Scientific Computing for Engineers: Spring 2011 – 3 Credits
This class is part of the Interdisciplinary Graduate Minor in Computational Science. See IGMCS for details.
Wednesdays from 1:30 – 4:15, Room 233 Claxton
Office hours: Wednesday 11:00 - 1:00, or by appointment
TA: Wes Alvaro, firstname.lastname@example.org
TA’s Office : 351 Claxton
TA’s Office Hours: Wednesday’s 10:00 – 12:00 or by appointment
There will be four major aspects of the course:
· Part I will start with current trends in high-end computing systems and environments, and continue with a practical short description on parallel programming with MPI, OpenMP, and Pthreads.
· Part II will illustrate the modeling of problems from physics and engineering in terms of partial differential equations (PDEs), and their numerical discretization using finite difference, finite element, and spectral approximation.
· Part III will be on solvers: both iterative for the solution of sparse problems of part II, and direct for dense matrix problems. Algorithmic and practical implementation aspects will be covered.
· Finally in Part IV, various software tools will be surveyed and used. This will include PETSc, Sca/LAPACK, MATLAB, and some tools and techniques for scientific debugging and performance analysis.
The grade would be based on homework, a midterm project, a final project, and a final project presentation. Topics for the final project would be flexible according to the student's major area of research.
And the course mailing list: email@example.com
Book for the Class:
Edited by Jack Dongarra, Ian Foster, Geoffrey Fox, William Gropp, Ken Kennedy, Linda Torczon, Andy White, October 2002, 760 pages, ISBN 1-55860-871-0, Morgan Kaufmann Publishers.
Lecture Notes: (Tentative outline of the class)
Read Chapter 1, 2, and 9
Homework 1 (due January 26, 2011)
Homework 2 (due February 2, 2011)
Read Chapter 3
Read Chapter 20
Read Chapter 21
Homework 3 (due February 23, 2011)
Parallel programming paradigms and their performances -2
Read Chapter 11
MPI Dynamic Processes
Homework 4 (due March 2nd, 2011)
Homework 5 (due March 9th, 2011)
Read Chapter 9
HPC Performance Issues and Systems
Read Chapter 3
Homework 6 (due March 23rd, 2011)
Homework 7 (due March 30th, 2011)
March 16 – Spring Break
11. March 30 (Dr. Tomov)
Read Chapter 20 and 21
14. April 20 (Dr. Dongarra)
Read Chapter 20
Class Final reports
Order of presentation:
10:00 Tingxing Dong
10:20 Shuang Gao
10:40 Chuanjun He
11:00 Huang Huang
11:20 Yulu Jia
12:20 Bryan Hunter
12:40 Nicholas Lineback
1:00 Rui Ma
1:20 Mouge Mohagheghi
1:40 Henian Xia
Here are some ideas for projects:
Additional Reading Materials
Message Passing Systems
Several implementations of the MPI standard are available today. The most widely used open source MPI implementations are Open MPI and MPICH.
Here is the link to the MPI Forum.
Other useful reference material
· Here are pointers to specs on various processors:
· Introduction to message passing systems and parallel computing
``Message Passing Interfaces'', Special issue of Parallel Computing, vol 20(4), April 1994.
Ian Foster, Designing and Building Parallel Programs, see http://www-unix.mcs.anl.gov/dbpp/
Alice Koniges, ed., Industrial Strength Parallel Computing, ISBN1-55860-540-1, Morgan Kaufmann Publishers, San Francisco, 2000.
Ananth Gramma et al., Introduction to Parallel Computing, 2nd edition, Pearson Education Limited, 2003.
Michael Quinn, Parallel Programming: Theory and Practice, McGraw-Hill, 1993
David E. Culler & Jaswinder Pal Singh, Parallel Computer Architecture, Morgan Kaufmann, 1998, see http://www.cs.berkeley.edu/%7Eculler/book.alpha/index.html
George Almasi and Allan Gottlieb, Highly Parallel Computing, Addison Wesley, 1993
Matthew Sottile, Timothy Mattson, and Craig Rasmussen, Introduction to Concurrency in Programming Languages, Chapman & Hall, 2010
· Other relevant books
Stephen Chapman, Fortran 95/2003 for Scientists and Engineers, McGraw-Hill, 2007
Stephen Chapman, MATLAB Programming for Engineers, Thompson, 2007
Barbara Chapman, Gabriele Jost, Ruud van der Pas, and David J. Kuck, Using OpenMP: Portable Shared Memory Paralllel Programming, MIT Press, 2007
Tarek El-Ghazawi, William Carlson, Thomas Sterling, Katherine Yelick, UPC: Distributed Shared Memory Programming, John Wiley & Sons, 2005
David Bailey, Robert Lucas, Samuel Williams, eds., Performance Tuning of Scientific Applications, Chapman & Hall, 2010
Message Passing Standards
``MPI - The Complete Reference, Volume 1, The
MPI-1 Core, Second Edition'',
``MPI: The Complete
Reference - 2nd Edition: Volume 2 - The MPI-2 Extensions'',
MPI-2.1 Standard, September 2008
PDF format: http://www.mpi-forum.org/docs/mpi21-report.pdf
MPI-2.2 Standard, September 2009
On-line Documentation and Information about Machines
Other Scientific Computing Information Sites
· AIST Parallel and High Performance Application Software Exchange (in Japan)
(includes information on parallel computing conferences and journals)
Related On-line Books/Textbooks
· Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods, SIAM Publication, Philadelphia, 1994.
· LAPACK Users' Guide (Second Edition), SIAM Publications, Philadelphia, 1995.
· Using MPI: Portable Parallel Programming with the Message-Passing Interface by W. Gropp, E. Lusk, and A. Skjellum
· Parallel Computing Works, by G. Fox, R. Williams, and P. Messina (Morgan Kaufmann Publishers)
· Designing and Building Parallel Programs. A dead-tree version of this book is available by Addison-Wesley.
· Introduction to High-Performance Scientific Computing, by Victor Eijkhout with Edmond Chow, Robert Van De Geijn, February 2010
· Introduction to Parallel Computing, by Blaise Barney
Performance Analysis Tools Websites
Other Online Software and Documentation
· Matlab documentation is available from several sources, most notably by typing ``help'' into the Matlab command window. A primer (for version 4.0/4.1 of Matlab, not too different from the current version) is available in either postscript or pdf.
· SuperLU is a fast implementations of sparse Gaussian elimination for sequential and parallel computers, respectively.
· Sources of test matrices for sparse matrix algorithms
· Templates for the solution of linear systems, a collection of iterative methods, with advice on which ones to use. The web site includes on-line versions of the book (in html and postscript) as well as software.
· Templates for the Solution of Algebraic Eigenvalue Problems is a survey of algorithms and software for solving eigenvalue problems. The web site points to an html version of the book, as well as software.
· MGNet is a repository for information and software for Multigrid and Domain Decomposition methods, which are widely used methods for solving linear systems arising from PDEs.
· Resources for Parallel and High Performance Computing
· ACTS (Advanced CompuTational Software) is a set of software tools that make it easier for programmers to write high performance scientific applications for parallel computers.
· Issues related to Computer Arithmetic and Error Analysis
· Efficient software for very high precision floating point arithmetic
· The IEEE floating point standard is currently being updated. To find out what issues the standard committee is considering, look here.Jack Dongarra