New Fast and Accurate Jacobi Svd Algorithm: I. Lapack Working Note 169
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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. -
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. -
Jacobi-Davidson, Gauss-Seidel and Successive Over-Relaxation For
Applied Mathematics and Computational Intelligence Volume 6, 2017 [41-52] Jacobi‐Davidson, Gauss‐Seidel and Successive Over‐Relaxation for Solving Systems of Linear Equations Fatini Dalili Mohammed1,a and Mohd Rivaieb 1Department of Computer Sciences and Mathematics, Universiti Teknologi MARA (UiTM) Terengganu, Campus Kuala Terengganu, Malaysia ABSTRACT Linear systems are applied in many applications such as calculating variables, rates, budgets, making a prediction and others. Generally, there are two techniques of solving system of linear equation including direct methods and iterative methods. Some basic solution methods known as direct methods are ineffective in solving many equations in large systems due to slower computation. Due to inability of direct methods, iterative methods are practical to be used in large systems of linear equations as they do not need much storage. In this project, three indirect methods are used to solve large system of linear equations. The methods are Jacobi Davidson, Gauss‐Seidel and Successive Over‐ Relaxation (SOR) which are well known in the field of numerical analysis. The comparative results analysis of the three methods is considered. These three methods are compared based on number of iterations, CPU time and error. The numerical results show that Gauss‐Seidel method and SOR method with ω=1.25 are more efficient than others. This research allows researcher to appreciate the use of iterative techniques for solving systems of linear equations that is widely used in industrial applications. Keywords: system of linear equation, iterative method, Jacobi‐Davidson, Gauss‐Seidel, Successive Over‐Relaxation 1. INTRODUCTION Linear systems are important in our real life. They are applied in various applications such as in calculating variables, rates, budgets, making a prediction and others. -
A Study on Comparison of Jacobi, Gauss-Seidel and Sor Methods For
International Journal of Mathematics Trends and Technology (IJMTT) – Volume 56 Issue 4- April 2018 A Study on Comparison of Jacobi, Gauss- Seidel and Sor Methods for the Solution in System of Linear Equations #1 #2 #3 *4 Dr.S.Karunanithi , N.Gajalakshmi , M.Malarvizhi , M.Saileshwari #Assistant Professor ,* Research Scholar Thiruvalluvar University,Vellore PG & Research Department of Mathematics,Govt.Thirumagal Mills College,Gudiyattam,Vellore Dist,Tamilnadu,India-632602 Abstract — This paper presents three iterative methods for the solution of system of linear equations has been evaluated in this work. The result shows that the Successive Over-Relaxation method is more efficient than the other two iterative methods, number of iterations required to converge to an exact solution. This research will enable analyst to appreciate the use of iterative techniques for understanding the system of linear equations. Keywords — The system of linear equations, Iterative methods, Initial approximation, Jacobi method, Gauss- Seidel method, Successive Over- Relaxation method. 1. INTRODUCTION AND PRELIMINARIES Numerical analysis is the area of mathematics and computer science that creates, analyses, and implements algorithms for solving numerically the problems of continuous mathematics. Such problems originate generally from real-world applications of algebra, geometry and calculus, and they involve variables which vary continuously. These problems occur throughout the natural sciences, social science, engineering, medicine, and business. The solution of system of linear equations can be accomplished by a numerical method which falls in one of two categories: direct or iterative methods. We have so far discussed some direct methods for the solution of system of linear equations and we have seen that these methods yield the solution after an amount of computation that is known advance. -
New Fast and Accurate Jacobi Svd Algorithm: I
NEW FAST AND ACCURATE JACOBI SVD ALGORITHM: I. ZLATKO DRMAC· ¤ AND KRESIMIR· VESELIC¶ y Abstract. This paper is the result of contrived e®orts to break the barrier between numerical accuracy and run time e±ciency in computing the fundamental decomposition of numerical linear algebra { the singular value decomposition (SVD) of a general dense matrix. It is an unfortunate fact that the numerically most accurate one{sided Jacobi SVD algorithm is several times slower than generally less accurate bidiagonalization based methods such as the QR or the divide and conquer algorithm. Despite its sound numerical qualities, the Jacobi SVD is not included in the state of the art matrix computation libraries and it is even considered obsolete by some leading researches. Our quest for a highly accurate and e±cient SVD algorithm has led us to a new, superior variant of the Jacobi algorithm. The new algorithm has inherited all good high accuracy properties, and it outperforms not only the best implementations of the one{sided Jacobi algorithm but also the QR algorithm. Moreover, it seems that the potential of the new approach is yet to be fully exploited. Key words. Jacobi method, singular value decomposition, eigenvalues AMS subject classi¯cations. 15A09, 15A12, 15A18, 15A23, 65F15, 65F22, 65F35 1. Introduction. In der Theorie der SÄacularstÄorungenund der kleinen Oscil- lationen wird man auf ein System lineÄarerGleichungen gefÄurt,in welchem die Co- e±cienten der verschiedenen Unbekanten in Bezug auf die Diagonale symmetrisch sind, die ganz constanten Glieder fehlen und zu allen in der Diagonale be¯ndlichen Coe±cienten noch dieselbe GrÄo¼e ¡x addirt ist. -
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. -
Solving Linear Systems: Iterative Methods and Sparse Systems
Solving Linear Systems: Iterative Methods and Sparse Systems COS 323 Last time • Linear system: Ax = b • Singular and ill-conditioned systems • Gaussian Elimination: A general purpose method – Naïve Gauss (no pivoting) – Gauss with partial and full pivoting – Asymptotic analysis: O(n3) • Triangular systems and LU decomposition • Special matrices and algorithms: – Symmetric positive definite: Cholesky decomposition – Tridiagonal matrices • Singularity detection and condition numbers Today: Methods for large and sparse systems • Rank-one updating with Sherman-Morrison • Iterative refinement • Fixed-point and stationary methods – Introduction – Iterative refinement as a stationary method – Gauss-Seidel and Jacobi methods – Successive over-relaxation (SOR) • Solving a system as an optimization problem • Representing sparse systems Problems with large systems • Gaussian elimination, LU decomposition (factoring step) take O(n3) • Expensive for big systems! • Can get by more easily with special matrices – Cholesky decomposition: for symmetric positive definite A; still O(n3) but halves storage and operations – Band-diagonal: O(n) storage and operations • What if A is big? (And not diagonal?) Special Example: Cyclic Tridiagonal • Interesting extension: cyclic tridiagonal • Could derive yet another special case algorithm, but there’s a better way Updating Inverse • Suppose we have some fast way of finding A-1 for some matrix A • Now A changes in a special way: A* = A + uvT for some n×1 vectors u and v • Goal: find a fast way of computing (A*)-1 -
Numerical Mathematics
4 Iterative Methods for Solving Linear Systems Iterative methods formally yield the solution x of a linear system after an infinite number of steps. At each step they require the computation of the residual of the system. In the case of a full matrix, their computational cost is therefore of the order of n2 operations for each iteration, to be 2 3 compared with an overall cost of the order of 3 n operations needed by direct methods. Iterative methods can therefore become competitive with direct methods provided the number of iterations that are required to con- verge (within a prescribed tolerance) is either independent of n or scales sublinearly with respect to n. In the case of large sparse matrices, as discussed in Section 3.9, direct methods may be unconvenient due to the dramatic fill-in, although ex- tremely efficient direct solvers can be devised on sparse matrices featuring special structures like, for example, those encountered in the approximation of partial differential equations (see Chapters 12 and 13). Finally, we notice that, when A is ill-conditioned, a combined use of direct and iterative methods is made possible by preconditioning techniques that will be addressed in Section 4.3.2. 4.1 On the Convergence of Iterative Methods The basic idea of iterative methods is to construct a sequence of vectors x(k) that enjoy the property of convergence x = lim x(k), (4.1) k →∞ 124 4. Iterative Methods for Solving Linear Systems where x is the solution to (3.2). In practice, the iterative process is stopped at the minimum value of n such that x(n) x <ε, where ε is a fixed tolerance and is any convenient vector∥ norm.− ∥ However, since the exact solution is obviously∥·∥ not available, it is necessary to introduce suitable stopping criteria to monitor the convergence of the iteration (see Section 4.6). -
Linear Iterative Methods
Chapter 6 Linear Iterative Methods 6.1 Motivation In Chapter 3 we learned that, in general, solving the linear system of equations n n n 3 Ax = b with A C ⇥ and b C requires (n ) operations. This is too 2 2 O expensive in practice. The high cost begs the following questions: Are there lower cost options? Is an approximation of x good enough? How would such an approximation be generated? Often times we can find schemes that have a much lower cost of computing an approximate solution to x. As an alternative to the direct methods that we studied in the previous chapters, in the present chapter we will describe so called iteration methods for n 1 constructing sequences, x k 1 C , with the desire that x k x := A− b, { }k=1 ⇢ ! as k . The idea is that, given some ">0, we look for a k N such that !1 2 x x " k − k k with respect to some norm. In this context, " is called the stopping tolerance. In other words, we want to make certain the error is small in norm. But a word of caution. Usually, we do not have a direct way of approximating the error. The residual is more readily available. Suppose that x k is an ap- proximation of x = A 1b. The error is e = x x and the residual is − k − k r = b Ax = Ae . Recall that, k − k k e r k k k (A)k k k. x b k k k k r k Thus, when (A) is large, k b k , which is easily computable, may not be a good k k ek indicator of the size of the relative error k x k , which is not directly computable.