An Improved Algorithm for Computing the Singular Value Decomposition
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Life As a Developer of Numerical Software
A Brief History of Numerical Libraries Sven Hammarling NAG Ltd, Oxford & University of Manchester First – Something about Jack Jack’s thesis (August 1980) 30 years ago! TOMS Algorithm 589 Small Selection of Jack’s Projects • Netlib and other software repositories • NA Digest and na-net • PVM and MPI • TOP 500 and computer benchmarking • NetSolve and other distributed computing projects • Numerical linear algebra Onto the Rest of the Talk! Rough Outline • History and influences • Fortran • Floating Point Arithmetic • Libraries and packages • Proceedings and Books • Summary Ada Lovelace (Countess Lovelace) Born Augusta Ada Byron 1815 – 1852 The language Ada was named after her “Is thy face like thy mother’s, my fair child! Ada! sole daughter of my house and of my heart? When last I saw thy young blue eyes they smiled, And then we parted,-not as now we part, but with a hope” Childe Harold’s Pilgramage, Lord Byron Program for the Bernoulli Numbers Manchester Baby, 21 June 1948 (Replica) 19 Kilburn/Tootill Program to compute the highest proper factor 218 218 took 52 minutes 1.5 million instructions 3.5 million store accesses First published numerical library, 1951 First use of the word subroutine? Quality Numerical Software • Should be: – Numerically stable, with measures of quality of solution – Reliable and robust – Accompanied by test software – Useful and user friendly with example programs – Fully documented – Portable – Efficient “I have little doubt that about 80 per cent. of all the results printed from the computer are in error to a much greater extent than the user would believe, ...'' Leslie Fox, IMA Bulletin, 1971 “Giving business people spreadsheets is like giving children circular saws. -
Numerical and Parallel Libraries
Numerical and Parallel Libraries Uwe Küster University of Stuttgart High-Performance Computing-Center Stuttgart (HLRS) www.hlrs.de Uwe Küster Slide 1 Höchstleistungsrechenzentrum Stuttgart Numerical Libraries Public Domain commercial vendor specific Uwe Küster Slide 2 Höchstleistungsrechenzentrum Stuttgart 33. — Numerical and Parallel Libraries — 33. 33-1 Overview • numerical libraries for linear systems – dense – sparse •FFT • support for parallelization Uwe Küster Slide 3 Höchstleistungsrechenzentrum Stuttgart Public Domain Lapack-3 linear equations, eigenproblems BLAS fast linear kernels Linpack linear equations Eispack eigenproblems Slatec old library, large functionality Quadpack numerical quadrature Itpack sparse problems pim linear systems PETSc linear systems Netlib Server best server http://www.netlib.org/utk/papers/iterative-survey/packages.html Uwe Küster Slide 4 Höchstleistungsrechenzentrum Stuttgart 33. — Numerical and Parallel Libraries — 33. 33-2 netlib server for all public domain numerical programs and libraries http://www.netlib.org Uwe Küster Slide 5 Höchstleistungsrechenzentrum Stuttgart Contents of netlib access aicm alliant amos ampl anl-reports apollo atlas benchmark bib bibnet bihar blacs blas blast bmp c c++ cephes chammp cheney-kincaid clapack commercial confdb conformal contin control crc cumulvs ddsv dierckx diffpack domino eispack elefunt env f2c fdlibm fftpack fishpack fitpack floppy fmm fn fortran fortran-m fp gcv gmat gnu go graphics harwell hence hompack hpf hypercube ieeecss ijsa image intercom itpack -
Jack Dongarra: Supercomputing Expert and Mathematical Software Specialist
Biographies Jack Dongarra: Supercomputing Expert and Mathematical Software Specialist Thomas Haigh University of Wisconsin Editor: Thomas Haigh Jack J. Dongarra was born in Chicago in 1950 to a he applied for an internship at nearby Argonne National family of Sicilian immigrants. He remembers himself as Laboratory as part of a program that rewarded a small an undistinguished student during his time at a local group of undergraduates with college credit. Dongarra Catholic elementary school, burdened by undiagnosed credits his success here, against strong competition from dyslexia.Onlylater,inhighschool,didhebeginto students attending far more prestigious schools, to Leff’s connect material from science classes with his love of friendship with Jim Pool who was then associate director taking machines apart and tinkering with them. Inspired of the Applied Mathematics Division at Argonne.2 by his science teacher, he attended Chicago State University and majored in mathematics, thinking that EISPACK this would combine well with education courses to equip Dongarra was supervised by Brian Smith, a young him for a high school teaching career. The first person in researcher whose primary concern at the time was the his family to go to college, he lived at home and worked lab’s EISPACK project. Although budget cuts forced Pool to in a pizza restaurant to cover the cost of his education.1 make substantial layoffs during his time as acting In 1972, during his senior year, a series of chance director of the Applied Mathematics Division in 1970– events reshaped Dongarra’s planned career. On the 1971, he had made a special effort to find funds to suggestion of Harvey Leff, one of his physics professors, protect the project and hire Smith. -
Randnla: Randomized Numerical Linear Algebra
review articles DOI:10.1145/2842602 generation mechanisms—as an algo- Randomization offers new benefits rithmic or computational resource for the develop ment of improved algo- for large-scale linear algebra computations. rithms for fundamental matrix prob- lems such as matrix multiplication, BY PETROS DRINEAS AND MICHAEL W. MAHONEY least-squares (LS) approximation, low- rank matrix approxi mation, and Lapla- cian-based linear equ ation solvers. Randomized Numerical Linear Algebra (RandNLA) is an interdisci- RandNLA: plinary research area that exploits randomization as a computational resource to develop improved algo- rithms for large-scale linear algebra Randomized problems.32 From a foundational per- spective, RandNLA has its roots in theoretical computer science (TCS), with deep connections to mathemat- Numerical ics (convex analysis, probability theory, metric embedding theory) and applied mathematics (scientific computing, signal processing, numerical linear Linear algebra). From an applied perspec- tive, RandNLA is a vital new tool for machine learning, statistics, and data analysis. Well-engineered implemen- Algebra tations have already outperformed highly optimized software libraries for ubiquitous problems such as least- squares,4,35 with good scalability in par- allel and distributed environments. 52 Moreover, RandNLA promises a sound algorithmic and statistical foundation for modern large-scale data analysis. MATRICES ARE UBIQUITOUS in computer science, statistics, and applied mathematics. An m × n key insights matrix can encode information about m objects ˽ Randomization isn’t just used to model noise in data; it can be a powerful (each described by n features), or the behavior of a computational resource to develop discretized differential operator on a finite element algorithms with improved running times and stability properties as well as mesh; an n × n positive-definite matrix can encode algorithms that are more interpretable in the correlations between all pairs of n objects, or the downstream data science applications. -
Copyright © by SIAM. Unauthorized Reproduction of This Article Is Prohibited. PARALLEL BIDIAGONALIZATION of a DENSE MATRIX 827
SIAM J. MATRIX ANAL. APPL. c 2007 Society for Industrial and Applied Mathematics Vol. 29, No. 3, pp. 826–837 ∗ PARALLEL BIDIAGONALIZATION OF A DENSE MATRIX † ‡ ‡ § CARLOS CAMPOS , DAVID GUERRERO , VICENTE HERNANDEZ´ , AND RUI RALHA Abstract. A new stable method for the reduction of rectangular dense matrices to bidiagonal form has been proposed recently. This is a one-sided method since it can be entirely expressed in terms of operations with (full) columns of the matrix under transformation. The algorithm is well suited to parallel computing and, in order to make it even more attractive for distributed memory systems, we introduce a modification which halves the number of communication instances. In this paper we present such a modification. A block organization of the algorithm to use level 3 BLAS routines seems difficult and, at least for the moment, it relies upon level 2 BLAS routines. Nevertheless, we found that our sequential code is competitive with the LAPACK DGEBRD routine. We also compare the time taken by our parallel codes and the ScaLAPACK PDGEBRD routine. We investigated the best data distribution schemes for the different codes and we can state that our parallel codes are also competitive with the ScaLAPACK routine. Key words. bidiagonal reduction, parallel algorithms AMS subject classifications. 15A18, 65F30, 68W10 DOI. 10.1137/05062809X 1. Introduction. The problem of computing the singular value decomposition (SVD) of a matrix is one of the most important operations in numerical linear algebra and is employed in a variety of applications. The SVD is defined as follows. × For any rectangular matrix A ∈ Rm n (we will assume that m ≥ n), there exist ∈ Rm×m ∈ Rn×n ΣA ∈ Rm×n two orthogonal matrices U and V and a matrix Σ = 0 , t where ΣA = diag (σ1,...,σn) is a diagonal matrix, such that A = UΣV . -
Minimum-Residual Methods for Sparse Least-Squares Using Golub-Kahan Bidiagonalization a Dissertation Submitted to the Institute
MINIMUM-RESIDUAL METHODS FOR SPARSE LEAST-SQUARES USING GOLUB-KAHAN BIDIAGONALIZATION A DISSERTATION SUBMITTED TO THE INSTITUTE FOR COMPUTATIONAL AND MATHEMATICAL ENGINEERING AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY David Chin-lung Fong December 2011 © 2011 by Chin Lung Fong. All Rights Reserved. Re-distributed by Stanford University under license with the author. This dissertation is online at: http://purl.stanford.edu/sd504kj0427 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Michael Saunders, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Margot Gerritsen I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Walter Murray Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. iii iv ABSTRACT For 30 years, LSQR and its theoretical equivalent CGLS have been the standard iterative solvers for large rectangular systems Ax = b and least-squares problems min Ax b . They are analytically equivalent − to symmetric CG on the normal equation ATAx = ATb, and they reduce r monotonically, where r = b Ax is the k-th residual vector. -
Evolving Software Repositories
1 Evolving Software Rep ositories http://www.netli b.org/utk/pro ject s/esr/ Jack Dongarra UniversityofTennessee and Oak Ridge National Lab oratory Ron Boisvert National Institute of Standards and Technology Eric Grosse AT&T Bell Lab oratories 2 Pro ject Fo cus Areas NHSE Overview Resource Cataloging and Distribution System RCDS Safe execution environments for mobile co de Application-l evel and content-oriented to ols Rep ository interop erabili ty Distributed, semantic-based searching 3 NHSE National HPCC Software Exchange NASA plus other agencies funded CRPC pro ject Center for ResearchonParallel Computation CRPC { Argonne National Lab oratory { California Institute of Technology { Rice University { Syracuse University { UniversityofTennessee Uniform interface to distributed HPCC software rep ositories Facilitation of cross-agency and interdisciplinary software reuse Material from ASTA, HPCS, and I ITA comp onents of the HPCC program http://www.netlib.org/nhse/ 4 Goals: Capture, preserve and makeavailable all software and software- related artifacts pro duced by the federal HPCC program. Soft- ware related artifacts include algorithms, sp eci cations, designs, do cumentation, rep ort, ... Promote formation, growth, and interop eration of discipline-oriented rep ositories that organize, evaluate, and add value to individual contributions. Employ and develop where necessary state-of-the-art technologies for assisting users in nding, understanding, and using HPCC software and technologies. 5 Bene ts: 1. Faster development of high-quality software so that scientists can sp end less time writing and debugging programs and more time on research problems. 2. Less duplication of software development e ort by sharing of soft- ware mo dules. -
Restarted Lanczos Bidiagonalization for the SVD in Slepc
Scalable Library for Eigenvalue Problem Computations SLEPc Technical Report STR-8 Available at http://slepc.upv.es Restarted Lanczos Bidiagonalization for the SVD in SLEPc V. Hern´andez J. E. Rom´an A. Tom´as Last update: June, 2007 (slepc 2.3.3) Previous updates: { About SLEPc Technical Reports: These reports are part of the documentation of slepc, the Scalable Library for Eigenvalue Problem Computations. They are intended to complement the Users Guide by providing technical details that normal users typically do not need to know but may be of interest for more advanced users. Restarted Lanczos Bidiagonalization for the SVD in SLEPc STR-8 Contents 1 Introduction 2 2 Description of the Method3 2.1 Lanczos Bidiagonalization...............................3 2.2 Dealing with Loss of Orthogonality..........................6 2.3 Restarted Bidiagonalization..............................8 2.4 Available Implementations............................... 11 3 The slepc Implementation 12 3.1 The Algorithm..................................... 12 3.2 User Options...................................... 13 3.3 Known Issues and Applicability............................ 14 1 Introduction The singular value decomposition (SVD) of an m × n complex matrix A can be written as A = UΣV ∗; (1) ∗ where U = [u1; : : : ; um] is an m × m unitary matrix (U U = I), V = [v1; : : : ; vn] is an n × n unitary matrix (V ∗V = I), and Σ is an m × n diagonal matrix with nonnegative real diagonal entries Σii = σi for i = 1;:::; minfm; ng. If A is real, U and V are real and orthogonal. The vectors ui are called the left singular vectors, the vi are the right singular vectors, and the σi are the singular values. In this report, we will assume without loss of generality that m ≥ n. -
2 Accessing Matlab at ER4
Department of Electrical Engineering EE281 Intro duction to MATLAB on the Region IV Computing Facilities 1 What is Matlab? Matlab is a high-p erformance interactive software package for scienti c and enginnering numeric computation. Matlab integrates numerical analysis, matrix computation, signal pro cessing, and graphics in an easy-to-use envi- ronment without traditional programming. The name Matlab stands for matrix laboratory. Matlab was originally written to provide easy access to the matrix software develop ed by the LIN- PACK and EISPACK pro jects. Matlab is an interactive system whose basic data element is a matrix that do es not require dimensioning. Furthermore, problem solutions are expressed in Matlab almost exactly as they are written mathematically. Matlab has evolved over the years with inputs from many users. Matlab Toolboxes are sp ecialized collections of Matlab les designed for solving particular classes of functions. Currently available to olb oxes include: signal pro cessing control system optimization neural networks system identi cation robust control analysis splines symb olic mathematics image pro cessing statistics 2 Accessing Matlab at ER4 Sit down at a workstation. Log on. login: smithj <press return> password: 1234js <press return> Use the mouse button to view the Ro ot Menu. Drag the cursor to \Design Tools" then to \Matlab." Release the mouse button. You are now running the Matlab interactive software package. The prompt is a double \greater than" sign. You may use emacs line editor commands and the arrow keys while typing in Matlab. 1 3 An Intro ductory Demonstration Execute the following command to view aquick intro duction to Matlab. -
Cache Efficient Bidiagonalization Using BLAS 2.5 Operators Howell, G. W. and Demmel, J. W. and Fulton, C. T. and Hammarling, S
Cache Efficient Bidiagonalization Using BLAS 2.5 Operators Howell, G. W. and Demmel, J. W. and Fulton, C. T. and Hammarling, S. and Marmol, K. 2006 MIMS EPrint: 2006.56 Manchester Institute for Mathematical Sciences School of Mathematics The University of Manchester Reports available from: http://eprints.maths.manchester.ac.uk/ And by contacting: The MIMS Secretary School of Mathematics The University of Manchester Manchester, M13 9PL, UK ISSN 1749-9097 Cache Efficient Bidiagonalization Using BLAS 2.5 Operators∗ G. W. Howell North Carolina State University Raleigh, North Carolina 27695 J. W. Demmel University of California, Berkeley Berkeley, California 94720 C. T. Fulton Florida Institute of Technology Melbourne, Florida 32901 S. Hammarling Numerical Algorithms Group Oxford, United Kingdom K. Marmol Harris Corporation Melbourne, Florida 32901 March 23, 2006 ∗ This research was supported by National Science Foundation Grant EIA-0103642. Abstract On cache based computer architectures using current standard al- gorithms, Householder bidiagonalization requires a significant portion of the execution time for computing matrix singular values and vectors. In this paper we reorganize the sequence of operations for Householder bidiagonalization of a general m × n matrix, so that two ( GEMV) vector-matrix multiplications can be done with one pass of the unre- duced trailing part of the matrix through cache. Two new BLAS 2.5 operations approximately cut in half the transfer of data from main memory to cache. We give detailed algorithm descriptions and com- pare timings with the current LAPACK bidiagonalization algorithm. 1 Introduction A primary constraint on execution speed is the “von Neumann” bottleneck in delivering data to the CPU. -
CS 267 Dense Linear Algebra: History and Structure, Parallel Matrix
Quick review of earlier lecture •" What do you call •" A program written in PyGAS, a Global Address CS 267 Space language based on Python… Dense Linear Algebra: •" That uses a Monte Carlo simulation algorithm to approximate π … History and Structure, •" That has a race condition, so that it gives you a Parallel Matrix Multiplication" different funny answer every time you run it? James Demmel! Monte - π - thon ! www.cs.berkeley.edu/~demmel/cs267_Spr16! ! 02/25/2016! CS267 Lecture 12! 1! 02/25/2016! CS267 Lecture 12! 2! Outline Outline •" History and motivation •" History and motivation •" What is dense linear algebra? •" What is dense linear algebra? •" Why minimize communication? •" Why minimize communication? •" Lower bound on communication •" Lower bound on communication •" Parallel Matrix-matrix multiplication •" Parallel Matrix-matrix multiplication •" Attaining the lower bound •" Attaining the lower bound •" Other Parallel Algorithms (next lecture) •" Other Parallel Algorithms (next lecture) 02/25/2016! CS267 Lecture 12! 3! 02/25/2016! CS267 Lecture 12! 4! CS267 Lecture 2 1 Motifs What is dense linear algebra? •" Not just matmul! The Motifs (formerly “Dwarfs”) from •" Linear Systems: Ax=b “The Berkeley View” (Asanovic et al.) •" Least Squares: choose x to minimize ||Ax-b||2 Motifs form key computational patterns •" Overdetermined or underdetermined; Unconstrained, constrained, or weighted •" Eigenvalues and vectors of Symmetric Matrices •" Standard (Ax = λx), Generalized (Ax=λBx) •" Eigenvalues and vectors of Unsymmetric matrices -
Comparison of Numerical Methods and Open-Source Libraries for Eigenvalue Analysis of Large-Scale Power Systems
applied sciences Article Comparison of Numerical Methods and Open-Source Libraries for Eigenvalue Analysis of Large-Scale Power Systems Georgios Tzounas , Ioannis Dassios * , Muyang Liu and Federico Milano School of Electrical and Electronic Engineering, University College Dublin, Belfield, Dublin 4, Ireland; [email protected] (G.T.); [email protected] (M.L.); [email protected] (F.M.) * Correspondence: [email protected] Received: 30 September 2020; Accepted: 24 October 2020; Published: 28 October 2020 Abstract: This paper discusses the numerical solution of the generalized non-Hermitian eigenvalue problem. It provides a comprehensive comparison of existing algorithms, as well as of available free and open-source software tools, which are suitable for the solution of the eigenvalue problems that arise in the stability analysis of electric power systems. The paper focuses, in particular, on methods and software libraries that are able to handle the large-scale, non-symmetric matrices that arise in power system eigenvalue problems. These kinds of eigenvalue problems are particularly difficult for most numerical methods to handle. Thus, a review and fair comparison of existing algorithms and software tools is a valuable contribution for researchers and practitioners that are interested in power system dynamic analysis. The scalability and performance of the algorithms and libraries are duly discussed through case studies based on real-world electrical power networks. These are a model of the All-Island Irish Transmission System with 8640 variables; and, a model of the European Network of Transmission System Operators for Electricity, with 146,164 variables. Keywords: eigenvalue analysis; large non-Hermitian matrices; numerical methods; open-source libraries 1.