Linear Algebra Overview
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A Comparative Evaluation of Matlab, Octave, R, and Julia on Maya 1 Introduction
A Comparative Evaluation of Matlab, Octave, R, and Julia on Maya Sai K. Popuri and Matthias K. Gobbert* Department of Mathematics and Statistics, University of Maryland, Baltimore County *Corresponding author: [email protected], www.umbc.edu/~gobbert Technical Report HPCF{2017{3, hpcf.umbc.edu > Publications Abstract Matlab is the most popular commercial package for numerical computations in mathematics, statistics, the sciences, engineering, and other fields. Octave is a freely available software used for numerical computing. R is a popular open source freely available software often used for statistical analysis and computing. Julia is a recent open source freely available high-level programming language with a sophisticated com- piler for high-performance numerical and statistical computing. They are all available to download on the Linux, Windows, and Mac OS X operating systems. We investigate whether the three freely available software are viable alternatives to Matlab for uses in research and teaching. We compare the results on part of the equipment of the cluster maya in the UMBC High Performance Computing Facility. The equipment has 72 nodes, each with two Intel E5-2650v2 Ivy Bridge (2.6 GHz, 20 MB cache) proces- sors with 8 cores per CPU, for a total of 16 cores per node. All nodes have 64 GB of main memory and are connected by a quad-data rate InfiniBand interconnect. The tests focused on usability lead us to conclude that Octave is the most compatible with Matlab, since it uses the same syntax and has the native capability of running m-files. R was hampered by somewhat different syntax or function names and some missing functions. -
Plotting Direction Fields in Matlab and Maxima – a Short Tutorial
Plotting direction fields in Matlab and Maxima – a short tutorial Luis Carvalho Introduction A first order differential equation can be expressed as dx x0(t) = = f(t; x) (1) dt where t is the independent variable and x is the dependent variable (on t). Note that the equation above is in normal form. The difficulty in solving equation (1) depends clearly on f(t; x). One way to gain geometric insight on how the solution might look like is to observe that any solution to (1) should be such that the slope at any point P (t0; x0) is f(t0; x0), since this is the value of the derivative at P . With this motivation in mind, if you select enough points and plot the slopes in each of these points, you will obtain a direction field for ODE (1). However, it is not easy to plot such a direction field for any function f(t; x), and so we must resort to some computational help. There are many computational packages to help us in this task. This is a short tutorial on how to plot direction fields for first order ODE’s in Matlab and Maxima. Matlab Matlab is a powerful “computing environment that combines numeric computation, advanced graphics and visualization” 1. A nice package for plotting direction field in Matlab (although resourceful, Matlab does not provide such facility natively) can be found at http://math.rice.edu/»dfield, contributed by John C. Polking from the Dept. of Mathematics at Rice University. To install this add-on, simply browse to the files for your version of Matlab and download them. -
Redberry: a Computer Algebra System Designed for Tensor Manipulation
Redberry: a computer algebra system designed for tensor manipulation Stanislav Poslavsky Institute for High Energy Physics, Protvino, Russia SRRC RF ITEP of NRC Kurchatov Institute, Moscow, Russia E-mail: [email protected] Dmitry Bolotin Institute of Bioorganic Chemistry of RAS, Moscow, Russia E-mail: [email protected] Abstract. In this paper we focus on the main aspects of computer-aided calculations with tensors and present a new computer algebra system Redberry which was specifically designed for algebraic tensor manipulation. We touch upon distinctive features of tensor software in comparison with pure scalar systems, discuss the main approaches used to handle tensorial expressions and present the comparison of Redberry performance with other relevant tools. 1. Introduction General-purpose computer algebra systems (CASs) have become an essential part of many scientific calculations. Focusing on the area of theoretical physics and particularly high energy physics, one can note that there is a wide area of problems that deal with tensors (or more generally | objects with indices). This work is devoted to the algebraic manipulations with abstract indexed expressions which forms a substantial part of computer aided calculations with tensors in this field of science. Today, there are many packages both on top of general-purpose systems (Maple Physics [1], xAct [2], Tensorial etc.) and standalone tools (Cadabra [3,4], SymPy [5], Reduce [6] etc.) that cover different topics in symbolic tensor calculus. However, it cannot be said that current demand on such a software is fully satisfied [7]. The main difference of tensorial expressions (in comparison with ordinary indexless) lies in the presence of contractions between indices. -
Data Visualization in Python
Data visualization in python Day 2 A variety of packages and philosophies • (today) matplotlib: http://matplotlib.org/ – Gallery: http://matplotlib.org/gallery.html – Frequently used commands: http://matplotlib.org/api/pyplot_summary.html • Seaborn: http://stanford.edu/~mwaskom/software/seaborn/ • ggplot: – R version: http://docs.ggplot2.org/current/ – Python port: http://ggplot.yhathq.com/ • Bokeh (live plots in your browser) – http://bokeh.pydata.org/en/latest/ Biocomputing Bootcamp 2017 Matplotlib • Gallery: http://matplotlib.org/gallery.html • Top commands: http://matplotlib.org/api/pyplot_summary.html • Provides "pylab" API, a mimic of matlab • Many different graph types and options, some obscure Biocomputing Bootcamp 2017 Matplotlib • Resulting plots represented by python objects, from entire figure down to individual points/lines. • Large API allows any aspect to be tweaked • Lengthy coding sometimes required to make a plot "just so" Biocomputing Bootcamp 2017 Seaborn • https://stanford.edu/~mwaskom/software/seaborn/ • Implements more complex plot types – Joint points, clustergrams, fitted linear models • Uses matplotlib "under the hood" Biocomputing Bootcamp 2017 Others • ggplot: – (Original) R version: http://docs.ggplot2.org/current/ – A recent python port: http://ggplot.yhathq.com/ – Elegant syntax for compactly specifying plots – but, they can be hard to tweak – We'll discuss this on the R side tomorrow, both the basics of both work similarly. • Bokeh – Live, clickable plots in your browser! – http://bokeh.pydata.org/en/latest/ -
Performance Analysis of Effective Symbolic Methods for Solving Band Matrix Slaes
Performance Analysis of Effective Symbolic Methods for Solving Band Matrix SLAEs Milena Veneva ∗1 and Alexander Ayriyan y1 1Joint Institute for Nuclear Research, Laboratory of Information Technologies, Joliot-Curie 6, 141980 Dubna, Moscow region, Russia Abstract This paper presents an experimental performance study of implementations of three symbolic algorithms for solving band matrix systems of linear algebraic equations with heptadiagonal, pen- tadiagonal, and tridiagonal coefficient matrices. The only assumption on the coefficient matrix in order for the algorithms to be stable is nonsingularity. These algorithms are implemented using the GiNaC library of C++ and the SymPy library of Python, considering five different data storing classes. Performance analysis of the implementations is done using the high-performance computing (HPC) platforms “HybriLIT” and “Avitohol”. The experimental setup and the results from the conducted computations on the individual computer systems are presented and discussed. An analysis of the three algorithms is performed. 1 Introduction Systems of linear algebraic equations (SLAEs) with heptadiagonal (HD), pentadiagonal (PD) and tridiagonal (TD) coefficient matrices may arise after many different scientific and engineering prob- lems, as well as problems of the computational linear algebra where finding the solution of a SLAE is considered to be one of the most important problems. On the other hand, special matrix’s char- acteristics like diagonal dominance, positive definiteness, etc. are not always feasible. The latter two points explain why there is a need of methods for solving of SLAEs which take into account the band structure of the matrices and do not have any other special requirements to them. One possible approach to this problem is the symbolic algorithms. -
CAS (Computer Algebra System) Mathematica
CAS (Computer Algebra System) Mathematica- UML students can download a copy for free as part of the UML site license; see the course website for details From: Wikipedia 2/9/2014 A computer algebra system (CAS) is a software program that allows [one] to compute with mathematical expressions in a way which is similar to the traditional handwritten computations of the mathematicians and other scientists. The main ones are Axiom, Magma, Maple, Mathematica and Sage (the latter includes several computer algebras systems, such as Macsyma and SymPy). Computer algebra systems began to appear in the 1960s, and evolved out of two quite different sources—the requirements of theoretical physicists and research into artificial intelligence. A prime example for the first development was the pioneering work conducted by the later Nobel Prize laureate in physics Martin Veltman, who designed a program for symbolic mathematics, especially High Energy Physics, called Schoonschip (Dutch for "clean ship") in 1963. Using LISP as the programming basis, Carl Engelman created MATHLAB in 1964 at MITRE within an artificial intelligence research environment. Later MATHLAB was made available to users on PDP-6 and PDP-10 Systems running TOPS-10 or TENEX in universities. Today it can still be used on SIMH-Emulations of the PDP-10. MATHLAB ("mathematical laboratory") should not be confused with MATLAB ("matrix laboratory") which is a system for numerical computation built 15 years later at the University of New Mexico, accidentally named rather similarly. The first popular computer algebra systems were muMATH, Reduce, Derive (based on muMATH), and Macsyma; a popular copyleft version of Macsyma called Maxima is actively being maintained. -
SNC: a Cloud Service Platform for Symbolic-Numeric Computation Using Just-In-Time Compilation
This article has been accepted for publication in a future issue of this journal, but has not been fully edited. Content may change prior to final publication. Citation information: DOI 10.1109/TCC.2017.2656088, IEEE Transactions on Cloud Computing IEEE TRANSACTIONS ON CLOUD COMPUTING 1 SNC: A Cloud Service Platform for Symbolic-Numeric Computation using Just-In-Time Compilation Peng Zhang1, Member, IEEE, Yueming Liu1, and Meikang Qiu, Senior Member, IEEE and SQL. Other types of Cloud services include: Software as a Abstract— Cloud services have been widely employed in IT Service (SaaS) in which the software is licensed and hosted in industry and scientific research. By using Cloud services users can Clouds; and Database as a Service (DBaaS) in which managed move computing tasks and data away from local computers to database services are hosted in Clouds. While enjoying these remote datacenters. By accessing Internet-based services over lightweight and mobile devices, users deploy diversified Cloud great services, we must face the challenges raised up by these applications on powerful machines. The key drivers towards this unexploited opportunities within a Cloud environment. paradigm for the scientific computing field include the substantial Complex scientific computing applications are being widely computing capacity, on-demand provisioning and cross-platform interoperability. To fully harness the Cloud services for scientific studied within the emerging Cloud-based services environment computing, however, we need to design an application-specific [4-12]. Traditionally, the focus is given to the parallel scientific platform to help the users efficiently migrate their applications. In HPC (high performance computing) applications [6, 12, 13], this, we propose a Cloud service platform for symbolic-numeric where substantial effort has been given to the integration of computation– SNC. -
Fenics-Shells Release 2018.1.0
FEniCS-Shells Release 2018.1.0 Aug 02, 2021 Contents 1 Subpackages 1 2 Module contents 13 3 Documented demos 15 4 FEniCS-Shells 61 Bibliography 65 Python Module Index 67 Index 69 i ii CHAPTER 1 Subpackages 1.1 fenics_shells.analytical package 1.1.1 Submodules 1.1.2 fenics_shells.analytical.lovadina_clamped module Analytical solution for clamped Reissner-Mindlin plate problem from Lovadina et al. 1.1.3 fenics_shells.analytical.simply_supported module Analytical solution for simply-supported Reissner-Mindlin square plate under a uniform transverse load. 1.1.4 fenics_shells.analytical.vonkarman_heated module Analytical solution for elliptic orthotropic von Karman plate with lenticular thickness subject to a uniform field of inelastic curvatures. fenics_shells.analytical.vonkarman_heated.analytical_solution(Ai, Di, a_rad, b_rad) 1 FEniCS-Shells, Release 2018.1.0 1.1.5 Module contents 1.2 fenics_shells.common package 1.2.1 Submodules 1.2.2 fenics_shells.common.constitutive_models module fenics_shells.common.constitutive_models.psi_M(k, **kwargs) Returns bending moment energy density calculated from the curvature k using: Isotropic case: .. math:: D = frac{E*t^3}{24(1 - nu^2)} W_m(k, ldots) = D*((1 - nu)*tr(k**2) + nu*(tr(k))**2) Parameters • k – Curvature, typically UFL form with shape (2,2) (tensor). • **kwargs – Isotropic case: E: Young’s modulus, Constant or Expression. nu: Poisson’s ratio, Constant or Expression. t: Thickness, Constant or Expression. Returns UFL form of bending stress tensor with shape (2,2) (tensor). fenics_shells.common.constitutive_models.psi_N(e, **kwargs) Returns membrane energy density calculated from e using: Isotropic case: .. math:: B = frac{E*t}{2(1 - nu^2)} N(e, ldots) = B(1 - nu)e + nu mathrm{tr}(e)I Parameters • e – Membrane strain, typically UFL form with shape (2,2) (tensor). -
Fenics-HPC: Automated Predictive High-Performance Finite Element
FEniCS-HPC: Automated predictive high-performance finite element computing with applications in aerodynamics Johan Hoffman1, Johan Jansson2, and Niclas Jansson3 1 Computational Technology Laboratory, School of Computer Science and Communication, KTH, Stockholm, Sweden and BCAM - Basque Center for Applied Mathematics, Bilbao, Spain [email protected] 2 BCAM - Basque Center for Applied Mathematics, Bilbao, Spain and Computational Technology Laboratory, School of Computer Science and Communication, KTH, Stockholm, Sweden [email protected] 3 RIKEN Advanced Institute for Computational Science, Kobe, Japan [email protected] Abstract. Developing multiphysics finite element methods (FEM) and scalable HPC implementations can be very challenging in terms of soft- ware complexity and performance, even more so with the addition of goal-oriented adaptive mesh refinement. To manage the complexity we in this work present general adaptive stabilized methods with automated implementation in the FEniCS-HPC automated open source software framework. This allows taking the weak form of a partial differential equation (PDE) as input in near-mathematical notation and automati- cally generating the low-level implementation source code and auxiliary equations and quantities necessary for the adaptivity. We demonstrate new optimal strong scaling results for the whole adaptive framework applied to turbulent flow on massively parallel architectures down to 25000 vertices per core with ca. 5000 cores with the MPI-based PETSc backend and for assembly down to 500 vertices per core with ca. 20000 cores with the PGAS-based JANPACK backend. As a demonstration of the high impact of the combination of the scalability together with the adaptive methodology allowing prediction of gross quantities in turbulent flow we present an application in aerodynamics of a full DLR-F11 aircraft in connection with the HiLift-PW2 benchmarking workshop with good match to experiments. -
New Directions in Symbolic Computer Algebra 3.5 Year Doctoral Research Student Position Leading to a Phd in Maths Supervisor: Dr
Cadabra: new directions in symbolic computer algebra 3:5 year doctoral research student position leading to a PhD in Maths supervisor: Dr. Kasper Peeters, [email protected] Project description The Cadabra software is a new approach to symbolic computer algebra. Originally developed to solve problems in high-energy particle and gravitational physics, it is now attracting increas- ing attention from other disciplines which deal with aspects of tensor field theory. The system was written from the ground up with the intention of exploring new ideas in computer alge- bra, in order to help areas of applied mathematics for which suitable tools have so far been inadequate. The system is open source, built on a C++ graph-manipulating core accessible through a Python layer in a notebook interface, and in addition makes use of other open maths libraries such as SymPy, xPerm, LiE and Maxima. More information and links to papers using the software can be found at http://cadabra.science. With increasing attention and interest from disciplines such as earth sciences, machine learning and condensed matter physics, we are now looking for an enthusiastic student who is interested in working on this highly multi-disciplinary computer algebra project. The aim is to enlarge the capabilities of the system and bring it to an ever widening user base. Your task will be to do research on new algorithms and take responsibility for concrete implemen- tations, based on the user feedback which we have collected over the last few years. There are several possibilities to collaborate with people in some of the fields listed above, either in the Department of Mathematical Sciences or outside of it. -
Principal Components Analysis Tutorial 4 Yang
Principal Components Analysis Tutorial 4 Yang 1 Objectives Understand the principles of principal components analysis (PCA) Know the principal components analysis method Study the PCA function of sickit-learn.decomposition Process the data set by the PCA of sickit-learn Learn to apply PCA in a reality example 2 Principal Components Analysis Method: ̶ Subtract the mean ̶ Calculate the covariance matrix ̶ Calculate the eigenvectors and eigenvalues of the covariance matrix ̶ Choosing components and forming a feature vector ̶ Deriving the new data set 3 Example 1 x y 퐷푎푡푎 = 2.5 2.4 0.5 0.7 2.2 2.9 1.9 2.2 3.1 3.0 2.3 2.7 2 1.6 1 1.1 1.5 1.6 1.1 0.9 4 sklearn.decomposition.PCA It uses the LAPACK implementation of the full SVD or a randomized truncated SVD by the method of Halko et al. 2009, depending on the shape of the input data and the number of components to extract. It can also use the scipy.sparse.linalg ARPACK implementation of the truncated SVD. Notice that this class does not upport sparse input. 5 Parameters of PCA n_components: Number of components to keep. svd_solver: if n_components is not set: n_components == auto: default, if the input data is larger than 500x500 min (n_samples, n_features), default=None and the number of components to extract is lower than 80% of the smallest dimension of the data, then the more efficient ‘randomized’ method is enabled. if n_components == ‘mle’ and svd_solver == ‘full’, Otherwise the exact full SVD is computed and Minka’s MLE is used to guess the dimension optionally truncated afterwards. -
Sage Tutorial (Pdf)
Sage Tutorial Release 9.4 The Sage Development Team Aug 24, 2021 CONTENTS 1 Introduction 3 1.1 Installation................................................4 1.2 Ways to Use Sage.............................................4 1.3 Longterm Goals for Sage.........................................5 2 A Guided Tour 7 2.1 Assignment, Equality, and Arithmetic..................................7 2.2 Getting Help...............................................9 2.3 Functions, Indentation, and Counting.................................. 10 2.4 Basic Algebra and Calculus....................................... 14 2.5 Plotting.................................................. 20 2.6 Some Common Issues with Functions.................................. 23 2.7 Basic Rings................................................ 26 2.8 Linear Algebra.............................................. 28 2.9 Polynomials............................................... 32 2.10 Parents, Conversion and Coercion.................................... 36 2.11 Finite Groups, Abelian Groups...................................... 42 2.12 Number Theory............................................. 43 2.13 Some More Advanced Mathematics................................... 46 3 The Interactive Shell 55 3.1 Your Sage Session............................................ 55 3.2 Logging Input and Output........................................ 57 3.3 Paste Ignores Prompts.......................................... 58 3.4 Timing Commands............................................ 58 3.5 Other IPython