Janssen / Nielsen Parallel Computing in Quantum Chemistry

Erscheinungsjahr 2008
ISBN: 978-1-4200-5165-0
Verlag: Taylor & Francis
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 232 Seiten

An In-Depth View of Hardware Issues, Programming Practices, and Implementation of Key Methods Exploring the challenges of parallel programming from the perspective of quantum chemists, Parallel Computing in Quantum Chemistry thoroughly covers topics relevant to designing and implementing parallel quantum chemistry programs. Focusing on good parallel program design and performance analysis, the first part of the book deals with parallel computer architectures and parallel computing concepts and terminology. The authors discuss trends in hardware, methods, and algorithms; parallel computer architectures and the overall system view of a parallel computer; message-passing; parallelization via multi-threading; measures for predicting and assessing the performance of parallel algorithms; and fundamental issues of designing and implementing parallel programs. The second part contains detailed discussions and performance analyses of parallel algorithms for a number of important and widely used quantum chemistry procedures and methods. The book presents schemes for the parallel computation of two-electron integrals, details the Hartree–Fock procedure, considers the parallel computation of second-order Møller–Plesset energies, and examines the difficulties of parallelizing local correlation methods. Through a solid assessment of parallel computing hardware issues, parallel programming practices, and implementation of key methods, this invaluable book enables readers to develop efficient quantum chemistry software capable of utilizing large-scale parallel computers.

Zielgruppe

Quantum chemistry software developers and users; researchers, professionals, and advanced undergraduate students in chemistry, biochemistry, and chemical physics; computer scientists; hardware developers.

Autoren/Hrsg.

Janssen, Curtis L.

Nielsen, Ida M. B.

Fachgebiete

• Mathematik | Informatik EDV | Informatik Informatik
• Naturwissenschaften Chemie Physikalische Chemie Quantenchemie, Theoretische Chemie

Inhaltsverzeichnis

Parallel Computing Concepts and Terminology
Introduction
Parallel Computing in Quantum Chemistry: Past and Present
Trends in Hardware Development
Trends in Parallel Software Development
Parallel Computer Architectures
Flynn’s Classification Scheme
Network Architecture
Node Architecture
MIMD System Architecture
Further Reading
Communication via Message-Passing
Point-to-Point Communication Operations
Collective Communication Operations
One-Sided Communication Operations
Further Reading
Multi-Threading
Pitfalls of Multi-Threading
Thread-Safety
Comparison of Multi-Threading and Message-Passing
Hybrid Programming
Further Reading
Parallel Performance Evaluation
Network Performance Characteristics
Performance Measures for Parallel Programs
Performance Modeling
Presenting and Evaluating Performance Data: A Few Caveats
Further Reading
Parallel Program Design
Distribution of Work
Distribution of Data
Designing a Communication Scheme
Design Example: Matrix-Vector Multiplication
Summary of Key Points of Parallel Program Design
Further Reading
Applications of Parallel Programming in Quantum Chemistry
Two-Electron Integral Evaluation
Basics of Integral Computation
Parallel Implementation Using Static Load Balancing
Parallel Implementation Using Dynamic Load Balancing
The Hartree–Fock Method
The Hartree–Fock Equations
The Hartree–Fock Procedure
Parallel Fock Matrix Formation with Replicated Data
Parallel Fock Matrix Formation with Distributed Data
Further Reading
Second-Order Møller–Plesset Perturbation Theory
The Canonical MP2 Equations
A Scalar Direct MP2 Algorithm
Parallelization with Minimal Modifications
High-Performance Parallelization
Performance of the Parallel Algorithms
Further Reading
Local Møller–Plesset Perturbation Theory
The LMP2 Equations
A Scalar LMP2 Algorithm
Parallel LMP2
Appendix A: A Brief Introduction to MPI
Appendix B: Pthreads: Explicit Use of Threads
Appendix C: OpenMP: Compiler Extensions for Multi-Threading
Index
References appear at the end of each chapter.