
CS 59431778 Understanding Parallel Computing:
Spring 2005 – 3 Credits Wednesdays from 1:30 – 4:15 Room C211 Prof. Jack Dongarra with help
from Drs. George Bosilca, Graham Fagg, Victor Eijkhout, Julien Langou, Shirley
Moore, Dan Terpstra, and Felix Wolf Email: dongarra@cs.utk.edu Phone: 8659748295 Fax:
8659748296 Office
hours: Wednesday 11:00  1:00, or by appointment TA: Fengguang Song, song@cs.utk.edu
O :
307 Claxton Complex, 9740517 OH:
10am11am TR, or by request Class
Roster If your name is not on the list or some
information is incorrect, please send mail to TA:
Huadong Liu hliu@cs.utk.edu Andy
Perkins aperkins@cs.utk.edu Jon Scharff scharff@cs.utk.edu Sergei Shinkarev shinkare@cs.utk.edu
Fengguang Song (TA) song@cs.utk.edu Jiayi Wu wu@cs.utk.edu Yun Zhang yzhang@cs.utk.edu And the course
mailing list: cs594pa@klutz.cs.utk.edu
Book for the Class: The Sourcebook of Parallel Computing, Edited by Jack
Dongarra, Ian Foster, Geoffrey Fox, William Gropp, Ken Kennedy, Linda
Torczon, Andy White, October 2002, 760 pages, ISBN 1558608710, Morgan
Kaufmann Publishers. Lecture
Notes: (Tentative outline of the class) 1. January
12 Introduction
to High Performance Computing Chapter 1 Homework
1 (due January 26, 2005) 2. January
19 Homework
2 (due February 2, 2005) Chapter 10 Chapter 11 3. January
26 (We are meeting at the regular time and place (no seminar): Parallel
Programming Considerations Homework
3 (due February 9, 2005) Chapter 3 Chapter 14 4. February
2 The first hour of class will
be for the seminar by: Dr. Julien Langou, 1:30 p.m.
 2:30 p.m. Claxton Complex, Room 205 “Recent Improvements on the
Kernel Operations Used in Iterative Methods” Memory
Hierarchy and Cache continued Homework
4 (due February 16, 2005) 5. February
9 Message
Passing (updated 2/10/05) Homework
05 (due February 23, 2005) Chapter 10 6. February
16 Message
Passing continued (updated 2/23) For Homework see last slide
from lecture How
to do homework (due March 2, 2005) Chapter 11 7. February
23 Remainder
of slides from Week 5 Chapter 20 8. March
2 Dense Linear Algebra
continued part
1, part
2 Chapter 20 9. March
9 Iterative
Linear Algebra Methods Chapter 20 10. March
16 Iterative
Linear Algebra Methods continued Chapter 21 March 23 –
Spring Break 11. March
30 Homework
08 (due April 13, 2005) Chapter 14 pp 409  442 12. April
6 Grid
Computing continued; Felix Wolf 13. April
13 Tools for Debugging and Performance Analysis; part1,
part2,
part3 Homework
09 (due April 20, 2005) Felix Wolf and Dan Terpstra Chapter 15 14. April
20 Tools for Debugging and Performance Analysis;
part1, part2 continued 15. April
25– Last Class (Note this is Monday) Class reports We will start at 1:00 and
plan to finish by 5:00 · Projects (due April 2005) Additional
Message Passing
Systems.
The PVM home page. Other useful reference material
· Here’s a pointer to specs on various processors: http://www.geek.com/procspec/procspec.htm A
good introduction to message passing systems.
``Message Passing Interfaces'', Special issue of Parallel Computing , vol 20(4), April 1994. A paper by members of the PVM team on the differences between PVM
and MPI. Geist, G.A, J.A. Kohl, P.M. Papadopoulos, `` PVM and MPI: A
Comparison of Features '', Calculateurs Paralleles , 8(2), pp. 137150, June, 1996.
Papers by members of the MPI team on the differences between PVM
and MPI. ``Why are PVM and MPI So Different'', William Gropp and Ewing Lusk
(submitted to The Fourth European PVM  MPI Users' Group Meeting) and ``PVM and MPI are completely different'', William Gropp and Ewing
Lusk, to appear in the journal Future Generation Computer Systems, 1998. Ian Foster, Designing and Building Parallel Programs, see http://wwwunix.mcs.anl.gov/dbpp/
Alice Koniges,
ed.,
Industrial Strength Parallel Computing, ISBN1558605401,
Morgan Kaufmann Publishers, Michael Quinn, Parallel Programming, see http://web.engr.oregonstate.edu/~quinn/Comparison.htm David E. Culler & Jaswinder
Pal Singh, Parallel Computer Architecture, see http://www.cs.berkeley.edu/%7Eculler/book.alpha/index.html George Almasi and Allan Gottlieb,
Highly Parallel Computing Standard
Books on Message Passing
``MPI  The Complete Reference, Volume 1, The MPI1
Core, Second Edition'', ``Using
MPI,'' ``MPI:
The Complete Reference  2nd Edition: Volume 2  The MPI2 Extensions'', Online
Documentation and Information about Machines ·
Overview of Recent
Supercomputers, Aad J. van der
Steen and Jack J. Dongarra, 2004.
·
Catalog of Commercial
Hardware and Software Vendors Other Parallel Information Sites · NHSE  National
HPCC Software Exchange · Netlib Repository at UTK/ORNL · LAPACK · GAMS  Guide
to Available Math Software · Center for Research
on Parallel Computation (CRPC) · Supercomputing & Parallel
Computing: Conferences · Supercomputing & Parallel
Computing: Journals · High
Performance Fortran (HPF) reports · High
Performance Fortran Resource List · Major Science Research Institutions from
Caltech · Message
Passing Interface (MPI) Forum · High Performance
Fortran Forum · OpenMP · PVM
· DoD High Performance Computing Modernization Program · DoE Accelerated Strategic Computing Initiative (ASCI)
· National Computational Science
Alliance Related Online Textbooks · Templates for the Solution of Linear Systems:
Building Blocks for Iterative Methods, · PVM
 A Users' Guide and Tutorial for Networked Parallel Computing, MIT Press, · MPI
: A MessagePassing Interface Standard · LAPACK
Users' Guide (Second Edition), · MPI:
The Complete Reference, MIT Press, · Using
MPI: Portable Parallel Programming with the MessagePassing Interface by
W. Gropp, E. Lusk, and A. Skjellum · Parallel Computing
Works, by G. Fox, R. Williams, and P. Messina (Morgan Kaufmann
Publishers) · Computational
Science Education Project · Designing and Building Parallel Programs.
A deadtree version of this book is available by AddisonWesley. · High
Performance Fortran (HPF), a course offered by For
performance analysis: · Raj Jain, The Art of Computer
Systems Performance Analysis. John Wiley, 1991. Papers
on performance analysis tools: · Ruth A. Aydt,
"The Pablo SelfDefining Data Format," November 1997, click here. · Jeffrey K. Hollingsworth, Barton P. Miller,
Marcelo J. R. Gongalves, Oscar Naim,
Zhichen Xu and Ling Zheng,
"MDL: A Language and Compiler for Dynamic Program Instrumentation",
International Conference on Parallel Architectures and Compilation
Techniques, San Francisco, CA, November 1997, click here.
· Barton P. Miller, Mark D. Callaghan,
Jonathan M. Cargille, Jeffrey K. Hollingsworth, R.
Bruce Irvin, Karen L. Karavanic, Krishna Kunchithapadam and Tia Newhall.
"The Paradyn Parallel Performance Measurement
Tools", IEEE Computer 28(11), (November 1995). click here. · Steven T. Hackstadt
and Allen D. Malony, "Distributed Array Query and Visualization for High
Performance Fortran, February 1996. · Jerry Yan and Sekhar Sarukkai and Pankaj Mehra, "Performance
Measurement, Visualization and Modeling of Parallel and Distributed Programs
using the AIMS toolkit", Software Practice and Experience 25(4), April
1995, 429461 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. · Netlib, a repository of numerical software and related documentation · Netlib Search Facility, a way to search for the software on Netlib that you need · GAMS  Guide to Available Math Software, another search facility to find numerical software · Linear Algebra Software Libraries and Collections · LAPACK, stateoftheart software for dense numerical linear algebra on workstations and sharedmemory parallel computers. Written in Fortran. · CLAPACK, a C version of
LAPACK. · ScaLAPACK, a partial version of LAPACK for distributedmemory parallel computers. · LINPACK and EISPACK are precursors of LAPACK, dealing with linear systems and eigenvalue problems, respectively. · SuperLU is a fast implementations of sparse Gaussian elimination for sequential and parallel computers, respectively. · Sources of test matrices for sparse matrix algorithms · University of Florida Sparse Matrix Collection · Templates for the solution of linear systems, a collection of iterative methods, with advice on which ones to use. The web site includes online 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. · Updated survey of sparse direct linear equation solvers, by Xiaoye Li · 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 · Millennium a UC Berkeley campuswide parallel computing resource · Resources for CS 267, Applications of Parallel Computers · 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. · PETSc: Portable, Extensible, Toolkit for Scientific Computation · Issues related to Computer Arithmetic and Error Analysis · Efficient software for very high precision floating point arithmetic · Notes on IEEE Floating Point Arithmetic, by Prof. W. Kahan · Other notes on arithmetic, error analysis, etc. by Prof. W. Kahan · Report on arithmetic error that cause the Ariane 5 Rocket Crash Jack Dongarra4/24/2005 