High Performance Parallelism Pearls, Vol. 2

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High Performance Parallelism Pearls Volume Two: Multicore and Many-core Programming Approaches
Acquiring Editor: Todd green Editorial Project Manager: Lindsay lawrence Project Manager: Mohana natarajan Designer Maria Ines Cruz Cover Background: Photo of the COSMOS@ DiRAC SGI UV2000 based Supercomputer manufactured by SGl, Inc and operated by the Stephen Haw king Centre for Theoretical Cosmology, University of Cambridge. Photo courtesy of Philip mynott Cover Foreground: 3D visualization of statistical fluctuations in the Cosmic Microwave Background, the remnant of the first measurable light after the Big Bang. CMB data is from the Planck satellite and is the topic of Chapter 10 providing insights into new physics and how the universe evolved. Visualization rendered with Intel,'s OsPray ray tracing open source software by Gregory P. Johnson and Timothy Rowley, Intel Corporation Morgan Kaufmann is an imprint of elsevier 225 Wyman Street, Waltham, MA 02451, USA Copyright 2015 Elsevier Inc. All rights reserved Except as follows Intel Corporation retains the copyright to their original software programming codes used in this work Chapter 9: Copyright C 2015 Elsevier Inc. All rights reserved JSA, LLC, Contract no. DE-AC05-06OR23177 Chapter 25: Copyright C 2015 Elsevier Inc. All rights reserved UT-Battelle, LLC, Contract no DE-AC05-76RLO1830 No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publishers permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be foundatourwebsitewww.elsevier.com/permissions This book and the individual contributions contained in it are protected under copyright by the Publisher(other than as may be noted herein) Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress ISBN:978-0-12-8038192 For information on all Morgan Kaufmann publications visitourwebsiteathttp://store.elseviercom Working together to grow libraries in ELSEVIER Interna iona developing countries www.elsevier.com.www.bookaid.org Contributors Jefferson amstutz SURVICE Engineering, USA Jefferson is a Software Engineer in the Applied Technology Operation of sUrvICE engineering company his work lever ages advances in massively parallel computing architectures to solve a variety of physics-based simulation problems in domains such as ballistic vulnerability analysis, radio frequency propagation, and soft-body simulation Cedric andreolli ntel Corporation, France Cedric is an Application Engineer in the Energy team where he helps optimize customer applications running on Intel platforms for the oil and gas industry xviii Contributors Meenakshi arunachalam Intel Corporation, USA Meena is a Performance Architect working on performance analysis and modeling of workloads on Intel Xeon and Intel Xeon Phi products. She works on projections and modeling of key workloads and industry benchmarks. She builds in- sights using her models and tools including microarchitec ture analyses and optimizing application performance as seen by the user gauray bansa ntel Corporation, USA Gaurav is an hpc Software applications engineer in the soft ware and Services Group. His focus is on enabling and mod- ernizing applications in the manufacturing vertical, such as computational fluid dynamics and structural analysis, in- cluding advantage of the Intel's current and future generation multicore and many-core platforms Martin berzins SCI Institute School of Computing, University of Utah, USA Martin is a Professor of Computer Science in the School of Computing and the scientific Computing and Imaging Insti- tute at the University of Utah His broad research interests include parallel software for use on modern heterogeneous computer architectures Contributors xix Paul besl Intel Corporation, USA Paul works in the Software and Services group with a focus on CAE applications used by manufacturing organizations. Paul is also chair of the spec graphics Workstation Performance Group Ashraf bhuiyan Intel Corporation, USA Ashraf is a Software Engineer, specializing in code optimiza tion, and has helped projects including amber utilize paral lelism. Prior to Intel, he worked on Nsf funded projects as a multicore optimization expert Stephen Blair-Chappell ntel Corporation, United Kingdo Stephen is a Technical Consulting Engineer at Intel, and has worked in the compiler team for the last 15 years. Stephens provides consulting and training to the Intel Parallel com puting Centers in EMEA. Stephen is an author of the book Parallel programming with Intel Parallel studio XE XX Contributors Leonardo borges ntel Corporation, USA Leo is a senior Staff engineer and has been engaged with the Intel Many Integrated Core program from its early days. He specializes in HPc applying his background in numerical analysis and in developing parallel numerical math libraries Leo is focused on optimization work related to the oil and gas dust James P. Briggs University of Cambridge, UK James is a Parallel Programmer at the cosmos iPCc at the Stephen hawking Centre for Theoretical Cosmology at the University of cambridge. He works with scientists to modern ize and optimize cosmology codes for modern and future ar chitectures. His interests are in computational astrophysics and parallel and high-performance computing Mikhail Brinsky ntel Corporation, russia Mikhail is a Software Development Engineer working in the Software and services group with focus on the Intel MPl Library development. Mikhail has a strong background on numerical modeling for applied physics Contributors Michal Brylinski Department of Biological Sciences, Louisiana State University, USA Michal runs a Computational Systems Biology Lab, where most of the projects lie at the intersection of structural biol ogy, bioinformatics, and high-performance computing He is actively involved in the design and development of novel al- gorithms and codes for drug discovery and repositioning. He is highly interested in the application of massively paralle hardware accelerators in structural bioinformatics func tional genomics, cheminformatics, and pharmacogenomics He also teaches courses on computational biology, biophys- ics, physical chemistry, and molecular dynamics Vlad cali Intel Corporation, Roman Vlad is a software Engineer at Intel working on performance analysis and characterization of HPc applications. He focuses on the impact that various architectural features like vectorization and prefetching have on application performance James dina Intel Corporation, USA James is a Software Architect working in the area of High Performance Computing. He has served on the MPI Forum for several years and was a contributor to the mpi30 spec ification. Jim was previously the James Wallace Givens post doctoral fellow at Argonne National Laboratory. His research interests include parallel programming models, high performance fabrics, scalable runtime systems, distributed algorithms, scientific computing, and computer architecture xxii Contributors Jussi enkovaara CSC. Finland Jussi is a Senior Application Scientist in High-Performance Computing support at CSC and a docent of computational physics in Aalto University, Finland. Among others, he is interested in numerical methods for electronic structure simulations and utilizing python in the context of high performance computing. He is one of the key developers of the density-functional-theory-based software package GPAW Rob farber Tech Enablement. com USA Rob is a consultant with an extensive background in hPc and a long history of working with national laboratories and corpo rations engaged in HPc optimization work. rob has authored/ edited several books on GPU programming and is the ceo/ Publisher of tech enablement com Julia fedorova el Corporation russia Julia is a Principal Engineer in the Software and Services Group where she works on performance profiling and analysis tools including Intel vTune Amplifier XE. Recently, she has been focusing on gPU compute analysis. She loves the chal- lenge of optimizing software and improving the tools they de velop through this experience Contributors xxi Wei p feinstein Louisiana state University, USA Wei works in the HPc group assisting researchers from differ- ent disciplines to efficiently utilize computer cluster re sources. She is also a computational biologist interested in developing algorithms for computational biophysics with ap- plications in drug discovery. She develops high-performance parallel and heterogeneous codes to boost the performance of applications in biology. In addition, Wei co-leads the TEsC echnologies for EXtreme Scale Computing) team, where a group of interdisciplinary graduate students at LsU collabo- rate to improve the performance of various domain science projects using hardware accelerators Evan felix Pacific Northwest National Laboratory(PNNl), Usa Evan is a research Scientist and HPC Engineer in the Environ mental Molecular Sciences Laboratory, a department of en ergy (doe) users facility at pnnl. he is a senior member of the team that runs the Molecular Science Computing Facility, which provides supercomputing resources and archive capa bilities for researchers at pnnl, and at universities and labo ratories around the world. This team has deployed systems that have ranked highly on the top500. org supercomputer list, and maintains a multi- petabyte data archive. He works on numer- ous open-source projects, many of which are used to maintain monitor, and deploy supercomputing systems R. Fergusson University of Cambridge, UK James is a Lecturer in the department of applied Mathemat- ics and Theoretical Physics. His work mainly concerns con necting theoretical models of the very early universe with observational data. he is a mem ber of the planck satellite on and has done extensive work in the field of nol Gaussianity, producing the strongest available constraints on non-standard models of inflation 【实例截图】
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