method was introduced by Griewank and Walther (2002) for solving nonlinear equations. It generates dense approximations of the Jacobian and thus is not applicable to large-scale sparse problems. To overcome this difficulty, we propose sparse extensions of the TR1 update and give some convergence analysis. The numerical experiments show that some of our extensions are superior to the TR1 update method. Some convergence analysis is also presented.

关键词： TR1 update Broyden rank-one update sparsity

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Fast active-set-type algorithms for L1-regularized linear regression

Fast active-set-type algorithms for L1-regularized linear re...

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13th International Conference on Artificial Intelligence and Statistics, AISTATS 2010

作者： Kim, Jingu Park, Haesun School of Computational Science and Engineering College of Computing Georgia Institute of Technology United States

In this paper, we investigate new active-settype methods for l 1-regularized linear regression that overcome some difficulties of existing active set methods. By showing a relationship between l 1-regularized linear regression and the linear complementarity problem with bounds, we present a fast active-set-type method, called block principal pivoting. This method accelerates computation by allowing exchanges of several variables among working sets. We further provide an improvement of this method, discuss its properties, and also explain a connection to the structure learning of Gaussian graphical models. Experimental comparisons on synthetic and real data sets show that the proposed method is significantly faster than existing active set methods and competitive against recently developed iterative methods.

关键词： Linear regression

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Skel: Generative software for producing skeletal I/O applications

Skel: Generative software for producing skeletal I/O applica...

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7th IEEE International Conference on e-science Workshops, escienceW 201

作者： Logan, Jeremy Klasky, Scott Lofstead, Jay Abbasi, Hasan Ethier, Stéphane Grout, Ray Ku, Seung-Hoe Liu, Qing Ma, Xiaosong Parashar, Manish Podhorszki, Norbert Schwan, Karsten Wolf, Matthew Oak Ridge National Laboratory Oak Ridge TN United States Sandia National Laboratories Albuquerque NM United States National Institute for Computational Sciences University of Tennessee Oak Ridge TN United States Department of Electrical and Computer Engineering Rutgers the State University of New Jersey Piscataway NJ United States Courant Institute of Mathematical Sciences New York University New York NY United States Department of Computer Science North Carolina State University Raleigh NC United States Plasma Physics Laboratory Princeton University Princeton NJ United States National Renewable Energy Laboratory Golden CO United States College of Computing Georgia Tech. Atlanta GA United States

ISBN: (纸本)9780769545981

Massively parallel computations consist of a mixture of computation, communication, and I/O. Of these three components, implementing an effective parallel I/O solution has often been overlooked by application scientists and has typically been added to large scale simulations only when existing serial techniques have failed. As scientists' teams scaled their codes to run on hundreds of processors, it was common to call on an I/O expert to implement a set of more scalable I/O routines. These routines were easily separated from the calculations and communication, and in many cases, an I/O kernel was derived from the application which could be used for testing I/O performance independent of the application. These I/O kernels developed a life of their own used as a broad measure for comparing different I/O techniques. Unfortunately, as years passed and computation and communication changes required changes to the I/O, the separate I/O kernel used for benchmarking remained static, no longer providing an accurate indicator of the I/O performance of the simulation, and making I/O research less relevant for the application scientists. In this paper we describe a new approach to this problem where I/O kernels are replaced with skeletal I/O applications that are automatically generated from an abstract set of simulation I/O parameters. We realize this abstraction by leveraging the ADIOS [1] middleware's XML I/O specification with additional runtime parameters. Skeletal applications offer all of the benefits of I/O kernels including allowing I/O optimizations to focus on useful I/O patterns. Moreover, since they are automatically generated, it is easy to produce an updated I/O skeleton whenever the simulation's I/O changes. In this paper we analyze the performance of automatically generated I/O skeletal applications for the S3D and GTS codes. We show that these skeletal applications achieve performance comparable to that of the production applications. We wrap up the paper with

关键词： Benchmarking

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Novel Multi-Symplectic Integrators for Nonlinear Fourth-Order Schrodinger Equation with Trapped Term

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Communications in computational Physics 2010年第3期7卷 613-630页

作者： Jialin Hong Linghua Kong State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and System ScienceChinese Academy of SciencesP.O.Box 2719Beijing 100190China School of Mathematics and Information Science Jiangxi Normal UniversityNanchangJiangxi 330022China

The multi-symplectic Runge-Kutta (MSRK) methods and multi-symplecticFourier spectral (MSFS) methods will be employed to solve the fourth-orderSchrodinger equations with trapped term. Using the idea of split-step numericalmethod and the MSRK methods, we devise a new kind of multi-symplectic integrators, which is called split-step multi-symplectic (SSMS) methods. The numerical experiments show that the proposed SSMS methods are more efficient than the conventionalmulti-symplectic integrators with respect to the the numerical accuracy and conservation perserving properties.

关键词： Schrodinger equation with trapped term multi-symplectic scheme Fourier spectral method conservation law split-step method

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A Multitier System for the Verification, Visualization and Management of CHIMERA

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Procedia Computer science 2011年 4卷 2076-2085页

作者： E.J. Lingerfelt O.E.B. Messer J.A. Osborne R.D. Budiardja A. Mezzacappa Computer Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge TN 37831-6354 Leadership Computing Facility Oak Ridge National Laboratory Oak Ridge TN 37831-6354 Department of Physics and Astronomy University of Tennessee Knoxville TN 37996-1200 Department of Electrical Engineering and Computer Science University of Tennessee Knoxville TN 37996-2100 NSF Teragrid XD RDAVCenter National Institute for Computational Sciences University of Tennessee Knoxville TN 37996-2100 Physics Division Oak Ridge National Laboratory Oak Ridge TN 37831-6354

CHIMERA is a multi-dimensional radiation hydrodynamics code designed to study core-collapse supernovae. The code is made up of three essentially independent parts: a hydrodynamics module, a nuclear burning module, and a neutrino transport solver combined within an operator-split approach. Given CHIMERA's complexity and pace of ongoing development, a new support system, Bellerophon, has been designed and implemented to perform automated verification, visualization and management tasks while integrating with other workflow systems utilized by CHIMERA's development group. In order to achieve these goals, a multitier approach has been adopted. By integrating supercomputing platforms, visualization clusters, a dedicated web server and a client-side desktop application, this system attempts to provide an encapsulated, end-to-end solution to these needs.

关键词： Supernovae Visualization Regression test Code verification Multitier system

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iVisClassifier: An interactive visual analytics system for classification based on supervised dimension reduction

iVisClassifier: An interactive visual analytics system for c...

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1st IEEE Conference on Visual Analytics science and Technology, VAST 10

作者： Choo, Jaegul Lee, Hanseung Kihm, Jaeyeon Park, Haesun School of Computational Science and Engineering Georgia Institute of Technology United States School of Electrical and Computer Engineering Georgia Institute of Technology United States School of Interactive Computing Georgia Institute of Technology United States

ISBN: (纸本)9781424494866

We present an interactive visual analytics system for classification, iVisClassifier, based on a supervised dimension reduction method, linear discriminant analysis (LDA). Given high-dimensional data and associated cluster labels, LDA gives their reduced dimensional representation, which provides a good overview about the cluster structure. Instead of a single two- or three-dimensional scatter plot, iVisClassifier fully interacts with all the reduced dimensions obtained by LDA through parallel coordinates and a scatter plot. Furthermore, it significantly improves the interactivity and interpretability of LDA. LDA enables users to understand each of the reduced dimensions and how they influence the data by reconstructing the basis vector into the original data domain. By using heat maps, iVisClassifier gives an overview about the cluster relationship in terms of pairwise distances between cluster centroids both in the original space and in the reduced dimensional space. Equipped with these functionalities, iVisClassifier supports users' classification tasks in an efficient way. Using several facial image data, we show how the above analysis is performed. ©2010 IEEE.

关键词： Clustering algorithms

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Fast facial fitting based on mixture appearance model with 3D constraint

Fast facial fitting based on mixture appearance model with 3...

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Chinese Conference on Pattern Recognition

作者： Huang, Xiangsheng Gong, Lujin Wang, Xiaoyan Institute of Automation Chinese Academy of Sciences Beijing 100190 China State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing AMSS Beijing 100190 China College of Computer Science and Technology Zhejiang University of Technology Hangzhou 310023 China

ISBN: (纸本)9781424472109

Fast facial points fitting plays an important role in applications such as Human-Computer Interaction, entertainment, surveillance, and is highly relevant to the techniques of facial expression analysis, face recognition, 3D face model generation, etc. Active Appearance Models (AAMs) are generative models commonly used to fit face. They are sensitive to illumination and expression changes because they use only raw intensity to build observation models. In this paper, a real time facial points fitting approach using mixture observation models is presented. Furthermore, the 3D modes are used to constrain the AAM so that it can only generate model instances that can also be generated with the 3D modes. Finally, we give a derivative process for fast energy minimization using the inverse compositional algorithm. A coarse-to-fine fitting strategy is used for realtime and robust facial points fitting. We apply this algorithm to facial expression cloning of 3D Avatar system. Experimental results demonstrate that fitting the AAM with mixture observation models and 3D constraint outperforms other classical algorithms. ©2010 IEEE.

关键词： Mixtures

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Interactively exploring elimination orderings in symbolic sparse Cholesky factorization

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Procedia Computer science 2010年第1期1卷 867-874页

作者： Michael Lülfesmann Simon R. Leßenich H. Martin Bücker Institute for Scientic Computing Center for Computational Engineering Science RWTH Aachen University D-52056 Aachen Germany

When large sparse symmetric systems of linear equations are solved by the Cholesky factorization, nonzero elements can be generated at positions where the original matrix contains zero elements. This phenomenon is called fill-in and it is often crucial in large-scale problems. The symbolic Cholesky factorization solely takes into account the nonzero structure of a sparse matrix to determine the nonzero structure of its Cholesky factor. Sequences of elimination graphs are typically used to model this combinatorial problem. We propose an interactive educational module to visualize and explore the symbolic Cholesky factorization in terms of both elimination graphs and matrix representation. We describe the design and implementation of this interactive module that is intended to be used in a face-to-face learning environment.

关键词： Combinatorial scientific computing Symbolic sparse Cholesky factorization Exploration and visualization of elimination graphs and matrix representation Interactive educational module Face-to-face learning environment

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