Parallel Computing in Quantum Chemistry

by Janssen; Curtis L.

• ISBN13: 9781420051643
• ISBN10: 1420051644
• Edition: 1st
• Format: Hardcover
• Copyright: 2008-04-09
• Publisher: CRC Press

Summary

An In-Depth View of Hardware Issues, Programming Practices, and Implementation of Key MethodsExploring the challenges of parallel programming from the perspective of quantum chemists, Parallel Computing in Quantum Chemistrythoroughly 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 numberof important and widely used quantum chemistry procedures and methods. The book presents schemes for the parallel computation of two-electron integrals, details the Hartreea??Fock procedure, considers the parallel computation of second-order M??llera??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.

Table of Contents

Parallel Computing Concepts and Terminology
Introduction	p. 3
Parallel Computing in Quantum Chemistry: Past and Present	p. 4
Trends in Hardware Development	p. 5
Moore's Law	p. 5
Clock Speed and Performance	p. 6
Bandwidth and Latency	p. 7
Supercomputer Performance	p. 8
Trends in Parallel Software Development	p. 10
Responding to Changes in Hardware	p. 10
New Algorithms and Methods	p. 10
New Programming Models	p. 12
References	p. 13
Parallel Computer Architectures	p. 17
Flynn's Classification Scheme	p. 17
Single-Instruction, Single-Data	p. 17
Single-Instruction, Multiple-Data	p. 18
Multiple-Instruction, Multiple-Data	p. 18
Network Architecture	p. 19
Direct and Indirect Networks	p. 19
Routing	p. 20
Network Performance	p. 23
Network Topology	p. 25
Crossbar	p. 26
Ring	p. 27
Mesh and Torus	p. 27
Hypercube	p. 28
Fat Tree	p. 28
Bus	p. 30
Ad Hoc Grid	p. 31
Node Architecture	p. 31
MIMD System Architecture	p. 34
Memory Hierarchy	p. 35
Persistent Storage	p. 35
Local Storage	p. 37
Network Storage	p. 37
Trends in Storage	p. 38
Reliability	p. 38
Homogeneity and Heterogeneity	p. 39
Commodity versus Custom Computers	p. 40
Further Reading	p. 42
References	p. 43
Communication via Message-Passing	p. 45
Point-to-Point Communication Operations	p. 46
Blocking Point-to-Point Operations	p. 46
Non-Blocking Point-to-Point Operations	p. 47
Collective Communication Operations	p. 49
One-to-All Broadcast	p. 50
All-to-All Broadcast	p. 51
All-to-One Reduction and All-Reduce	p. 54
One-Sided Communication Operations	p. 55
Further Reading	p. 56
References	p. 56
Multi-Threading	p. 59
Pitfalls of Multi-Threading	p. 61
Thread-Safety	p. 64
Comparison of Multi-Threading and Message-Passing	p. 65
Hybrid Programming	p. 66
Further Reading	p. 69
References	p. 70
Parallel Performance Evaluation	p. 71
Network Performance Characteristics	p. 71
Performance Measures for Parallel Programs	p. 74
Speedup and Efficiency	p. 74
Scalability	p. 79
Performance Modeling	p. 80
Modeling the Execution Time	p. 80
Performance Model Example: Matrix-Vector Multiplication	p. 83
Presenting and Evaluating Performance Data: A Few Caveats	p. 86
Further Reading	p. 90
References	p. 90
Parallel Program Design	p. 93
Distribution of Work	p. 94
Static Task Distribution	p. 95
Round-Robin and Recursive Task Distributions	p. 96
Dynamic Task Distribution	p. 99
Manager-Worker Model	p. 99
Decentralized Task Distribution	p. 101
Distribution of Data	p. 101
Designing a Communication Scheme	p. 104
Using Collective Communication	p. 104
Using Point-to-Point Communication	p. 105
Design Example: Matrix-Vector Multiplication	p. 107
Using a Row-Distributed Matrix	p. 108
Using a Block-Distributed Matrix	p. 109
Summary of Key Points of Parallel Program Design	p. 112
Further Reading	p. 114
References	p. 114
Applications of Parallel Programming in Quantum Chemistry
Two-Electron Integral Evaluation	p. 117
Basics of Integral Computation	p. 117
Parallel Implementation Using Static Load Balancing	p. 119
Parallel Algorithms Distributing Shell Quartets and Pairs	p. 119
Performance Analysis	p. 121
Determination of the Load Imbalance Factor k(p)	p. 122
Determination of [mu] and [sigma] for Integral Computation	p. 123
Predicted and Measured Efficiencies	p. 124
Parallel Implementation Using Dynamic Load Balancing	p. 125
Parallel Algorithm Distributing Shell Pairs	p. 126
Performance Analysis	p. 128
Load Imbalance	p. 128
Communication Time	p. 128
Predicted and Measured Efficiencies	p. 129
References	p. 130
The Hartree-Fock Method	p. 131
The Hartree-Fock Equations	p. 131
The Hartree-Fock Procedure	p. 133
Parallel Fock Matrix Formation with Replicated Data	p. 135
Parallel Fock Matrix Formation with Distributed Data	p. 138
Further Reading	p. 145
References	p. 146
Second-Order Moller-Plesset Perturbation Theory	p. 147
The Canonical MP2 Equations	p. 147
A Scalar Direct MP2 Algorithm	p. 149
Parallelization with Minimal Modifications	p. 151
High-Performance Parallelization	p. 154
Performance of the Parallel Algorithms	p. 158
Further Reading	p. 164
References	p. 164
Local Moller-Plesset Perturbation Theory	p. 167
The LMP2 Equations	p. 167
A Scalar LMP2 Algorithm	p. 169
Parallel LMP2	p. 170
Two-Electron Integral Transformation	p. 171
Computation of the Residual	p. 173
Parallel Performance	p. 174
References	p. 177
Appendices
A Brief Introduction to MPI	p. 181
Pthreads: Explicit Use of Threads	p. 189
OpenMP: Compiler Extensions for Multi-Threading	p. 195
Index	p. 205
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