Chapter 1. Preliminaries
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(LINUX) Computer in Three Parts
Science on a (LINUX) computer in three parts Introductory short couse, Part II Thorsten Becker University of Southern California, Los Angeles September 2007 The first part dealt with ● UNIX: what and why ● File system, Window managers ● Shell environment ● Editing files ● Command line tools ● Scripts and GUIs ● Virtualization Contents part II ● Typesetting ● Programming – common languages – philosophy – compiling, debugging, make, version control – C and F77 interfacing – libraries and packages ● Number crunching ● Visualization tools Programming: Traditional languages in the natural sciences ● Fortran: higher level, good for math – F77: legacy, don't use (but know how to read) – F90/F95: nice vector features, finally implements C capabilities (structures, memory allocation) ● C: low level (e.g. pointers), better structured – very close to UNIX philosophy – structures offer nice way of modular programming, see Wikipedia on C ● I recommend F95, and use C happily myself Programming: Some Languages that haven't completely made it to scientific computing ● C++: object oriented programming model – reusable objects with methods and such – can be partly realized by modular programming in C ● Java: what's good for commercial projects (or smart, or elegant) doesn't have to be good for scientific computing ● Concern about portability as well as general access Programming: Compromises ● Python – Object oriented – Interpreted – Interfaces easily with F90/C – Numerous scientific packages Programming: Other interpreted, high- abstraction languages -
4.4 Improper Integrals 135
4.4 Improper Integrals 135 converges (with parameters as shown above) on the very first extrapolation, after just 5 calls to trapzd, while qsimp requires 8 calls (8 times as many evaluations of the integrand) and qtrap requires 13 calls (making 256 times as many evaluations of the integrand). CITED REFERENCES AND FURTHER READING: http://www.nr.com or call 1-800-872-7423 (North America only), or send email to [email protected] (outside North Amer readable files (including this one) to any server computer, is strictly prohibited. To order Numerical Recipes books or CDROMs, v Permission is granted for internet users to make one paper copy their own personal use. Further reproduction, or any copyin Copyright (C) 1986-1992 by Cambridge University Press. Programs Copyright (C) 1986-1992 by Numerical Recipes Software. Sample page from NUMERICAL RECIPES IN FORTRAN 77: THE ART OF SCIENTIFIC COMPUTING (ISBN 0-521-43064-X) Stoer, J., and Bulirsch, R. 1980, Introduction to Numerical Analysis (New York: Springer-Verlag), §§3.4–3.5. Dahlquist, G., and Bjorck, A. 1974, Numerical Methods (Englewood Cliffs, NJ: Prentice-Hall), §§7.4.1–7.4.2. Ralston, A., and Rabinowitz, P. 1978, A First Course in Numerical Analysis, 2nd ed. (New York: McGraw-Hill), §4.10–2. 4.4 Improper Integrals For our present purposes, an integral will be “improper” if it has any of the following problems: • its integrand goes to a finite limiting value at finite upper and lower limits, but cannot be evaluated right on one of those limits (e.g., sin x/x at x =0) • its upper limit is ∞ , or its lower limit is −∞ • it has an integrable singularity at either limit (e.g., x−1/2 at x =0) • it has an integrable singularity at a known place between its upper and lower limits • it has an integrable singularity at an unknown place between its upper and lower limits ∞ −1 If an integral is infinite (e.g., 1 x dx), or does not exist in a limiting sense ∞ (e.g., −∞ cos xdx), we do not call it improper; we call it impossible. -
3.2 Rational Function Interpolation and Extrapolation
104 Chapter 3. Interpolation and Extrapolation do 11 i=1,n Here we find the index ns of the closest table entry, dift=abs(x-xa(i)) if (dift.lt.dif) then ns=i dif=dift endif c(i)=ya(i) and initialize the tableau of c’s and d’s. d(i)=ya(i) http://www.nr.com or call 1-800-872-7423 (North America only), or send email to [email protected] (outside North Amer readable files (including this one) to any server computer, is strictly prohibited. To order Numerical Recipes books or CDROMs, v Permission is granted for internet users to make one paper copy their own personal use. Further reproduction, or any copyin Copyright (C) 1986-1992 by Cambridge University Press. Programs Copyright (C) 1986-1992 by Numerical Recipes Software. Sample page from NUMERICAL RECIPES IN FORTRAN 77: THE ART OF SCIENTIFIC COMPUTING (ISBN 0-521-43064-X) enddo 11 y=ya(ns) This is the initial approximation to y. ns=ns-1 do 13 m=1,n-1 For each column of the tableau, do 12 i=1,n-m we loop over the current c’s and d’s and update them. ho=xa(i)-x hp=xa(i+m)-x w=c(i+1)-d(i) den=ho-hp if(den.eq.0.)pause ’failure in polint’ This error can occur only if two input xa’s are (to within roundoff)identical. den=w/den d(i)=hp*den Here the c’s and d’s are updated. c(i)=ho*den enddo 12 if (2*ns.lt.n-m)then After each column in the tableau is completed, we decide dy=c(ns+1) which correction, c or d, we want to add to our accu- else mulating value of y, i.e., which path to take through dy=d(ns) the tableau—forking up or down. -
Linear Algebra Libraries
Linear Algebra Libraries Claire Mouton [email protected] March 2009 Contents I Requirements 3 II CPPLapack 4 III Eigen 5 IV Flens 7 V Gmm++ 9 VI GNU Scientific Library (GSL) 11 VII IT++ 12 VIII Lapack++ 13 arXiv:1103.3020v1 [cs.MS] 15 Mar 2011 IX Matrix Template Library (MTL) 14 X PETSc 16 XI Seldon 17 XII SparseLib++ 18 XIII Template Numerical Toolkit (TNT) 19 XIV Trilinos 20 1 XV uBlas 22 XVI Other Libraries 23 XVII Links and Benchmarks 25 1 Links 25 2 Benchmarks 25 2.1 Benchmarks for Linear Algebra Libraries . ....... 25 2.2 BenchmarksincludingSeldon . 26 2.2.1 BenchmarksforDenseMatrix. 26 2.2.2 BenchmarksforSparseMatrix . 29 XVIII Appendix 30 3 Flens Overloaded Operator Performance Compared to Seldon 30 4 Flens, Seldon and Trilinos Content Comparisons 32 4.1 Available Matrix Types from Blas (Flens and Seldon) . ........ 32 4.2 Available Interfaces to Blas and Lapack Routines (Flens and Seldon) . 33 4.3 Available Interfaces to Blas and Lapack Routines (Trilinos) ......... 40 5 Flens and Seldon Synoptic Comparison 41 2 Part I Requirements This document has been written to help in the choice of a linear algebra library to be included in Verdandi, a scientific library for data assimilation. The main requirements are 1. Portability: Verdandi should compile on BSD systems, Linux, MacOS, Unix and Windows. Beyond the portability itself, this often ensures that most compilers will accept Verdandi. An obvious consequence is that all dependencies of Verdandi must be portable, especially the linear algebra library. 2. High-level interface: the dependencies should be compatible with the building of the high-level interface (e. -
C++ API for BLAS and LAPACK
2 C++ API for BLAS and LAPACK Mark Gates ICL1 Piotr Luszczek ICL Ahmad Abdelfattah ICL Jakub Kurzak ICL Jack Dongarra ICL Konstantin Arturov Intel2 Cris Cecka NVIDIA3 Chip Freitag AMD4 1Innovative Computing Laboratory 2Intel Corporation 3NVIDIA Corporation 4Advanced Micro Devices, Inc. February 21, 2018 This research was supported by the Exascale Computing Project (17-SC-20-SC), a collaborative effort of two U.S. Department of Energy organizations (Office of Science and the National Nuclear Security Administration) responsible for the planning and preparation of a capable exascale ecosystem, including software, applications, hardware, advanced system engineering and early testbed platforms, in support of the nation's exascale computing imperative. Revision Notes 06-2017 first publication 02-2018 • copy editing, • new cover. 03-2018 • adding a section about GPU support, • adding Ahmad Abdelfattah as an author. @techreport{gates2017cpp, author={Gates, Mark and Luszczek, Piotr and Abdelfattah, Ahmad and Kurzak, Jakub and Dongarra, Jack and Arturov, Konstantin and Cecka, Cris and Freitag, Chip}, title={{SLATE} Working Note 2: C++ {API} for {BLAS} and {LAPACK}}, institution={Innovative Computing Laboratory, University of Tennessee}, year={2017}, month={June}, number={ICL-UT-17-03}, note={revision 03-2018} } i Contents 1 Introduction and Motivation1 2 Standards and Trends2 2.1 Programming Language Fortran............................ 2 2.1.1 FORTRAN 77.................................. 2 2.1.2 BLAST XBLAS................................. 4 2.1.3 Fortran 90.................................... 4 2.2 Programming Language C................................ 5 2.2.1 Netlib CBLAS.................................. 5 2.2.2 Intel MKL CBLAS................................ 6 2.2.3 Netlib lapack cwrapper............................. 6 2.2.4 LAPACKE.................................... 7 2.2.5 Next-Generation BLAS: \BLAS G2"..................... -
GNU Scientific Library – 設計と実装の指針
GNU Scienti¯c Library { 設計と実装の指針 マーク・ガラッシ (Mark Galassi) Los Alamos National Laboratory ジェイムズ・ティラー (James Theiler) Astrophysics and Radiation Measurements Group, Los Alamos National Laboratory ブライアン・ガウ (Brian Gough) Network Theory Limited とみながだいすけ訳 (translation: Daisuke Tominaga) 産業技術総合研究所 生命情報工学研究センター Copyright °c 1996,1997,1998,1999,2000,2001,2004 The GSL Project. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modi¯ed versions of this manual under the con- ditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another lan- guage, under the above conditions for modi¯ed versions, except that this permission notice may be stated in a translation approved by the Foundation. このライセンスの文面をつけさえすれば、この文書をそのままの形でコピー、再配布して構 いません。また、この文書を改編したものについても、同じライセンスにしたがうのであれ ば、コピー、再配布して構いません。この文書を翻訳したものについても、米フリーソフト ウェア財団 (the Free Software Foundation) が認可した翻訳済みのライセンス文面を添付す れば、コピー、再配布して構いません。 そういうわけで、この日本語に翻訳した文書は、GFDL 1.3 にしたがった複製、再配布を認 めるものとします。ライセンスの詳細はこの文書に添付されています。 平成 21 年 6 月 4 日 とみながだいすけ i Table of Contents GSL について :::::::::::::::::::::::::::::::::::::::: 1 1 目標 :::::::::::::::::::::::::::::::::::::::::::::: 2 2 開発への参加:::::::::::::::::::::::::::::::::::::: 4 2.1 パッケージ ::::::::::::::::::::::::::::::::::::::::::::::::::::: -
Numerical Methods in Engineering with MATLAB R
P1: PHB cuus734 CUUS734/Kiusalaas 0 521 19133 3 August 29, 2009 12:17 This page intentionally left blank ii P1: PHB cuus734 CUUS734/Kiusalaas 0 521 19133 3 August 29, 2009 12:17 Numerical Methods in Engineering with MATLAB R Second Edition Numerical Methods in Engineering with MATLAB R is a text for engi- neering students and a reference for practicing engineers. The choice of numerical methods was based on their relevance to engineering prob- lems. Every method is discussed thoroughly and illustrated with prob- lems involving both hand computation and programming. MATLAB M-files accompany each method and are available on the book Web site. This code is made simple and easy to understand by avoiding com- plex bookkeeping schemes while maintaining the essential features of the method. MATLAB was chosen as the example language because of its ubiquitous use in engineering studies and practice. This new edi- tion includes the new MATLAB anonymous functions, which allow the programmer to embed functions into the program rather than storing them as separate files. Other changes include the addition of rational function interpolation in Chapter 3, the addition of Ridder’s method in place of Brent’s method in Chapter 4, and the addition of the downhill simplex method in place of the Fletcher–Reeves method of optimization in Chapter 10. Jaan Kiusalaas is a Professor Emeritus in the Department of Engineer- ing Science and Mechanics at the Pennsylvania State University. He has taught numerical methods, including finite element and boundary ele- ment methods, for more than 30 years. He is also the co-author of four other books – Engineering Mechanics: Statics, Engineering Mechanics: Dynamics, Mechanics of Materials,andNumerical Methods in Engineer- ing with Python, Second Edition. -
NUMERICAL RECIPES in FORTRAN 77: the ART of SCIENTIFIC COMPUTING (ISBN 0-521-43064-X) Copyright (C) 1986-1992 by Cambridge University Press
Numerical Recipes http://www.nr.com or call 1-800-872-7423 (North America only), or send email to [email protected] (outside North Amer readable files (including this one) to any server computer, is strictly prohibited. To order Numerical Recipes books or CDROMs, v Permission is granted for internet users to make one paper copy their own personal use. Further reproduction, or any copyin Copyright (C) 1986-1992 by Cambridge University Press. Programs Copyright (C) 1986-1992 by Numerical Recipes Software. Sample page from NUMERICAL RECIPES IN FORTRAN 77: THE ART OF SCIENTIFIC COMPUTING (ISBN 0-521-43064-X) in Fortran 77 The Art of Scientific Computing Second Edition Volume 1 of Fortran Numerical Recipes William H. Press Harvard-Smithsonian Center for Astrophysics Saul A. Teukolsky Department of Physics, Cornell University William T. Vetterling Polaroid Corporation Brian P. Flannery g of machine- EXXON Research and Engineering Company isit website ica). Published by the Press Syndicate of the University of Cambridge The Pitt Building, Trumpington Street, Cambridge CB2 1RP 40 West 20th Street, New York, NY 10011-4211, USA 10 Stamford Road, Oakleigh, Melbourne 3166, Australia Copyright c Cambridge University Press 1986, 1992 except for §13.10, which is placed into the public domain, and except for all other computer programs and procedures, which are http://www.nr.com or call 1-800-872-7423 (North America only), or send email to [email protected] (outside North Amer readable files (including this one) to any server computer, is strictly prohibited. To order Numerical Recipes books or CDROMs, v Permission is granted for internet users to make one paper copy their own personal use. -
A Framework for Developing Finite Element Codes for Multi- Disciplinary Applications
A Framework for Developing Finite Element Codes for Multi- Disciplinary Applications Pooyan Dadvand Eugenio Oñate Monograph CIMNE Nº-109, January 2008 A Framework for Developing Finite Element Codes for Multi-Disciplinary Applications Pooyan Dadvand Eugenio Oñate Monograph CIMNE Nº-109, January 2008 Centro Internacional de Métodos Numéricos en Ingeniería Gran Capitán s/n, 08034 Barcelona, España CENTRO INTERNACIONAL DE MÉTODOS NUMÉRICOS EN INGENIERÍA Edificio C1, Campus Norte UPC Gran Capitán s/n 08034 Barcelona, Spain Primera edición: Januray 2008 A FRAMEWORK FOR DEVELOPING FINITE ELEMENT CODES FOR MULTI-DISCIPLINARY APPLICATIONS Monografía CIMNE M109 Los autores To Hengameh Abstract The world of computing simulation has experienced great progresses in recent years and requires more exigent multidisciplinary challenges to satisfy the new upcoming demands. Increasing the importance of solving multi-disciplinary problems makes developers put more attention to these problems and deal with difficulties involved in developing software in this area. Conventional finite element codes have several difficulties in dealing with multi-disciplinary problems. Many of these codes are designed and implemented for solving a certain type of problems, generally involving a single field. Extending these codes to deal with another field of analysis usually consists of several problems and large amounts of modifications and implementations. Some typical difficulties are: predefined set of degrees of freedom per node, data structure with fixed set of defined variables, global list of variables for all entities, domain based interfaces, IO restriction in reading new data and writing new results and algorithm definition inside the code. A common approach is to connect different solvers via a master program which implements the interaction algorithms and also transfers data from one solver to another. -
9.4 Newton-Raphson Method Using Derivative 355
9.4 Newton-Raphson Method Using Derivative 355 endif if(p.gt.0.) q=-q Check whether in bounds. p=abs(p) if(2.*p .lt. min(3.*xm*q-abs(tol1*q),abs(e*q))) then e=d Accept interpolation. d=p/q else d=xm Interpolation failed, use bisection. visit website http://www.nr.com or call 1-800-872-7423 (North America only),or send email to [email protected] (outside North America). readable files (including this one) to any servercomputer, is strictly prohibited. To order Numerical Recipes books,diskettes, or CDROMs Permission is granted for internet users to make one paper copy their own personal use. Further reproduction, or any copying of machine- Copyright (C) 1986-1992 by Cambridge University Press.Programs Numerical Recipes Software. Sample page from NUMERICAL RECIPES IN FORTRAN 77: THE ART OF SCIENTIFIC COMPUTING (ISBN 0-521-43064-X) e=d endif else Bounds decreasing too slowly, use bisection. d=xm e=d endif a=b Move last best guess to a. fa=fb if(abs(d) .gt. tol1) then Evaluate new trial root. b=b+d else b=b+sign(tol1,xm) endif fb=func(b) enddo 11 pause ’zbrent exceeding maximum iterations’ zbrent=b return END CITED REFERENCES AND FURTHER READING: Brent, R.P. 1973, Algorithms for Minimization without Derivatives (Englewood Cliffs, NJ: Prentice- Hall), Chapters 3, 4. [1] Forsythe, G.E., Malcolm, M.A., and Moler, C.B. 1977, Computer Methods for Mathematical Computations (Englewood Cliffs, NJ: Prentice-Hall), 7.2. § 9.4 Newton-Raphson Method Using Derivative Perhaps the most celebrated of all one-dimensional root-®ndingroutines is New- ton'smethod, also called the Newton-Raphson method. -
An Active-Library Based Investigation Into the Performance Optimisation of Linear Algebra and the Finite Element Method
Imperial College of Science, Technology and Medicine Department of Computing An Active-Library Based Investigation into the Performance Optimisation of Linear Algebra and the Finite Element Method Francis Prem Russell Submitted in part fulfilment of the requirements for the degree of Doctor of Philosophy in Computing and the Diploma of Imperial College, London, July 2011 Abstract In this thesis, I explore an approach called \active libraries". These are libraries that take part in their own optimisation, enabling both high-performance code and the presentation of intuitive abstractions. I investigate the use of active libraries in two domains. Firstly, dense and sparse linear algebra, particularly, the solution of linear systems of equations. Secondly, the specification and solution of finite element problems. Extending my earlier (MEng) thesis work, I describe the modifications to my linear algebra library \Desola" required to perform sparse-matrix code generation. I show that optimisations easily applied in the dense case using code-transformation must be applied at a higher level of abstraction in the sparse case. I present performance results for sparse linear system solvers generated using Desola and compare against an implementation using the Intel Math Kernel Library. I also present improved dense linear-algebra performance results. Next, I explore the active-library approach by developing a finite element library that captures runtime representations of basis functions, variational forms and sequences of operations be- tween discretised operators and fields. Using captured representations of variational forms and basis functions, I demonstrate optimisations to cell-local integral assembly that this approach enables, and compare against the state of the art. -
Numerical Recipes in C++ the Art of Scientific Computing Second Edition
Numerical Recipes in C++ The Art of Scientific Computing Second Edition William H. Press Los Alamos National Laboratory Saul A. Teukolsky Department of Physics, Cornell University William T. Vetterling Polaroid Corporation Brian P. Flannery EXXON Research and Engineering Company PUBLISHED BY THE PRESS SYNDICATE OF THE UNIVERSITY OF CAMBRIDGE The Pitt Building, Trumpington Street, Cambridge, United Kingdom CAMBRIDGE UNIVERSITY PRESS The Edinburgh Building, Cambridge CB2 2RU, UK 40 West 20th Street, New York, NY 10011-4211, USA 477 Williamstown Road, Port Melbourne, VIC, 3207, Australia Ruiz de Alarcon´ 13, 28014 Madrid, Spain Dock House, The Waterfront, Cape Town 8001, South Africa http://www.cambridge.org c Cambridge University Press 1988, 1992, 2002 except for §13.10 and Appendix B, which are placed into the public domain, and except for all other computer programs and procedures, which are c Numerical Recipes Software 1987, 1988, 1992, 1997, 2002 All Rights Reserved. This book is copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. Some sections of this book were originally published, in different form, in Computers in Physics magazine, c American Institute of Physics, 1988–1992. First Edition originally published 1988; Second Edition originally published 1992; C++ edition originally published 2002. This printing is corrected to software version 2.10 Printed in the United States of America Typeface Times 10/12 pt. System TEX[AU] Affiliations shown on title page are for purposes of identification only. No implication that the works contained herein were created in the course of employment is intended, nor is any knowledge of or endorsement of these works by the listed institutions to be inferred.