Software Tools, Algorithms and Applications

Table of Contents

Algorithms

1. Course Materials

   • Lecture slides: Statistics and Random Numbers, in preparation for Monte Carlo Integrals.
   • Background materials on Random Number Generators (RNG), from the CSEP book.
   • Lecture slides: ODE's and Computing Techniques for Particle Systems, and the same material appeared in written text.
   • Background materials on Ordinary Differential Equations, from the CSEP book.
   • Numerical Integration Module including details on Monte Carlo Methods.
   • Lecture slides:Adaptive Parallel Computing Techniques for Numerical Integration apply parallel computing to numerical integration.
   • Lecture slides: Iterative Methods for Partial Differential Equations.
   • Lecture slides:Motivation for Partial Differential Equations where this has extensive discussion of CFD and the Navier Stokes equation which was prepared for CPS713 and can be ignored here. The initial remarks on relative role of PDE's, Monte Carlo, and particle dynamics has value.
   • Further references are: Basic Discussion of PDE's in CSEP Project.
   • More examples in Material Balance Section.
   • A very good discussion of iterative methods is in Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods, by Dongarra et al.
   • A good introduction to numerical linear algebra comes from the HPSC group at the University of Colorado covering basic matrix analysis, elementary ODE's and Fourier Analysis.
   • The full HPSC material is available in postscript by ftp. You may need to fetch the numerical analysis module for use in the course.
   • Lecture slides: Linear Algebra Presentation that continues from the HPSC resource with eigenvalues and eigenvectors.
   • Lecture slides:Finite Element and Conjugate Gradient Presentation with analogies to minimization methods.
   • Lecture slides:Parallel Full Matrix Algorithms.
   • More parallel computing materials, algorithms, tutorials are available at Computational Science page.

2. General Resources

   • Parallel Computing Works! is an online book by G. C Fox, R. D. Williams, and P. C. Messina. A highly recommended book to read.
   • Designing and Building Parallel Programs by Ian Foster is an online book, a collection of public domain parallel software tools, a collection of Web Tours providing access to other information on Parallel Computing, and various educational resources.
   • Supercomputing and Parallel Computing Resources is a collection of pointers to various pages containing software resources.
   • Computational Science Resources is a collection of online resources in computational methods, application areas, roadmaps, courses, hardware, and software.
   • Parallel Computing is a one day course given by Minty, Davey, and Simpson of EPCC. There are also other related tools.
   • On mesh and grid generation take a look at Finite Element Mesh Generation.
   • For a good survey on N-Body Methods Resources, see this page at EPCC.
   • Global Educational Resources for HPC is quite a comprehensive collection of resources in parallel computing education, courses and tutorials, books online, bibliographies, software online, and parallel research groups.
   • Programming Tools--Languages and Libraries is a set of parallel software tools and libraries. Tools such as Scalable Unstructured Mesh Computation and libraries such as Chameleon, etc.
   • NAS Parallel Tools Group Hotlist of useful tools in design/analysis , programming models and paradigms, process control, debugging and performance analysis/visualization, etc.

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Programming Languages and Tools

1. Course Materials

   • World Wide Web

     • This is a link form CPS615 fall-95 on getting started on the World Wide Web.
     • From CPS615 fall-95, a link to a tutorial page entitled Tutorial on Creating Hypertext Documents. It also contains links to the abovementioned NCSA documents.

   • Fortran90 and HPF

     • Educational Materials for High Performance Fortran (HPF) and F90 is a collection of materials on learning HPF, programming background, applications, etc. using HPF.
     • Lecture slides:An Introduction to High Performance Fortran .

   • Message Passing Interface(MPI)

     • Lecture slides from fall 1995.
     • MPI resources page containing a set of educational materials as well as general resources.

2. General Resources

   • World Wide Web

     • The World Wide Web consortium (W3C) homepage.
     • The W3 consortium provides general information and history about the World Wide Web.
     • Also W3C provides all the information needed about the HyperText Markup Language (HTML).
     • A highly recommended starting point to HTML is the primer from NCSA entitled A Beginner's Guide to HTML.
     • Also, NCSA provides a simple and easy to follow primer on URLs entitled A Beginner's Guide to URLs.
     • NCSA HTTPd overview contains instructions on how to setup the server, tutorials and HTTPd Library.
     • The Common Gateway Interface, or CGI, is a standard for external gateway programs to interface with information servers such as HTTP servers.
     • Here is that good old fashion NCSA Mosaic homepage.

   • Fortran90 and HPF

     • EPCC: HPF Course Notes. This is a set of student notes for a course on HPF by Ewing, Richardson, and Simpson at the Edinburgh Parallel Computing Center. It contains 11 sections and one section of exercises.
     • HPF/F90 course slides. This set of slides were put together for a course entitled Writing Data Parallel Programs with High Performance Fortran at EPCC.
     • The Fortran Library (aka FLIB) is repository of fortran code mainly in Fortran90 and 77 to run various scientific and engineering tasks.
     • Tutorial for Compiling and Running XL Fortran Programs (for the SP2). This tutorial is for the IBM XL Fortran (or xlf) on the Cornell Theory Center's SP.
     • Fortran 90 FAQ, texts, programs, etc. is a large list of compilers, tests and benchmarks, libraries and utilities, examples and repositories of resources in Fortran.

   • Message Passing Interface(MPI)

     • MPI Quick Tutorials from Ohio Supercomputer Center. This is a set of easy and quick tutorials on MPI mainly for beginners.
     • more MPI resources from HPCC at Southampton containing pointers to other resources and archives with yet more resources on the subject.
     • MPI: The Complete Reference by Dongarra et al. is a complete MPI book online covering all aspects of MPI.
     • A list of MPI implementations for various systems from Ohio Supercomputer Center. This is quite a valuable list of both commercial as well as publicly available MPI implementations. Each entry gives the name of the package, author or owner, current version, MPI functions implemented, availability of the code, and supported systems.
     • MPI Tutorials is a list of tutorials as well as other documents on learning MPI such as FAQs, lessons learned, MPI-inspired definitions, and quick overviews from Argonne National Laboratory.
     • Directory of MPI resources at the Engineering Research Center of Mississippi State.
     • A list of Tutorials and Lab Exercises are available at the MPI's page of Cornell Theory Center.
     • Applications and Examples Using MPI maintained by David Walker at ORNL. It contains example programs for the nbody problem as well as examples for the 2D Laplace equation, etc.

   • Java

     • A set of parallel algorithms and animation are available at Parallel Algorithm Animation.
     • An archive of geometric algorithms in Java is available at JAVA Gallery of Geometric Algorithms.
     • The most widely studied and analyzed algorithms in the field of Computer Science are the sorting algorithms. Here are few of them implemented in Java.
     • Jon Hardwick of CMU has an excellent page for Java Optimization Resources. It lists resources for optimization as well as benchmarking and pointers to yet more resources.
     • MPI Java Wrapper is a set of Java Wrappers to MPI implemented using Java 1.0 native class interface.
     • Using Java and JavaScript in the Virtual Programming Laboratory (VPL). VPL is a Web-based virtual programming environment built based on a client-server architecture. The system can be accessed on any platform (Unix, PC, or Mac) using a standard Java-enabled browser.

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Areas of Applications

1. Course Materials

   • None is available.

2. General Resources

   • Computational Fluid Dynamics for Astrophysics is a lecture was given by Univ. of Tennessee and Oak Ridge as part of the Computational Science Education Project.
   • Earth Sciences Resources is essentially a collection of resources, etc. dealing with studies in Earch Science.
   • Atmospheric Sciences Resources. Web resources maintained by the US Geological Survey.
   • Biology Resources is a collection of pointers to resources in biology. Maintained by the US Geological Survey.
   • Molecular Modeling maintained by the Center for Molecular Modeling of the National Institute of Health. It points to software and hardware resources in the field of Molecular Modeling.
   • Computational Molecular Biology is a collection of resources and documents in Sequence Analysis, Molecular Biology Software, and other related resources. This page is maintained by the molecular biology section of NIH.
   • Physics Resources is a link to Mike Guidry's collection of physics resources. This is part of the Computational Science Education Projects.
   • Guide to Available Mathematical Software. NIST provides a comprehensive guide to wide range of available mathematical software listed by package name and module name with short abstracts of the module.
   • UCB/NASA Earth Observing System, Distributed Information System as part of NASA's EOS."End-to-End Problems in EOSDIS" is a NASA-sponsored multi-year project investigating alternative data management strategies for NASA's Earth Observing System (EOS).
   • Atmospheric Chemistry Model is a NASA-sponsored model to develop a state-of-the-art Earth System Model (ESM) that will be comprised of a coupled atmosphere and ocean system including chemical tracers that are found in, and may be exchanged between, the atmosphere and the oceans.
   • Real-World Solutions With Cray Research Systems is a sampling of case histories revealing the real-world impact of Cray systems in solving some challenging problems!
   • Here is a very interesting page containing a set of Parallel Algorithm Animation for various parallel algorithms.

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Computational Methods

1. Course Materials

   • None is available.

2. General Resources

   • Monte Carlo Methods (by Guidry et al.) for integration are rooted in the concept that a part of the function to be integrated over may be thought of as a normalized probability distribution over the region of integration.
   • Lectures in Various Computational Science Methods for the physical and life sciences presented at ORNL by Guidry and Strayer.
   • Presentations in Hypertext Format by Guidry et al. at ORNL as part of the CSEP.

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General References and Roadmaps

1. Course Materials

   • None is available.

2. General Resources

   • The NHSE HPCC Roadmap is a guide to High Performance Computing and Communications (HPCC) applications, algorithms, software and enabling technologies. It is developed as part of the National HPCC Software Exchange.
   • Sequence analysis tools for Protein identification, DNA -> Protein, similarity searches, pattern and profile searches , primary structure analysis, secondary structure prediction, transmembrane regions detection, etc.
   • Applications of Computational Geometry is a collection of various areas in which ideas from discrete and computational geometry (meaning mainly low-dimensional Euclidean geometry) meet some real world applications.
   • The topic of computational gene recognition has become more and more important as long DNA being sequenced in the Human Genome Project. Here is a bibliography in Computational Gene Recognition.
   • Supercomputing and Parallel Computing Resources of conferences, research groups, vendors, and supercomputers.

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