Using MPI-2 - Advanced Features.pdf

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Using MPI-2
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Scientific and Engineering Computation
Janusz Kowalik, editor
Data-Parallel Programming on MIMD Computers,
Philip J. Hatcher and Michael J. Quinn, 1991
Unstructured Scientific Computation on Scalable Multiprocessors,
edited by Piyush Mehrotra, Joel Saltz, and Robert Voigt, 1992
Parallel Computational Fluid Dynamics: Implementation and Results,
edited by Horst D. Simon, 1992
Enterprise Integration Modeling: Proceedings of the First International Conference,
edited by Charles J. Petrie, Jr., 1992
The High Performance Fortran Handbook,
Charles H. Koelbel, David B. Loveman, Robert S. Schreiber, Guy L. Steele Jr. and Mary E. Zosel, 1994
PVM: Parallel Virtual Machine–A Users' Guide and Tutorial for Network Parallel Computing,
Al Geist, Adam Beguelin, Jack Dongarra, Weicheng Jiang, Bob Manchek, and Vaidy Sunderam, 1994
Practical Parallel Programming,
Gregory V. Wilson, 1995
Enabling Technologies for Petaflops Computing,
Thomas Sterling, Paul Messina, and Paul H. Smith, 1995
An Introduction to High-Performance Scientific Computing,
Lloyd D. Fosdick, Elizabeth R. Jessup, Carolyn J. C. Schauble, and Gitta Domik, 1995
Parallel Programming Using C++,
edited by Gregory V. Wilson and Paul Lu, 1996
Using PLAPACK: Parallel Linear Algebra Package,
Robert A. van de Geijn, 1997
Fortran 95 Handbook,
Jeanne C. Adams, Walter S. Brainerd, Jeanne T. Martin, Brian T. Smith, Jerrold L. Wagener, 1997
MPI—The Complete Reference: Volume 1, The MPI Core,
Marc Snir, Steve Otto, Steven Huss-Lederman, David Walker, and Jack Dongarra, 1998
MPI—The Complete Reference: Volume 2, The MPI-2 Extensions,
William Gropp, Steven Huss-Lederman, Andrew Lumsdaine, Ewing Lusk, Bill Nitzberg,
William Saphir, and Marc Snir, 1998
A Programmer's Guide to ZPL,
Lawrence Snyder, 1999
How to Build a Beowulf,
Thomas L. Sterling, John Salmon, Donald J. Becker, and Daniel F. Savarese, 1999
Using MPI: Portable Parallel Programming with the Message-Passing Interface,
second edition,
William Gropp, Ewing Lusk, and Anthony Skjellum, 1999
Using MPI-2: Advanced Features of the Message-Passing Interface,
William Gropp, Ewing Lusk, and Rajeev Thakur, 1999
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Using MPI-2
Advanced Features of the Message-Passing Interface
William Gropp
Ewing Lusk
Rajeev Thakur
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© 1999 Massachusetts Institute of Technology
All rights reserved. No part of this book may be reproduced in any form by any electronic or mechanical means (including
photocopying, recording, or information storage and retrieval) without permission in writing from the publisher.
This book was set in
by the authors and was printed and bound in the United States of America.
Library of Congress Cataloging-in-Publication Data
Gropp, William.
Using MPI-2: advanced features of the message-passing interface /
William Gropp, Ewing Lusk, Rajeev Thakur.
p. cm.—(Scientific and engineering computation)
Includes bibliographical references and index.
ISBN 0-262-057133-1 (pb.: alk. paper)
1. Parallel programming (Computer science). 2. Parallel computers—
Programming. 3. Computer interfaces. I. Lusk, Ewing. II. Thakur,
Rajeev. III. Title. IV. Series.
QA76.642.G762
1999
005.2'75–dc21
99-042972
CIP
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To Christopher Gropp, Brigid Lusk, and Pratibha and Sharad Thakur
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Contents
Series Foreword
Preface
1
Introduction
1.1 Background
1.1.1 Ancient History
1.1.2 The MPI Forum
1.1.3 The MPI-2 Forum
1.2 What's New in MPI-2?
1.2.1 Parallel I/O
1.2.2 Remote Memory Operations
1.2.3 Dynamic Process Management
1.2.4 Odds and Ends
1.3 Reading This Book
2
Getting Started with MPI-2
2.1 Portable Process Startup
2.2 Parallel I/O
2.2.1 Non-Parallel I/O from an MPI Program
2.2.2 Non-MPI Parallel I/O from an MPI Program
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2.2.3 MPI I/O to Separate Files
2.2.4 Parallel MPI I/O to a Single File
2.2.5 Fortran 90 Version
2.2.6 Reading the File with a Different Number of Processes
2.2.7 C++ Version
2.2.8 Other Ways to Write to a Shared File
2.3 Remote Memory Access
2.3.1 The Basic Idea: Memory Windows
2.3.2 RMA Version of
cpi
2.4 Dynamic Process Management
2.4.1 Spawning Processes
2.4.2 Parallel
cp:
A Simple System Utility
2.5 More Info on
Info
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2.5.1 Motivation, Description, and Rationale
2.5.2 An Example from Parallel I/O
2.5.3 An Example from Dynamic Process Management
2.6 Summary
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Parallel I/O
3.1 Introduction
3.2 Using MPI for Simple I/O
3.2.1 Using Individual File Pointers
3.2.2 Using Explicit Offsets
3.2.3 Writing to a File
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3.3 Noncontiguous Accesses and Collective I/O
3.3.1 Noncontiguous Accesses
3.3.2 Collective I/O
3.4 Accessing Arrays Stored in Files
3.4.1 Distributed Arrays
3.4.2 A Word of Warning about Darray
3.4.3 Subarray Datatype Constructor
3.4.4 Local Array with Ghost Area
3.4.5 Irregularly Distributed Arrays
3.5 Nonblocking I/O and Split Collective I/O
3.6 Shared File Pointers
3.7 Passing Hints to the Implementation
3.8 Consistency Semantics
3.8.1 Simple Cases
3.8.2 Accessing a Common File Opened with
MPI_COMM_WORLD
3.8.3 Accessing a Common File Opened with
MPI_COMM_SELF
3.8.4 General Recommendation
3.9 File Interoperability
3.9.1 File Structure
3.9.2 File Data Representation
3.9.3 Use of Datatypes for Portability
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