1 Diagonally Dominant Matrices
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Recursive Approach in Sparse Matrix LU Factorization
51 Recursive approach in sparse matrix LU factorization Jack Dongarra, Victor Eijkhout and the resulting matrix is often guaranteed to be positive Piotr Łuszczek∗ definite or close to it. However, when the linear sys- University of Tennessee, Department of Computer tem matrix is strongly unsymmetric or indefinite, as Science, Knoxville, TN 37996-3450, USA is the case with matrices originating from systems of Tel.: +865 974 8295; Fax: +865 974 8296 ordinary differential equations or the indefinite matri- ces arising from shift-invert techniques in eigenvalue methods, one has to revert to direct methods which are This paper describes a recursive method for the LU factoriza- the focus of this paper. tion of sparse matrices. The recursive formulation of com- In direct methods, Gaussian elimination with partial mon linear algebra codes has been proven very successful in pivoting is performed to find a solution of Eq. (1). Most dense matrix computations. An extension of the recursive commonly, the factored form of A is given by means technique for sparse matrices is presented. Performance re- L U P Q sults given here show that the recursive approach may per- of matrices , , and such that: form comparable to leading software packages for sparse ma- LU = PAQ, (2) trix factorization in terms of execution time, memory usage, and error estimates of the solution. where: – L is a lower triangular matrix with unitary diago- nal, 1. Introduction – U is an upper triangular matrix with arbitrary di- agonal, Typically, a system of linear equations has the form: – P and Q are row and column permutation matri- Ax = b, (1) ces, respectively (each row and column of these matrices contains single a non-zero entry which is A n n A ∈ n×n x where is by real matrix ( R ), and 1, and the following holds: PPT = QQT = I, b n b, x ∈ n and are -dimensional real vectors ( R ). -
Abstract 1 Introduction
Implementation in ScaLAPACK of Divide-and-Conquer Algorithms for Banded and Tridiagonal Linear Systems A. Cleary Department of Computer Science University of Tennessee J. Dongarra Department of Computer Science University of Tennessee Mathematical Sciences Section Oak Ridge National Laboratory Abstract Described hereare the design and implementation of a family of algorithms for a variety of classes of narrow ly banded linear systems. The classes of matrices include symmetric and positive de - nite, nonsymmetric but diagonal ly dominant, and general nonsymmetric; and, al l these types are addressed for both general band and tridiagonal matrices. The family of algorithms captures the general avor of existing divide-and-conquer algorithms for banded matrices in that they have three distinct phases, the rst and last of which arecompletely paral lel, and the second of which is the par- al lel bottleneck. The algorithms have been modi ed so that they have the desirable property that they are the same mathematical ly as existing factorizations Cholesky, Gaussian elimination of suitably reordered matrices. This approach represents a departure in the nonsymmetric case from existing methods, but has the practical bene ts of a smal ler and more easily hand led reduced system. All codes implement a block odd-even reduction for the reduced system that al lows the algorithm to scale far better than existing codes that use variants of sequential solution methods for the reduced system. A cross section of results is displayed that supports the predicted performance results for the algo- rithms. Comparison with existing dense-type methods shows that for areas of the problem parameter space with low bandwidth and/or high number of processors, the family of algorithms described here is superior. -
On Multigrid Methods for Solving Electromagnetic Scattering Problems
On Multigrid Methods for Solving Electromagnetic Scattering Problems Dissertation zur Erlangung des akademischen Grades eines Doktor der Ingenieurwissenschaften (Dr.-Ing.) der Technischen Fakultat¨ der Christian-Albrechts-Universitat¨ zu Kiel vorgelegt von Simona Gheorghe 2005 1. Gutachter: Prof. Dr.-Ing. L. Klinkenbusch 2. Gutachter: Prof. Dr. U. van Rienen Datum der mundliche¨ Prufung:¨ 20. Jan. 2006 Contents 1 Introductory remarks 3 1.1 General introduction . 3 1.2 Maxwell’s equations . 6 1.3 Boundary conditions . 7 1.3.1 Sommerfeld’s radiation condition . 9 1.4 Scattering problem (Model Problem I) . 10 1.5 Discontinuity in a parallel-plate waveguide (Model Problem II) . 11 1.6 Absorbing-boundary conditions . 12 1.6.1 Global radiation conditions . 13 1.6.2 Local radiation conditions . 18 1.7 Summary . 19 2 Coupling of FEM-BEM 21 2.1 Introduction . 21 2.2 Finite element formulation . 21 2.2.1 Discretization . 26 2.3 Boundary-element formulation . 28 3 4 CONTENTS 2.4 Coupling . 32 3 Iterative solvers for sparse matrices 35 3.1 Introduction . 35 3.2 Classical iterative methods . 36 3.3 Krylov subspace methods . 37 3.3.1 General projection methods . 37 3.3.2 Krylov subspace methods . 39 3.4 Preconditioning . 40 3.4.1 Matrix-based preconditioners . 41 3.4.2 Operator-based preconditioners . 42 3.5 Multigrid . 43 3.5.1 Full Multigrid . 47 4 Numerical results 49 4.1 Coupling between FEM and local/global boundary conditions . 49 4.1.1 Model problem I . 50 4.1.2 Model problem II . 63 4.2 Multigrid . 64 4.2.1 Theoretical considerations regarding the classical multi- grid behavior in the case of an indefinite problem . -
Overview of Iterative Linear System Solver Packages
Overview of Iterative Linear System Solver Packages Victor Eijkhout July, 1998 Abstract Description and comparison of several packages for the iterative solu- tion of linear systems of equations. 1 1 Intro duction There are several freely available packages for the iterative solution of linear systems of equations, typically derived from partial di erential equation prob- lems. In this rep ort I will give a brief description of a numberofpackages, and giveaninventory of their features and de ning characteristics. The most imp ortant features of the packages are which iterative metho ds and preconditioners supply; the most relevant de ning characteristics are the interface they present to the user's data structures, and their implementation language. 2 2 Discussion Iterative metho ds are sub ject to several design decisions that a ect ease of use of the software and the resulting p erformance. In this section I will give a global discussion of the issues involved, and how certain p oints are addressed in the packages under review. 2.1 Preconditioners A go o d preconditioner is necessary for the convergence of iterative metho ds as the problem to b e solved b ecomes more dicult. Go o d preconditioners are hard to design, and this esp ecially holds true in the case of parallel pro cessing. Here is a short inventory of the various kinds of preconditioners found in the packages reviewed. 2.1.1 Ab out incomplete factorisation preconditioners Incomplete factorisations are among the most successful preconditioners devel- op ed for single-pro cessor computers. Unfortunately, since they are implicit in nature, they cannot immediately b e used on parallel architectures. -
Accelerating the LOBPCG Method on Gpus Using a Blocked Sparse Matrix Vector Product
Accelerating the LOBPCG method on GPUs using a blocked Sparse Matrix Vector Product Hartwig Anzt and Stanimire Tomov and Jack Dongarra Innovative Computing Lab University of Tennessee Knoxville, USA Email: [email protected], [email protected], [email protected] Abstract— the computing power of today’s supercomputers, often accel- erated by coprocessors like graphics processing units (GPUs), This paper presents a heterogeneous CPU-GPU algorithm design and optimized implementation for an entire sparse iter- becomes challenging. ative eigensolver – the Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG) – starting from low-level GPU While there exist numerous efforts to adapt iterative lin- data structures and kernels to the higher-level algorithmic choices ear solvers like Krylov subspace methods to coprocessor and overall heterogeneous design. Most notably, the eigensolver technology, sparse eigensolvers have so far remained out- leverages the high-performance of a new GPU kernel developed side the main focus. A possible explanation is that many for the simultaneous multiplication of a sparse matrix and a of those combine sparse and dense linear algebra routines, set of vectors (SpMM). This is a building block that serves which makes porting them to accelerators more difficult. Aside as a backbone for not only block-Krylov, but also for other from the power method, algorithms based on the Krylov methods relying on blocking for acceleration in general. The subspace idea are among the most commonly used general heterogeneous LOBPCG developed here reveals the potential of eigensolvers [1]. When targeting symmetric positive definite this type of eigensolver by highly optimizing all of its components, eigenvalue problems, the recently developed Locally Optimal and can be viewed as a benchmark for other SpMM-dependent applications. -
Sparse Matrices and Iterative Methods
Iterative Methods Sparsity Sparse Matrices and Iterative Methods K. Cooper1 1Department of Mathematics Washington State University 2018 Cooper Washington State University Introduction Iterative Methods Sparsity Iterative Methods Consider the problem of solving Ax = b, where A is n × n. Why would we use an iterative method? I Avoid direct decomposition (LU, QR, Cholesky) I Replace with iterated matrix multiplication 3 I LU is O(n ) flops. 2 I . matrix-vector multiplication is O(n )... I so if we can get convergence in e.g. log(n), iteration might be faster. Cooper Washington State University Introduction Iterative Methods Sparsity Jacobi, GS, SOR Some old methods: I Jacobi is easily parallelized. I . but converges extremely slowly. I Gauss-Seidel/SOR converge faster. I . but cannot be effectively parallelized. I Only Jacobi really takes advantage of sparsity. Cooper Washington State University Introduction Iterative Methods Sparsity Sparsity When a matrix is sparse (many more zero entries than nonzero), then typically the number of nonzero entries is O(n), so matrix-vector multiplication becomes an O(n) operation. This makes iterative methods very attractive. It does not help direct solves as much because of the problem of fill-in, but we note that there are specialized solvers to minimize fill-in. Cooper Washington State University Introduction Iterative Methods Sparsity Krylov Subspace Methods A class of methods that converge in n iterations (in exact arithmetic). We hope that they arrive at a solution that is “close enough” in fewer iterations. Often these work much better than the classic methods. They are more readily parallelized, and take full advantage of sparsity. -
Scalable Stochastic Kriging with Markovian Covariances
Scalable Stochastic Kriging with Markovian Covariances Liang Ding and Xiaowei Zhang∗ Department of Industrial Engineering and Decision Analytics The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong Abstract Stochastic kriging is a popular technique for simulation metamodeling due to its flexibility and analytical tractability. Its computational bottleneck is the inversion of a covariance matrix, which takes O(n3) time in general and becomes prohibitive for large n, where n is the number of design points. Moreover, the covariance matrix is often ill-conditioned for large n, and thus the inversion is prone to numerical instability, resulting in erroneous parameter estimation and prediction. These two numerical issues preclude the use of stochastic kriging at a large scale. This paper presents a novel approach to address them. We construct a class of covariance functions, called Markovian covariance functions (MCFs), which have two properties: (i) the associated covariance matrices can be inverted analytically, and (ii) the inverse matrices are sparse. With the use of MCFs, the inversion-related computational time is reduced to O(n2) in general, and can be further reduced by orders of magnitude with additional assumptions on the simulation errors and design points. The analytical invertibility also enhance the numerical stability dramatically. The key in our approach is that we identify a general functional form of covariance functions that can induce sparsity in the corresponding inverse matrices. We also establish a connection between MCFs and linear ordinary differential equations. Such a connection provides a flexible, principled approach to constructing a wide class of MCFs. Extensive numerical experiments demonstrate that stochastic kriging with MCFs can handle large-scale problems in an both computationally efficient and numerically stable manner. -
Chapter 7 Iterative Methods for Large Sparse Linear Systems
Chapter 7 Iterative methods for large sparse linear systems In this chapter we revisit the problem of solving linear systems of equations, but now in the context of large sparse systems. The price to pay for the direct methods based on matrix factorization is that the factors of a sparse matrix may not be sparse, so that for large sparse systems the memory cost make direct methods too expensive, in memory and in execution time. Instead we introduce iterative methods, for which matrix sparsity is exploited to develop fast algorithms with a low memory footprint. 7.1 Sparse matrix algebra Large sparse matrices We say that the matrix A Rn is large if n is large, and that A is sparse if most of the elements are2 zero. If a matrix is not sparse, we say that the matrix is dense. Whereas for a dense matrix the number of nonzero elements is (n2), for a sparse matrix it is only (n), which has obvious implicationsO for the memory footprint and efficiencyO for algorithms that exploit the sparsity of a matrix. AdiagonalmatrixisasparsematrixA =(aij), for which aij =0for all i = j,andadiagonalmatrixcanbegeneralizedtoabanded matrix, 6 for which there exists a number p,thebandwidth,suchthataij =0forall i<j p or i>j+ p.Forexample,atridiagonal matrix A is a banded − 59 CHAPTER 7. ITERATIVE METHODS FOR LARGE SPARSE 60 LINEAR SYSTEMS matrix with p =1, xx0000 xxx000 20 xxx003 A = , (7.1) 600xxx07 6 7 6000xxx7 6 7 60000xx7 6 7 where x represents a nonzero4 element. 5 Compressed row storage The compressed row storage (CRS) format is a data structure for efficient represention of a sparse matrix by three arrays, containing the nonzero values, the respective column indices, and the extents of the rows. -
Problems in Abstract Algebra
STUDENT MATHEMATICAL LIBRARY Volume 82 Problems in Abstract Algebra A. R. Wadsworth 10.1090/stml/082 STUDENT MATHEMATICAL LIBRARY Volume 82 Problems in Abstract Algebra A. R. Wadsworth American Mathematical Society Providence, Rhode Island Editorial Board Satyan L. Devadoss John Stillwell (Chair) Erica Flapan Serge Tabachnikov 2010 Mathematics Subject Classification. Primary 00A07, 12-01, 13-01, 15-01, 20-01. For additional information and updates on this book, visit www.ams.org/bookpages/stml-82 Library of Congress Cataloging-in-Publication Data Names: Wadsworth, Adrian R., 1947– Title: Problems in abstract algebra / A. R. Wadsworth. Description: Providence, Rhode Island: American Mathematical Society, [2017] | Series: Student mathematical library; volume 82 | Includes bibliographical references and index. Identifiers: LCCN 2016057500 | ISBN 9781470435837 (alk. paper) Subjects: LCSH: Algebra, Abstract – Textbooks. | AMS: General – General and miscellaneous specific topics – Problem books. msc | Field theory and polyno- mials – Instructional exposition (textbooks, tutorial papers, etc.). msc | Com- mutative algebra – Instructional exposition (textbooks, tutorial papers, etc.). msc | Linear and multilinear algebra; matrix theory – Instructional exposition (textbooks, tutorial papers, etc.). msc | Group theory and generalizations – Instructional exposition (textbooks, tutorial papers, etc.). msc Classification: LCC QA162 .W33 2017 | DDC 512/.02–dc23 LC record available at https://lccn.loc.gov/2016057500 Copying and reprinting. Individual readers of this publication, and nonprofit libraries acting for them, are permitted to make fair use of the material, such as to copy select pages for use in teaching or research. Permission is granted to quote brief passages from this publication in reviews, provided the customary acknowledgment of the source is given. Republication, systematic copying, or multiple reproduction of any material in this publication is permitted only under license from the American Mathematical Society. -
Over-Scalapack.Pdf
1 2 The Situation: Parallel scienti c applications are typically Overview of ScaLAPACK written from scratch, or manually adapted from sequen- tial programs Jack Dongarra using simple SPMD mo del in Fortran or C Computer Science Department UniversityofTennessee with explicit message passing primitives and Mathematical Sciences Section Which means Oak Ridge National Lab oratory similar comp onents are co ded over and over again, co des are dicult to develop and maintain http://w ww .ne tl ib. org /ut k/p e opl e/J ackDo ngarra.html debugging particularly unpleasant... dicult to reuse comp onents not really designed for long-term software solution 3 4 What should math software lo ok like? The NetSolve Client Many more p ossibilities than shared memory Virtual Software Library Multiplicityofinterfaces ! Ease of use Possible approaches { Minimum change to status quo Programming interfaces Message passing and ob ject oriented { Reusable templates { requires sophisticated user Cinterface FORTRAN interface { Problem solving environments Integrated systems a la Matlab, Mathematica use with heterogeneous platform Interactiveinterfaces { Computational server, like netlib/xnetlib f2c Non-graphic interfaces Some users want high p erf., access to details {MATLAB interface Others sacri ce sp eed to hide details { UNIX-Shell interface Not enough p enetration of libraries into hardest appli- Graphic interfaces cations on vector machines { TK/TCL interface Need to lo ok at applications and rethink mathematical software { HotJava Browser -
Prospectus for the Next LAPACK and Scalapack Libraries
Prospectus for the Next LAPACK and ScaLAPACK Libraries James Demmel1, Jack Dongarra23, Beresford Parlett1, William Kahan1, Ming Gu1, David Bindel1, Yozo Hida1, Xiaoye Li1, Osni Marques1, E. Jason Riedy1, Christof Voemel1, Julien Langou2, Piotr Luszczek2, Jakub Kurzak2, Alfredo Buttari2, Julie Langou2, Stanimire Tomov2 1 University of California, Berkeley CA 94720, USA, 2 University of Tennessee, Knoxville TN 37996, USA, 3 Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA, 1 Introduction Dense linear algebra (DLA) forms the core of many scienti¯c computing appli- cations. Consequently, there is continuous interest and demand for the devel- opment of increasingly better algorithms in the ¯eld. Here 'better' has a broad meaning, and includes improved reliability, accuracy, robustness, ease of use, and most importantly new or improved algorithms that would more e±ciently use the available computational resources to speed up the computation. The rapidly evolving high end computing systems and the close dependence of DLA algo- rithms on the computational environment is what makes the ¯eld particularly dynamic. A typical example of the importance and impact of this dependence is the development of LAPACK [1] (and later ScaLAPACK [2]) as a successor to the well known and formerly widely used LINPACK [3] and EISPACK [3] libraries. Both LINPACK and EISPACK were based, and their e±ciency depended, on optimized Level 1 BLAS [4]. Hardware development trends though, and in par- ticular an increasing Processor-to-Memory speed gap of approximately 50% per year, started to increasingly show the ine±ciency of Level 1 BLAS vs Level 2 and 3 BLAS, which prompted e®orts to reorganize DLA algorithms to use block matrix operations in their innermost loops. -
A Parallel Solver for Graph Laplacians
A Parallel Solver for Graph Laplacians Tristan Konolige Jed Brown University of Colorado Boulder University of Colorado Boulder [email protected] ABSTRACT low energy components while maintaining coarse grid sparsity. We Problems from graph drawing, spectral clustering, network ow also develop a parallel algorithm for nding and eliminating low and graph partitioning can all be expressed in terms of graph Lapla- degree vertices, a technique introduced for a sequential multigrid cian matrices. ere are a variety of practical approaches to solving algorithm by Livne and Brandt [22], that is important for irregular these problems in serial. However, as problem sizes increase and graphs. single core speeds stagnate, parallelism is essential to solve such While matrices can be distributed using a vertex partition (a problems quickly. We present an unsmoothed aggregation multi- 1D/row distribution) for PDE problems, this leads to unacceptable grid method for solving graph Laplacians in a distributed memory load imbalance for irregular graphs. We represent matrices using a seing. We introduce new parallel aggregation and low degree elim- 2D distribution (a partition of the edges) that maintains load balance ination algorithms targeted specically at irregular degree graphs. for parallel scaling [11]. Many algorithms that are practical for 1D ese algorithms are expressed in terms of sparse matrix-vector distributions are not feasible for more general distributions. Our products using generalized sum and product operations. is for- new parallel algorithms are distribution agnostic. mulation is amenable to linear algebra using arbitrary distributions and allows us to operate on a 2D sparse matrix distribution, which 2 BACKGROUND is necessary for parallel scalability.