Parallel Scientific Computing in C++ and MPI: A Seamless Approach to Parallel Algorithms and their Implementation

Book Description

This book provides a seamless approach to numerical algorithms, modern programming techniques and parallel computing. These concepts and tools are usually taught serially across different courses and different textbooks, thus observing the connection between them. The necessity of integrating these subjects usually comes after such courses are concluded (e.g., during a first job or a thesis project), thus forcing the student to synthesize what is perceived to be three independent subfields into one in order to produce a solution. The book includes both basic and advanced topics and places equal emphasis on the discretization of partial differential equations and on solvers. Advanced topics include wavelets, high-order methods, non-symmetric systems and parallelization of sparse systems. A CD-ROM accompanies the text.

Customer Reviews:

101 things to do with your pet supercomputer.......2006-09-11

Scientific parallel computing is what this book is all about, and it does a very good job kneading MPI into the mathematical dough. The book assumes knowledge of mathematics (through Calculus, in some sections, and quite a bit of linear algebra) and little programming experience. This is not a book on C++ programming (not even close, and it does not pretend to be), nor is it a book on MPI programming, parallel computer design, or even the setting up of a suitable software development environment. In fact, it assumes all of the above, which leaves the way uncluttered for the exploration of the application of parallel algorithms upon familiar mathematical concepts.

An introductory C++ section is provided to get things rolling, though the level of C++ in the book amounts to simple classes and cin / cout in lieu of C's `printf' nonsense. This is good news, because it maintains the book's focus on the parallelization of mathematical procedures rather than on the irrelevant details of how cute it would all look wrapped up in a needlessly complex object hierarchy. Basic applied C++ and MPI, as and when needed to get the job done.

I personally use this text at home on my home-grown parallel Linux computer to investigate the partitioning of algorithms, such as going from a complex function to a Taylor series that may then be distributed to compute nodes.

Further MPI, C/C++, and extremely high-level parallel concepts are introduced through the book in a natural progression, as the problems at hand require their introduction. This keeps the book from being bogged down and off-topic. Kudos to the authors for remaining on course through a sea of such tempting distractions.
The book is the `how'. BYOW:)
ps: my CD was damaged so couldn't evaluate it.
4-stars

Should be improved........2006-02-20

The authors attempted to combine introductory material in C++, numerical methods and parallel computing. That is quite a brave endevaour. They certainly break the new ground writing an introductory material for a "simulation scientist", but I believe they have achieved mixed success.

On the one hand, the material they present on all subjects is really top quality, packed with 100% usefull information. Bibliography is also very good and usefull. But the organisation of the book is quite confusing. They introduce all the topics toogether - throughtout the book. Hence each chapter introduces some numerical algorithms, few new concepts in C++ and eventually MPI. I beleive a novice would experience serious difficulties following it. For example, authors introduce objects before introducing curly braces "{}" as scope delimiters and before semicolon ";" as statement delimiters.

Further, very soon after introducung the very basic concepts in C++, the authors move on to BLAS. BLAS is usefull, of course, but a novice in C++ may wonder why does he needs libraries written in Fortran, if C++ is a language of the choice for numerical computations. (At least it is claimed so by the authors).

Another confusing example is the one of memory memory access. In section 2.2.6 Memory Management, (pg. 41) the authors introduce basic concepts of memory management and how can loop constructs influence the efficiency of the code. Very usefull indeed, no question about it. But very soon bellow, in section 2.2.8 Exploiting the Structure of the Sparse Matrices, they come up with the claim (pg. 58): "... optimization-savy individuals, as the old saying goes, often miss the forest for the threes" :-( Hence, a novice reader might think: "Well, why do I need to worry about the memory management explained just 17 pages above?".

My most serious critic of this book by far (and I hope the authors will read this) are the contents pages. The contents list only chapters and first level sub-chapters. Secind level chapters are not present!!! That makes the book very hard to use as a reference material. That is really a pitty, since there is some good material in it which is hard to find and might stay hidden. (For example, the chapter I mentioned above: 2.2.6 Memory management is NOT in the contents, so I had to browse slowly throught the book to find it and refer it here). I suggest the authors introduce: "Contents at a glance" (the present one) and a "Detailed Contents", where one could find references to all the chapters in the book. The contents is THE reason why I gave this book 3 stars instead of 4. One it lost on the confusing organisation of the book.

I think the authors should have organised the book in four parts: 1 - Numerical algorithms, 2 - C++ and 3 - Parallel computing with MPI, 4 - Advanced topics. Part 1 could introduce numerical algorithms and have pointers to their implementations in Part 2 and corresponding parallel implementations in Part 3. Part 2 and 3 could have started with introductions, which a reader already familiar with those subjects, could skip. Part 4, could bring advanced topics, such as optimisation, BLAS, etc.

Bottom line, it is:

- brave and usefull endevaour,
- full of excellent material,
- organized confusingly,
- and has a very poor contents.

Buy it if you are simulation scientist or teacher, but prepare to struggle with its organisation and contents.

Combining mathematics with modern computing.......2005-09-30

The book contains advanced numerical mathematics algorithms and
fundamental elements of parallel computation.
It will be useful for those academic instructors who believe that students should be shown the entire solution process
from mathematical problem definition to computer implementation. It has been used as a textbook at several leading American and European universities.
The authors professors Karniadakis and Kilby are innovators who demonstrate that combining education of applied mathematics with computer science is possible and extremely useful for students and their future employers.

Great book to get acquainted with numerical analysis.......2005-06-02

This book is great in describing some of the most important concepts and algorithms needed for the beginning numerical analyst. The book claims that it can be picked up by a complete novice and teach C++, MPI, and scientfic computing. I would say that the math goes very quickly and not quite as rigorous as necessary for the typical novice. The C++ is pretty basic but still the book leaves the reader a sense of confusion. This is largely because the book treats a large amount of the library functions as black boxes. The MPI starts very basic and gradually introduces the major concepts.

My recommendation for anyone reading the book is to supplement it with a good linear algebra book (such as Demmel) and book on C++ (The C++ programming language). For further study on MPI, Using MPI would be a good supplement. That way whenever you have a concept that isn't fully described, you have a source to get it from.

The book gets a high rating for going over the right content and doing so in a applied manner that gives the reader the skills to become a numerical analyst.

Parallel Optimization: Theory, Algorithms, and Applications (Numerical Mathematics and Scientific Computation)

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For the dedicated specialist
Proximal point algorithms by Censor and Zenios

Parallel Optimization: Theory, Algorithms, and Applications (Numerical Mathematics and Scientific Computation)
Yair Censor , and Stavros A. Zenios
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Hardcover

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ASIN: 019510062X

Book Description

This book offers a unique pathway to methods of parallel optimization by introducing parallel computing ideas into both optimization theory and into some numerical algorithms for large-scale optimization problems. The three parts of the book bring together relevant theory, careful study of algorithms, and modeling of significant real world problems such as image reconstruction, radiation therapy treatment planning, financial planning, transportation and multi-commodity network flow problems, planning under uncertainty, and matrix balancing problems.

Customer Reviews:

For the dedicated specialist.......2004-07-19

This book is highly mathematical. It phrases its points as a series of theorems, with a number of case studies at the end. The theorems all stop just short legible technique. The examples, though exciting, all presuppose command of technique. I regret that I never found that missing piece within myself. That piece was the one that connects deep theorems about abstract N-dimensional pseudodistances into working fluency about CAT scans.

I did, however, get some understanding of the kinds of problems that the authors address. They are some of the analytic functions, with linear or nonlinear constraints. In particular, they are functions of high dimensions - thousands or millions of constraints - amenable to fairly fine-grained optimization. They are not discrete problems, like the Travelling Salesman. They are not problems with hugely jagged reward surfaces, like "motif finding" problems in bioinformatics. They are not genetic algorithms, Monte Carlo searches, or combinatorial problems. The authors do in fact parallelize a number of important optimization problems, including CAT scans, transportation planning, and radiation therapy, but not all optimization techniques.

Those problems span only a small part of the parallelizable world. The broad promise in the title "Parallel Optimization" was only partly kept. Some parallelization techniques were presented, as well as some interesting perspetives on numerical optimization. Optimization is a large field, however, and this is only a small map.

Still, for that range of problems, it seems to offer the right reader profound insight. I can not be sure, though, since I'm not the right reader. I give it three stars, just because I had to give something. Different people will assign this book very different value.

Proximal point algorithms by Censor and Zenios.......2003-03-05

Part I of this book starts with an aphorism,
attributed to H. von Helmholtz:
``The most practical thing in the world
is a good theory.''
The book does justice to von Helmholtz maxim.
The theory of Bregman distances is presented
in a clear, geometrical and intuitive way.
Part II of the book presents several important
and illustrative applications of Proximal Point
algorithms, to constrained optimization,
Maximum Entropy problems, financial stochastic
networks, and several other important areas.

Algorithms for Elliptic Problems, Efficient Sequential and Parallel Solvers (Mathematics and its Applications)

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Algorithms for Elliptic Problems, Efficient Sequential and Parallel Solvers (Mathematics and its Applications)
Marián Vajtersic
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 0792319184

Book Description

This volume deals with problems of modern effective algorithms for the numerical solution of the most frequently occurring elliptic partial differential equations. From the point of view of implementation, attention is paid to algorithms for both classical sequential and parallel computer systems.
The first two chapters are devoted to fast algorithms for solving the Poisson and biharmonic equation. In the third chapter, parallel algorithms for model parallel computer systems of the SIMD and MIMD types are described. The implementation aspects of parallel algorithms for solving model elliptic boundary value problems are outlined for systems with matrix, pipeline and multiprocessor parallel computer architectures. A modern and popular multigrid computational principle which offers a good opportunity for a parallel realization is described in the next chapter. More parallel variants based in this idea are presented, whereby methods and assignments strategies for hypercube systems are treated in more detail. The last chapter presents VLSI designs for solving special tridiagonal linear systems of equations arising from finite-difference approximations of elliptic problems.
For researchers interested in the development and application of fast algorithms for solving elliptic partial differential equations using advanced computer systems.

Average customer rating:

Applied Parallel Computing

Manufacturer: Springer
ProductGroup: Book
Binding: Paperback

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ASIN: 354043786X

Book Description

This book constitutes the refereed proceedings of the 6th International Conference on Applied Parallel Computing, PARA 2002, held in Espoo, Finland, in June 2002.The 50 revised full papers presented together with nine keynote lectures were carefully reviewed and selected for inclusion in the proceedings. The papers are organized in topical sections on data mining and knowledge discovery, parallel program development, practical experience in parallel computing, computer science, numerical algorithms with hierarchical memory optimization, numerical methods and algorithms, cluster computing, grid and network technologies, and physics and applications.

Applied Parallel Computing. Large Scale Scientific and Industrial Problems: 4th International Workshop, PARA'98, Umea, Sweden, June 14-17, 1998, Proceedings (Lecture Notes in Computer Science)

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Applied Parallel Computing. Large Scale Scientific and Industrial Problems: 4th International Workshop, PARA'98, Umea, Sweden, June 14-17, 1998, Proceedings (Lecture Notes in Computer Science)

Manufacturer: Springer
ProductGroup: Book
Binding: Paperback

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ASIN: 3540654143

Book Description

This book constitutes the carefully refereed proceedings of the 4th International Workshop on Applied Parallel Computing, PARA'98, held in Umea, Sweden, in June 1998.The 75 revised papers presented were carefully reviewed and selected for inclusion in the book. The papers address a variety of topics in large scale scientific and industrial-strength computing, in particular high-performance computing and networking; tools, languages, and environments for parallel processing; scientific visualization and virtual reality; and future directions in high-performance computing and communication.

Applied Parallel Computing: State of the Art in Scientific Computing. 8th International Workshop, PARA 2006, Umea, Sweden, June 18-21, 2006, Revised Selected Papers (Lecture Notes in Computer Science)

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Applied Parallel Computing: State of the Art in Scientific Computing. 8th International Workshop, PARA 2006, Umea, Sweden, June 18-21, 2006, Revised Selected Papers (Lecture Notes in Computer Science)

Manufacturer: Springer
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Binding: Paperback

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Book Description

This book constitutes the thoroughly refereed post-proceedings of the 8th International Workshop on Applied Parallel Computing, PARA 2006, held in Umeå, Sweden, in June 2006.

This volume contains 4 keynote lectures and 86 revised papers of 15 invited minisymposia arranged on the following topics: stretching time and length scales in biomolecular modelling, recent advances in dense linear algebra, cfd applications for high performance computing, hpc environments: visualization and parallelization tools, tools, frameworks and applications for high performance computing, grid data management, simulations in geophysics and space physics, tools for parallel performance analysis, grids for scientific computing, simulations of materials, novel data formats and algorithms for dense linear algebra computations, bioinformatics and computational biology, scientific visualization and hpc applications, software tools for parallel cfd applications, and multi-scale physics. The 45 revised full papers papers of the main track are organized in topical sections on partial differential equations, grid computing, parallel scientific computing algorithms, linear algebra, simulation environments, algorithms and applications for blue gene/L, scientific computing applications, scientific computing tools, parallel search algorithms, peer-to-peer computing, mobility and security, algorithms for single-chip multiprocessors.

Complexity of Sequential and Parallel Numerical Algorithms

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Complexity of Sequential and Parallel Numerical Algorithms

Manufacturer: Academic Press Inc.,U.S.
ProductGroup: Book
Binding: Hardcover

Euro-Par 2001 Parallel Processing: 7th International Euro-Par Conference Manchester, UK August 28-31, 2001 Proceedings (Lecture Notes in Computer Science)

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Euro-Par 2001 Parallel Processing: 7th International Euro-Par Conference Manchester, UK August 28-31, 2001 Proceedings (Lecture Notes in Computer Science)

Manufacturer: Springer
ProductGroup: Book
Binding: Paperback

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ASIN: 3540424954

Book Description

This book constitutes the refereed proceedings of the 7th European Conference on Parallel Computing, Euro-Par 2001, held in Manchester, UK in August 2001. The 69 revised regular papers and 39 research notes presented together with five invited contributions were carefully reviewed and selected from a total of 207 submissions. All aspects of parallel computing and its applications are addressed. There is section on tools and environments, performance evaluation, scheduling and load balancing, compilers, databases and knowledge discovery, complexity theory, high-performance computing applications, architecture, distributed systems and algorithms, programming, numerical algorithms, routing and interconnection networks, cluster computing, metacomputing and grid computing, parallel and distributed embedded systems, etc.

Euro-Par 2002. Parallel Processing: 8th International Euro-Par Conference Paderborn, Germany, August 27-30, 2002 Proceedings (Lecture Notes in Computer Science)

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Euro-Par 2002. Parallel Processing: 8th International Euro-Par Conference Paderborn, Germany, August 27-30, 2002 Proceedings (Lecture Notes in Computer Science)

Manufacturer: Springer
ProductGroup: Book
Binding: Paperback

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ASIN: 3540440496

Book Description

This book constitutes the refereed proceedings of the 8th European Conference on Parallel Computing, Euro-Par 2002, held in Paderborn, Germany in August 2002.The 67 revised full papers and 55 research note papers presented together with 6 invited papers were carefully reviewed and selected from 265 submissions. The papers presented give a unique survey of the state of the art in parallel computing research, ranging from algorithms, software, hardware and application in various fields.

Euro-Par 2005 Parallel Processing: 11th International Euro-Par Conference, Lisbon, Portugal, August 30 - September 2, 2005, Proceedings (Lecture Notes in Computer Science)

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Euro-Par 2005 Parallel Processing: 11th International Euro-Par Conference, Lisbon, Portugal, August 30 - September 2, 2005, Proceedings (Lecture Notes in Computer Science)

Manufacturer: Springer
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Binding: Paperback

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ASIN: 3540287000

Book Description

This book constitutes the refereed proceedings of the 11th International Conference on Parallel Computing, Euro-Par 2005, held in Lisbon, Portugal, in August/September 2005.

The 120 revised papers presented together with 4 invited papers were carefully reviewed and selected from 388 submissions. The papers are organized in topical sections on support tools and environments, performance prediction and evaluation, scheduling and load balancing, compilers for high performance, parallel and distributed databases, data mining and knowledge discovery, grid and cluster computing: models, middleware and architectures, parallel computer architecture and instruction distributed systems and algorithms, parallel programming: models, methods, and languages, parallel numerical algorithms, distributed and high-performance multimedia, theory and algorithms for parallel computation, routing and communication in interconnection networks, mobile and ubiquitous computing, peer-to-peer and web computing, and applications of high-performance and grid computing.

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