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
2Mathematical and VisualizationSoftware
- By Ed Hall
- ITC Research Computing Support Group
- res-consult_at_virginia.edu
3Topics
- Problem solving environments
- Scientific computing libraries
- Data visualization tools
- Scientific word processing
- www.itc.virginia.edu/researchers/services.html
4General 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.
5More 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.
6Problem Solving Environments
- Matlab
- Mathematica
- Maple
- IDL
- LabVIEW
- Related Problem Solving Environments
- Comparison for Data Analysis
- www.scientificweb.de/ncrunch/
7MATLAB
- 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/
8Matlab 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.
9Matlab 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
10Matlab 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.
11Matlab 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
12Simulink
- 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/
13Matlab Examples
- Startup Matlab and from the command line type
- gtgtdemos
14Maple
- 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/
15Maple 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
16Maple 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
17Maple Examples
- Startup Maple graphic interface with xmaple and
select New Users Tour from the Help menu.
18Mathematica
- 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/
19Mathematica 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.
20Mathematica Key Features (cont.)
- Advanced Programming Methods.
- Tour of Features
- Educational Resources
- http//mathworld.wolfram.com
- http//integrals.wolfram.com
- http//functions.wolfram.com
-
21Mathematica 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/
22Mathematica 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
23Mathematica Inventor
- Stephen Wolfram, physicist
- www.stephenwolfram.com/about-sw/interviews/
- His Book New Kind of Science
- www.wolframscience.com/
24IDL
- 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/
25IDL 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
26IDL Functionality
- Functional Summary.
- www.rsinc.com/idl/idl55funcsum.pdf
- Wavelet Toolkit
- www.rsinc.com/idl/Wavelet.cfm
- Extensible with Fortran or C code
27IDL Examples
- Startup IDL graphic interface with idlde and type
in demo on the command line at bottom of window.
28LabVIEW
- 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
29LabVIEW (cont.)
- Many supplemental modules available with our site
license (see previous webpage) - Tutorial CDs available for checkout
30Related 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/
31Scientific Computing Libraries
- IMSL (International Mathematical and Statistical
Libraries) - Matlab C/C Libraries
- PETSc (Portable, Extensible Toolkit for
Scientific Computation) - TAO (Toolkit for Advanced Optimization)
32IMSL
- 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/
33Matlab C/C Math Libraries
- Overview
- www.mathworks.com/products/compiler/description/ma
th.shtml
34PETSc
- 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/
35TAO
- 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/
36Related Scientific Libraries
- GAMS (Guide to Available Mathematical Software)
- http//gams.nist.gov/
- Netlib (Network Library of Mathematical Software)
- www.netlib.org/
37Visualization Software
- NCAR (National Center for Atmospheric Research)
- IRIS Explorer
- OpenDX
- XGobi and XGvis
- Grace
38NCAR 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/
39IRIS 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/
40OpenDX
- Open source version of IBM Visualization Data
Explorer - General visualization environment
- www.opendx.org
- Available in Fall 2002
41XGobi and XGvis
- XGobi for multivariate data visualization.
- XGvis for multidimensional scaling.
- www.research.att.com/areas/stat/xgobi/
42Grace
- Wysiwyg for two-dimensional plots of numerical
data. - www.itc.virginia.edu/research/xmgrace/
43Scientific 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/