Optimization for the Molecular Dynamics Software GROMACS
In this chapter, we will first give a brief introduction about the GROMACS scientific computing software, and its experiment results based on a four-node HPC cluster. Furthermore, we propose and analyze the optimizations for GROMACS.
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The Student Supercomputer Challenge Guide From Supercomputing Competition to the Next HPC Generation
The Student Supercomputer Challenge Guide
ASC Community
The Student Supercomputer Challenge Guide From Supercomputing Competition to the Next HPC Generation
123
ASC Community Inspur (Beijing) Electronic Information Industry Co., Ltd Beijing China
ISBN 978-981-10-3730-6 ISBN 978-981-10-3731-3 https://doi.org/10.1007/978-981-10-3731-3
(eBook)
Jointly published with Science Press, Beijing, China The print edition is not for sale in China Mainland. Customers from China Mainland please order the print book from: Science Press, Beijing, China. ISBN of the China Mainland edition: 978-7-03-047163-5 Library of Congress Control Number: 2018934873 © Science Press and Springer Nature Singapore Pte Ltd. 2018 This work is subject to copyright. All rights are reserved by the Publishers, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publishers, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publishers nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publishers remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd. part of Springer Nature The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore
Foreword
Nowadays, supercomputers are widely used in areas such as weather prediction, geophysics exploration, earth modeling, developments of new material and drug, as well as automobile and aircraft designs. In the meantime, supercomputing is also an important method for dealing with essential social and economic issues. For example, decisions can be made faster and more effective in environmental protection, gene sequencing, natural disaster prediction and Internet deep learning with the help of supercomputing. Recent years have witnessed the fast development in building more powerful supercomputers. The computing performance of top supercomputers has reached to over 50 Petaflops (PFLOPS), and will be soon approaching into Exaflops-scale era in future years. De
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