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This book presents advanced and practical techniques for performance optimization for highly parallel processing. Featuring various parallelization techniques in material science, it is a valuable resource for anyone developing software codes for computational sciences such as physics, chemistry, biology, earth sciences, space science, weather, disaster prevention and manufacturing, as well as for anyone using those software codes. Chapter 1 outlines supercomputers and includes a brief explanation of the history of hardware. Chapter 2 presents procedures for performance evaluation, while Chapter 3 describes the set of tuned applications in materials science, nanoscience and nanotechnology, earth science and engineering on the K computer. Introducing the order-N method, based on density functional theory (DFT) calculation, Chapter 4 explains how to extend the applicability of DFT to large-scale systems by reducing the computational complexity. Chapter 5 discusses acceleration and parallelization in classical molecular dynamics simulations, and lastly, Chapter 6 explains techniques for large-scale quantum chemical calculations, including the order-N method. This is the second of the two volumes that grew out of a series of lectures in the K computer project in Japan. The first volume addresses more basic techniques, and this second volume focuses on advanced and concrete techniques.
This book provides basic and practical techniques of parallel computing and related methods of numerical analysis for researchers who conduct numerical calculation and simulation. Although the techniques provided in this book are field-independent, these methods can be used in fields such as physics, chemistry, biology, earth sciences, space science, meteorology, disaster prevention, and manufacturing. In particular, those who develop software code in these areas will find this book useful. The contents are suitable for graduate students and researchers in computational science rather than novices at programming or informed experts in computer science. Starting with an introduction to the recent trends in computer architecture and parallel processing, Chapter 1 explains the basic knowledge of speedup programs with simple examples of numerical computing. Chapters 2 – 4 detail the basics of parallel programming, the message passing interface (MPI), and OpenMP and discuss hybrid parallelization techniques. Showing an actual example of adaptation, Chapter 5 gives an overview of performance tuning and communication optimizations. To deal with dense matrix calculations, Chapter 6 details the basics and practice of linear algebra calculation libraries BLAS and LAPACK, including some examples that can be easily reproduced by readers using free software. Focusing on sparse matrix calculations, Chapter 7 explains high performance algorithms for numerical linear algebra. Chapter 8 introduces the fast Fourier transform in large-scale systems from the basics. Chapter 9 explains optimization and related topics such as debug methods and version control systems. Chapter 10 discusses techniques for increasing computation accuracy as an essential topic in numerical calculation. This is the first of the two volumes that grew out of a series of lectures in the K computer project in Japan. The second volume will focus on advanced techniques and examples of applications in materials science.
This book constitutes the thoroughly refereed post-conference proceedings of the 12fth International Conference on High Performance Computing in Computational Science, VECPAR 2016, held in Porto, Portugal, in June 2016. The 20 full papers presented were carefully reviewed and selected from 36 submissions. The papers are organized in topical sections on applications; performance modeling and analysis; low level support; environments/libraries to support parallelization.
This is a textbook that teaches the bridging topics between numerical analysis, parallel computing, code performance, large scale applications.
An authoritative guide to today's revolution in "commodity supercomputing, " this book brings together more than 100 of the field's leading practitioners, providing a single source for up-to-the-minute information on virtually every key system issue associated with high-performance cluster computing.
This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS). The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to computer science with a special emphasis on industrially relevant applications. Presenting findings of one of Europe’s leading systems, this volume covers a wide variety of applications that deliver a high level of sustained performance. The book covers the main methods in high-performance computing. Its outstanding results in achieving the best performance for production codes are of particular interest for both scientists and engineers. The book comes with a wealth of color illustrations and tables of results.
The 5th edition of the VECPAR series of conferences marked a change of the conference title. The full conference title now reads VECPAR 2002 — 5th Int- national Conference on High Performance Computing for Computational S- ence. This re?ects more accurately what has been the main emphasis of the conference since its early days in 1993 – the use of computers for solving pr- lems in science and engineering. The present postconference book includes the best papers and invited talks presented during the three days of the conference, held at the Faculty of Engineering of the University of Porto (Portugal), June 26–28 2002. The book is organized into 8 chapters, which as a whole appeal to a wide research community, from those involved in the engineering applications to those interested in the actual details of the hardware or software implementation, in line with what, in these days, tends to be considered as Computational Science and Engineering (CSE). The book comprises a total of 49 papers, with a prominent position reserved for the four invited talks and the two ?rst prizes of the best student paper competition.
This book provides a non-technical introduction to High Performance Computing applications together with advice about how beginners can start to write parallel programs. The authors show what HPC can offer geographers and social scientists and how it can be used in GIS. They provide examples of where it has already been used and suggestions for other areas of application in geography and the social sciences. Case studies drawn from geography explain the key principles and help to understand the logic and thought processes that lie behind the parallel programming.
These multiple volumes (LNCS volumes 6016, 6017, 6018 and 6019) consist of the peer-reviewed papers from the 2010 International Conference on Compu- tional Science and Its Applications (ICCSA2010)held in Fukuoka, Japanduring March23–26,2010.ICCSA2010wasasuccessfuleventintheInternationalC- ferences on Computational Science and Its Applications (ICCSA) conference - ries, previouslyheld in Suwon, South Korea (2009), Perugia, Italy (2008), Kuala Lumpur, Malaysia (2007), Glasgow, UK (2006), Singapore (2005), Assisi, Italy (2004), Montreal, Canada (2003), and (as ICCS) Amsterdam, The Netherlands (2002) and San Francisco, USA (2001). Computational science is a main pillar of most of the present research, - dustrial and commercial activities and plays a unique role in exploiting ICT - novative technologies. The ICCSA conference series has been providing a venue to researchers and industry practitioners to discuss new ideas, to share complex problems and their solutions, and to shape new trends in computational science. ICCSA 2010 was celebrated at the host university, Kyushu Sangyo Univ- sity, Fukuoka, Japan, as part of the university’s 50th anniversary.We would like to thank Kyushu Sangyo University for hosting ICCSA this year, and for - cluding this international event in their celebrations. Also for the ?rst time this year, ICCSA organized poster sessions that present on-going projects on various aspects of computational sciences.