Introduction to ITC Research Computing Support at U.Va. September, 2002 Presented by the ITC Researc - PowerPoint PPT Presentation

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Introduction to ITC Research Computing Support at U.Va. September, 2002 Presented by the ITC Researc

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Title: Introduction to ITC Research Computing Support at U.Va. September, 2002 Presented by the ITC Researc


1
Introduction to ITC Research
Computing Support at U.Va. September,
2002Presented by theITC Research Computing
Support Group David Drake,
Kathy Gerber, Ed Hall, Tim F. Jost Tolson
  • Overview of Research Hardware, Software, Support
    Storage Tuesday, September 10
  • Statistical Software Thursday, September 12
  • Mathematical Visualization Software Tuesday,
    September 17, 330 PM
  • High Performance Computing Thursday, September
    19, 330 PM
  • FEMLAB Seminar Multiphysics Modeling Friday,
    Sept. 27 at 1000 AM
  • Introduction to IDL Wednesday, October 9 at
    Noon
  • Databases and the Web Wednesday, October 23 at
    Noon
  • Maple 8 Wednesday, November 20 at Noon

2
Mathematical and VisualizationSoftware
  • By Ed Hall
  • ITC Research Computing Support Group
  • res-consult_at_virginia.edu

3
Topics
  • Problem solving environments
  • Scientific computing libraries
  • Data visualization tools
  • Scientific word processing
  • www.itc.virginia.edu/researchers/services.html

4
General Advice
  • Branches of science theory, experiment,
    computation.
  • The purpose of computing is insight, not
    pictures/numbers.
  • Use software to vary parameters, modify problem,
    play around.
  • Take advantage of software tools.

5
More General Advice
  • If the answer is highly sensitive to
    perturbations, youve probably asked the wrong
    question. (unless you are modeling a chaotic
    process)
  • Scientific calculation must be stable before
    being accurate.
  • Large scale computations will inevitably be
    carried out in parallel.

6
Problem Solving Environments
  • Matlab
  • Mathematica
  • Maple
  • IDL
  • LabVIEW
  • Related Problem Solving Environments
  • Comparison for Data Analysis
  • www.scientificweb.de/ncrunch/

7
MATLAB
  • MATrix LABoratory, Cleve Moler founder.
  • Integrates mathematical computing, visualization,
    and extensible programming language
  • Command line as well as Graphic interface
  • Interactive and batch processing
  • Widely used in science and engineering
  • www.itc.virginia.edu/research/matlab/

8
Matlab Key Features
  • Numeric computing for quick and accurate results.
  • Graphics to visualize and analyze data.
  • Discipline specific toolboxes.
  • www.mathworks.com/products/products_by_category.sh
    tml
  • Tools for building custom GUIs.
  • Interfaces to External Languages C/C, Fortran,
    Java, LabVIEW.

9
Matlab Key Features (cont.)
  • Support for wide range of Input/Output.
  • Conversion of Matlab applications to C/C with
    the Matlab Compiler for speed and dissemination.
  • Matlab programs platform independent.
  • Relatively easy to learn programming language

10
Matlab Applications
  • Data analysis and exploration.
  • Visualization and image processing.
  • Algorithm prototyping and development.
  • Modeling and simulation.
  • Programming and application development.
  • Application areas for other PSEs as well.

11
Matlab Functionality
  • Linear algebra and matrix computations.
  • Fourier and statistical analysis functions.
  • Differential equation solvers.
  • Sparse matrix support.
  • Trigonometric and other fundamental math
    operations.
  • Multidimensional data support.
  • www.mathworks.com/products/matlab/functions/functi
    ons.shtml

12
Simulink
  • Interactive Tool for modeling, simulating, and
    analyzing dynamic systems.
  • Visual programming using graphical block
    diagrams.
  • Simulation applications include DSP, control
    system, and communication systems design.
  • www.mathworks.com/products/simulink/

13
Matlab Examples
  • Startup Matlab and from the command line type
  • gtgtdemos

14
Maple
  • Numeric and symbolic computation.
  • Arbitrary precision numeric calculations.
  • Math functionality, graphics capabilities, and
    extensible programming language.
  • Math typeset document and command line
    interfaces.
  • Integration with NAG Numeric Libraries.
  • www.itc.virginia.edu/research/maple/

15
Maple Key Features
  • Maple Application Center
  • Maple PowerTools
  • Maple Student Center
  • Web connectivity TC/IP sockets, XML and MathML
    2.0.
  • Application connectivity Java, C, Fortran,
    Matlab, or MS Excel
  • Code Generation for Java, C, or Fortran

16
Maple Functionality
  • Over 3,000 computational functions.
  • Symbolic and numeric coverage of many areas of
    mathematics.
  • Algebra, Calculus, Differential Equations, Linear
    Algebra, Vector Calculus, Visualization, etc.
  • www.maplesoft.com/products/Maple8/functionality.sh
    tml

17
Maple Examples
  • Startup Maple graphic interface with xmaple and
    select New Users Tour from the Help menu.

18
Mathematica
  • Numeric and symbolic computation.
  • Arbitrary precision numeric calculations.
  • Math functionality, graphics capabilities, and
    extensible programming language.
  • Math typeset document and command line interface.
  • www.itc.virginia.edu/research/mathematica/

19
Mathematica Key Features
  • Sophisticated Technical Environment.
  • Notebook document for electronic and print
    distri-bution HTML, LaTeX, RTF, MathML, XML.
  • Fast numeric calculation.
  • Smart Numerics adaptively chooses best
    algorithm.
  • Fully integrated hypertext Help Browser.
  • MathLink protocol allows connection C/C,
    Fortran, Java, and LabVIEW J/Link for Java.

20
Mathematica Key Features (cont.)
  • Advanced Programming Methods.
  • Tour of Features
  • Educational Resources
  • http//mathworld.wolfram.com
  • http//integrals.wolfram.com
  • http//functions.wolfram.com

21
Mathematica Functionality
  • Standard Add-On Packages
  • Algebra,Calculus, Discrete Mathematics,
    Geometry, Graphics, Linear Algebra, Number
    Theory, and Statistics.
  • http//documents.wolfram.com/v4/index20.html
  • Application Packages
  • www.wolfram.com/products/applications/

22
Mathematica Examples
  • Startup Mathematica graphic interface and select
    Help Browser from Help Menu. Then select
    Getting Started Demos from Help Browser and
    then Tour of Mathematica

23
Mathematica Inventor
  • Stephen Wolfram, physicist
  • www.stephenwolfram.com/about-sw/interviews/
  • His Book New Kind of Science
  • www.wolframscience.com/

24
IDL
  • Interactive Data Language.
  • Data analysis and visualization software.
  • Numeric array-oriented like Matlab
  • Command line and graphic interface
  • Extensible programming language.
  • Widely used in astronomical, biomedical, and
    remote sensing imaging.
  • www.itc.virginia.edu/research/idl/

25
IDL Key Features
  • Supports many data formats
  • Math/Statistics functionality from Numerical
    Recipes
  • Multithreaded computations
  • Signal/Image Processing
  • GUI ToolKit and GUIBuilder
  • Data visualization
  • http//www.rsinc.com/idl/tour/index.asp

26
IDL Functionality
  • Functional Summary.
  • www.rsinc.com/idl/idl55funcsum.pdf
  • Wavelet Toolkit
  • www.rsinc.com/idl/Wavelet.cfm
  • Extensible with Fortran or C code

27
IDL Examples
  • Startup IDL graphic interface with idlde and type
    in demo on the command line at bottom of window.

28
LabVIEW
  • Provide virtual instrument interface for data
    acquisition, control, and analysis.
  • Dataflow Graphical programming environment.
  • Create standalone applications.
  • www.itc.virginia.edu/research/labview/
  • Hands-on Seminar Sept. 20

29
LabVIEW (cont.)
  • Many supplemental modules available with our site
    license (see previous webpage)
  • Tutorial CDs available for checkout

30
Related PSE Software
  • ANSYS Finite Element Analysis
  • www.itc.virginia.edu/research/ansys/
  • Abaqus Finite Element Analysis
  • www.itc.virginia.edu/research/abaqus/
  • Amber Assisted Model Building with Energy
    Refinement
  • www.itc.virginia.edu/research/amber/

31
Scientific Computing Libraries
  • IMSL (International Mathematical and Statistical
    Libraries)
  • Matlab C/C Libraries
  • PETSc (Portable, Extensible Toolkit for
    Scientific Computation)
  • TAO (Toolkit for Advanced Optimization)

32
IMSL
  • Fortran77/Fortran90 subroutines.
  • MPI-enhanced functionality for parallel
    computing.
  • www.vni.com/products/imsl/f90_mpi.html
  • Numerical Functionality.
  • www.vni.com/products/imsl/fortfunc.html
  • www.itc.virginia.edu/research/imsl/

33
Matlab C/C Math Libraries
  • Overview
  • www.mathworks.com/products/compiler/description/ma
    th.shtml

34
PETSc
  • Suite of data structures and routines for the
    scalable (parallel) solution of scientific
    applications modeled by partial differential
    equations
  • www.itc.virginia.edu/research/petsc/

35
TAO
  • Libraries aimed at the solution of large-scale
    optimization problems on high-performance
    architectures. Goals are portability,
    performance, scalable parallelism, and an
    interface independent of the architecture.
  • www.itc.virginia.edu/research/tao/

36
Related Scientific Libraries
  • GAMS (Guide to Available Mathematical Software)
  • http//gams.nist.gov/
  • Netlib (Network Library of Mathematical Software)
  • www.netlib.org/

37
Visualization Software
  • NCAR (National Center for Atmospheric Research)
  • IRIS Explorer
  • OpenDX
  • XGobi and XGvis
  • Grace

38
NCAR Graphic Libraries
  • Fortran/C graphic utilities.
  • http//ngwww.ucar.edu/ng4.2/whatisncarg.html
  • Examples.
  • http//ngwww.ucar.edu/ng4.2/examples.html
  • www.itc.virginia.edu/research/ncar/

39
IRIS Explorer
  • Visual programming environment for 3-D
    visualization.
  • Built using OpenGL.
  • Case Studies
  • www.nag.co.uk/visual/IE/iecbb/Posters/Index.html
  • www.itc.virginia.edu/research/iris/

40
OpenDX
  • Open source version of IBM Visualization Data
    Explorer
  • General visualization environment
  • www.opendx.org
  • Available in Fall 2002

41
XGobi and XGvis
  • XGobi for multivariate data visualization.
  • XGvis for multidimensional scaling.
  • www.research.att.com/areas/stat/xgobi/

42
Grace
  • Wysiwyg for two-dimensional plots of numerical
    data.
  • www.itc.virginia.edu/research/xmgrace/

43
Scientific Word Processing
  • LaTeX Standard for scientific word processing
    using typeset math notation.
  • Primarily supported on Unix platforms.
  • Emacs, Vim, and Nedit are LaTeX friendly editors.
  • Lyx provides WYSIWYG interface.
  • Conversion to HTML and PDF formats.
  • www.itc.virginia.edu/research/latex/
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