Petascale Computing: Algorithms and Applications (Chapman & Hall Crc Computational Science Series)

583 Pages·2007·9.54 MB·English

by  David A. Bader

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Chapman & Hall/CRC
Computational Science Series
SERiES EDiToR
Horst Simon
Associate Laboratory Director, Computing Sciences
Lawrence Berkeley National Laboratory
Berkeley, California, U.S.A.
AiMS AND SCoPE
This series aims to capture new developments and applications in the field of computational sci-
ence through the publication of a broad range of textbooks, reference works, and handbooks.
Books in this series will provide introductory as well as advanced material on mathematical, sta-
tistical, and computational methods and techniques, and will present researchers with the latest
theories and experimentation. The scope of the series includes, but is not limited to, titles in the
areas of scientific computing, parallel and distributed computing, high performance computing,
grid computing, cluster computing, heterogeneous computing, quantum computing, and their
applications in scientific disciplines such as astrophysics, aeronautics, biology, chemistry, climate
modeling, combustion, cosmology, earthquake prediction, imaging, materials, neuroscience, oil
exploration, and weather forecasting.
PuBliSHED TiTlES
PETASCALE COMPUTING: Algorithms and Applications
Edited by David A. Bader
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P c
etascale omPuting
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lgorithms and PPlications
EditEd by
daVid a. Bader
Georgia institute of technology
Atlanta, U.S.A.
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Chapman & Hall/CRC
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Library of Congress Cataloging‑in‑Publication Data
Petascale computing : algorithms and applications / editor, David A. Bader.
p. cm. ‑‑ (Computational science series)
Includes bibliographical references and index.
ISBN 978‑1‑58488‑909‑0 (hardback : alk. paper) 1. High performance
computing. 2. Petaflops computers. 3. Parallel processing (Electronic
computers) I. Bader, David A. II. Title. III. Series.
QA76.88.P475 2007
004’.35‑‑dc22 2007044024
Visit the Taylor & Francis Web site at
http://www.taylorandfrancis.com
and the CRC Press Web site at
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C9098_FM.indd 4 11/15/07 1:38:56 PM
To Sadie Rose
v

Chapman & Hall/CRC
Computational Science Series
Computationalscience,thescientificinvestigationofphysicalprocessesthrough
modellingandsimulationoncomputers,hasbecomegenerallyacceptedasthe
third pillar of science, complementing and extending theory and experimen-
tation. This view was probably first expressed in the mid-1980s. It grew out
ofanimpressivelistofaccomplishmentsinsuchdiverseareasasastrophysics,
aeronautics,chemistry,climatemodelling,combustion,cosmology,earthquake
prediction,imaging,materials,neuroscience,oilexploration,andweatherfore-
casting. Today, in the middle of the first decade of the 21st century, the pace
of innovation in information technology is accelerating, and consequently the
opportunities for computational science and engineering abound. Computa-
tionalscienceandengineering(CSE)todayservestoadvanceallofscienceand
engineering, and many areas of research in the future will be only accessible
to those with access to advanced computational technology and platforms.
Progress in research using high performance computing platforms has been
tightly linked to progress in computer hardware on one side and progress
in software and algorithms on the other, with both sides generally acknowl-
edged to contribute equally to the advances made by researchers using these
technologies. Withthearrivalofhighlyparallelcomputeplatformsinthemid-
1990s, several subtle changes occurred that changed the face of CSE in the
last decade. Because of the complexities of large-scale hardware systems and
the increasing sophistication of modelling software, including multi-physics
and multiscale simulation, CSE increasingly became a team science. The
most successful practitioners of CSE today are multidisciplinary teams that
include mathematicians and computer scientists. These teams have set up
a software infrastructure, including a support infrastructure, for large codes
thatarewellmaintainedandextensiblebeyondthesetoforiginaldevelopers.
The importance of CSE for the future of research accomplishments and
economic growth has been well established. “Computational science is now
indispensabletothesolutionofcomplexproblemsineverysector, fromtradi-
tional science and engineering domains to such key areas as national security,
public health, and economic innovation,” is the principal finding of the re-
cent report of the President’s Information Technology Advisory Committee
(PITAC) in the U.S. (President’s Information Technology Advisory Commit-
tee,ComputationalScience: EnsuringAmerica’sCompetitiveness ,Arlington,
Virginia: National Coordination Office for Information Technology Research
and Development, 2005, p. 2.)
vii
viii
As advances in computational science and engineering continue to grow at
a rapid pace, it becomes increasingly important to present the latest research
and applications to professionals working in the field. Therefore I welcomed
the invitation by Chapman & Hall/CRC Press to become series editor and
start this new series of books on computational science and engineering. The
series aims to capture new developments and applications in the field of com-
putationalscience,throughthepublicationofabroadrangeoftextbooks,ref-
erence works, and handbooks. By integrating mathematical, statistical, and
computational methods and techniques, the titles included in the series are
meanttoappealtostudents,researchers,andprofessionals,aswellasinterdis-
ciplinaryresearchersandpractitionerswhoareusersofcomputingtechnology
and practitioners of computational science. The inclusion of concrete exam-
ples and applications is highly encouraged. The scope of the series includes,
but is not limited to, titles in the areas of scientific computing, parallel and
distributed computing, high performance computing, grid computing, cluster
computing, heterogeneous computing, quantum computing, and their appli-
cation inscientific areas suchas astrophysics, aeronautics, biology, chemistry,
climate modelling, combustion, cosmology, earthquake prediction, imaging,
materials, neuroscience, oil exploration, and weather forecasting, and others.
With this goal in mind I am very pleased to introduce the first book in
the series, Petascale Computing: Algorithms and Applications, edited by my
goodcolleagueandfriendDavidBader. Thisbookgrewoutofaworkshopat
Schloss Dagstuhl in February 2006, and is a perfect start for the series. It is
probably the first book on real petascale computing. At the beginning of an
exciting new phase in high performance computing, just as we are about to
enter the age of petascale performance, the chapters in the book will form an
ideal starting point for further investigations. They summarize the state of
knowledge in algorithms and applications in 2007, just before the first peta-
scale systems will become available. In the same way as petascale computing
will open up new and unprecedented opportunities for research in computa-
tional science, I expect this current book to lead the new series to a deeper
understanding and appreciation of research in computational science and en-
gineering.
Berkeley, May 2007
Dr. Horst Simon
Series Editor
Associate Laboratory Director,
Computing Sciences
Lawrence Berkeley National Laboratory
Foreword
Over the last few decades, there have been innumerable science, engineering
and societal breakthroughs enabled by the development of high performance
computing(HPC)applications,algorithms,andarchitectures. Thesepowerful
tools have provided researchers, educators, and practitioners the ability to
computationally translate and harness data gathered from around the globe
into solutions for some of society’s most challenging questions and problems.
An important force which has continued to drive HPC has been a commu-
nityarticulationof“frontiermilestones,”i.e.,technicalgoalswhichsymbolize
the next level of progress within the field. In the 1990s, the HPC community
sought to achieve computing at the teraflop (1012 floating point operations
per second) level. Teraflop computing resulted in important new discoveries
such as the design of new drugs to combat HIV and other diseases; simula-
tions at unprecedented accuracy of natural phenomena such as earthquakes
andhurricanes; andgreaterunderstandingofsystemsaslargeastheuniverse
and smaller than the cell. Currently, we are about to compute on the first
architecturesatthepetaflop(1015 floatingpointoperationspersecond)level.
Some communities are already in the early stages of thinking about what
computingattheexaflop(1018 floatingpointoperationspersecond)levelwill
be like.
Indrivingtowardsthe“<nextfrontier>-flop,”theassumptionisthatachiev-
ingthenextfrontierinHPCarchitectureswillprovideimmensenewcapacity
and capability, will directly benefit the most resource-hungry users, and will
provide longer-term benefits to many others. However, large-scale HPC users
know that the ability to use frontier-level systems effectively is at least as
important as their increased capacity and capability, and that considerable
timeandhuman,software,andhardwareinfrastructurearegenerallyrequired
to get the most out of these extraordinary systems.
Experience indicates that the development of scalable algorithms, models,
simulations, analyses, libraries, and application components which can take
full advantage of frontier system capacities and capabilities can be as chal-
lenging as building and deploying the frontier system itself.
For application codes to sustain a petaflop in the next few years, hundreds
of thousands of processor cores or more will be needed, regardless of proces-
sor technology. Currently, few real existing HPC codes easily scale to this
regime, and major code development efforts are critical to achieve the poten-
tial of the new petaflop systems. Scaling to a petaflop will involve improving
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