High Performance Visualization

Author: E. Wes Bethel
Publisher: CRC Press
ISBN: 1439875723
Format: PDF, ePub, Mobi
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Visualization and analysis tools, techniques, and algorithms have undergone a rapid evolution in recent decades to accommodate explosive growth in data size and complexity and to exploit emerging multi- and many-core computational platforms. High Performance Visualization: Enabling Extreme-Scale Scientific Insight focuses on the subset of scientific visualization concerned with algorithm design, implementation, and optimization for use on today’s largest computational platforms. The book collects some of the most seminal work in the field, including algorithms and implementations running at the highest levels of concurrency and used by scientific researchers worldwide. After introducing the fundamental concepts of parallel visualization, the book explores approaches to accelerate visualization and analysis operations on high performance computing platforms. Looking to the future and anticipating changes to computational platforms in the transition from the petascale to exascale regime, it presents the main research challenges and describes several contemporary, high performance visualization implementations. Reflecting major concepts in high performance visualization, this book unifies a large and diverse body of computer science research, development, and practical applications. It describes the state of the art at the intersection of scientific visualization, large data, and high performance computing trends, giving readers the foundation to apply the concepts and carry out future research in this area.

High Performance Parallel I O

Author: Prabhat
Publisher: CRC Press
ISBN: 1466582340
Format: PDF, ePub, Mobi
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Gain Critical Insight into the Parallel I/O Ecosystem Parallel I/O is an integral component of modern high performance computing (HPC), especially in storing and processing very large datasets to facilitate scientific discovery. Revealing the state of the art in this field, High Performance Parallel I/O draws on insights from leading practitioners, researchers, software architects, developers, and scientists who shed light on the parallel I/O ecosystem. The first part of the book explains how large-scale HPC facilities scope, configure, and operate systems, with an emphasis on choices of I/O hardware, middleware, and applications. The book then traverses up the I/O software stack. The second part covers the file system layer and the third part discusses middleware (such as MPIIO and PLFS) and user-facing libraries (such as Parallel-NetCDF, HDF5, ADIOS, and GLEAN). Delving into real-world scientific applications that use the parallel I/O infrastructure, the fourth part presents case studies from particle-in-cell, stochastic, finite volume, and direct numerical simulations. The fifth part gives an overview of various profiling and benchmarking tools used by practitioners. The final part of the book addresses the implications of current trends in HPC on parallel I/O in the exascale world.

Contemporary High Performance Computing

Author: Jeffrey S. Vetter
Publisher: CRC Press
ISBN: 1351103954
Format: PDF
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Contemporary High Performance Computing: From Petascale toward Exascale focuses on the ecosystems surrounding the world’s leading centers for high performance computing (HPC). It covers many of the important factors involved in each ecosystem: computer architectures, software, applications, facilities, and sponsors. The first part of the book examines significant trends in HPC systems, including computer architectures, applications, performance, and software. It discusses the growth from terascale to petascale computing and the influence of the TOP500 and Green500 lists. The second part of the book provides a comprehensive overview of 18 HPC ecosystems from around the world. Each chapter in this section describes programmatic motivation for HPC and their important applications; a flagship HPC system overview covering computer architecture, system software, programming systems, storage, visualization, and analytics support; and an overview of their data center/facility. The last part of the book addresses the role of clouds and grids in HPC, including chapters on the Magellan, FutureGrid, and LLGrid projects. With contributions from top researchers directly involved in designing, deploying, and using these supercomputing systems, this book captures a global picture of the state of the art in HPC.

Industrial Applications of High Performance Computing

Author: Anwar Osseyran
Publisher: CRC Press
ISBN: 1466596813
Format: PDF, ePub, Mobi
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Industrial Applications of High-Performance Computing: Best Global Practices offers a global overview of high-performance computing (HPC) for industrial applications, along with a discussion of software challenges, business models, access models (e.g., cloud computing), public-private partnerships, simulation and modeling, visualization, big data analysis, and governmental and industrial influence. Featuring the contributions of leading experts from 11 different countries, this authoritative book: Provides a brief history of the development of the supercomputer Describes the supercomputing environments of various government entities in terms of policy and service models Includes a case study section that addresses more subtle and technical aspects of industrial supercomputing Shows how access to supercomputing matters, and how supercomputing can be used to solve large-scale and complex science and engineering problems Emphasizes the need for collaboration between companies, political organizations, government agencies, and entire nations Industrial Applications of High-Performance Computing: Best Global Practices supplies computer engineers and researchers with a state-of-the-art supercomputing reference. This book also keeps policymakers and industrial decision-makers informed about the economic impact of these powerful technological investments.

Introduction to High Performance Computing for Scientists and Engineers

Author: Georg Hager
Publisher: CRC Press
ISBN: 9781439811931
Format: PDF, ePub, Mobi
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Written by high performance computing (HPC) experts, Introduction to High Performance Computing for Scientists and Engineers provides a solid introduction to current mainstream computer architecture, dominant parallel programming models, and useful optimization strategies for scientific HPC. From working in a scientific computing center, the authors gained a unique perspective on the requirements and attitudes of users as well as manufacturers of parallel computers. The text first introduces the architecture of modern cache-based microprocessors and discusses their inherent performance limitations, before describing general optimization strategies for serial code on cache-based architectures. It next covers shared- and distributed-memory parallel computer architectures and the most relevant network topologies. After discussing parallel computing on a theoretical level, the authors show how to avoid or ameliorate typical performance problems connected with OpenMP. They then present cache-coherent nonuniform memory access (ccNUMA) optimization techniques, examine distributed-memory parallel programming with message passing interface (MPI), and explain how to write efficient MPI code. The final chapter focuses on hybrid programming with MPI and OpenMP. Users of high performance computers often have no idea what factors limit time to solution and whether it makes sense to think about optimization at all. This book facilitates an intuitive understanding of performance limitations without relying on heavy computer science knowledge. It also prepares readers for studying more advanced literature. Read about the authors’ recent honor: Informatics Europe Curriculum Best Practices Award for Parallelism and Concurrency

Combinatorial Scientific Computing

Author: Uwe Naumann
Publisher: CRC Press
ISBN: 1439827354
Format: PDF, ePub
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Combinatorial Scientific Computing explores the latest research on creating algorithms and software tools to solve key combinatorial problems on large-scale high-performance computing architectures. It includes contributions from international researchers who are pioneers in designing software and applications for high-performance computing systems. The book offers a state-of-the-art overview of the latest research, tool development, and applications. It focuses on load balancing and parallelization on high-performance computers, large-scale optimization, algorithmic differentiation of numerical simulation code, sparse matrix software tools, and combinatorial challenges and applications in large-scale social networks. The authors unify these seemingly disparate areas through a common set of abstractions and algorithms based on combinatorics, graphs, and hypergraphs. Combinatorial algorithms have long played a crucial enabling role in scientific and engineering computations and their importance continues to grow with the demands of new applications and advanced architectures. By addressing current challenges in the field, this volume sets the stage for the accelerated development and deployment of fundamental enabling technologies in high-performance scientific computing.

High Performance Computing

Author: John Levesque
Publisher: CRC Press
ISBN: 9781420077063
Format: PDF, Mobi
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High Performance Computing: Programming and Applications presents techniques that address new performance issues in the programming of high performance computing (HPC) applications. Omitting tedious details, the book discusses hardware architecture concepts and programming techniques that are the most pertinent to application developers for achieving high performance. Even though the text concentrates on C and Fortran, the techniques described can be applied to other languages, such as C++ and Java. Drawing on their experience with chips from AMD and systems, interconnects, and software from Cray Inc., the authors explore the problems that create bottlenecks in attaining good performance. They cover techniques that pertain to each of the three levels of parallelism: Message passing between the nodes Shared memory parallelism on the nodes or the multiple instruction, multiple data (MIMD) units on the accelerator Vectorization on the inner level After discussing architectural and software challenges, the book outlines a strategy for porting and optimizing an existing application to a large massively parallel processor (MPP) system. With a look toward the future, it also introduces the use of general purpose graphics processing units (GPGPUs) for carrying out HPC computations. A companion website at www.hybridmulticoreoptimization.com contains all the examples from the book, along with updated timing results on the latest released processors.

Introduction to HPC with MPI for Data Science

Author: Frank Nielsen
Publisher: Springer
ISBN: 3319219030
Format: PDF, ePub, Mobi
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This gentle introduction to High Performance Computing (HPC) for Data Science using the Message Passing Interface (MPI) standard has been designed as a first course for undergraduates on parallel programming on distributed memory models, and requires only basic programming notions. Divided into two parts the first part covers high performance computing using C++ with the Message Passing Interface (MPI) standard followed by a second part providing high-performance data analytics on computer clusters. In the first part, the fundamental notions of blocking versus non-blocking point-to-point communications, global communications (like broadcast or scatter) and collaborative computations (reduce), with Amdalh and Gustafson speed-up laws are described before addressing parallel sorting and parallel linear algebra on computer clusters. The common ring, torus and hypercube topologies of clusters are then explained and global communication procedures on these topologies are studied. This first part closes with the MapReduce (MR) model of computation well-suited to processing big data using the MPI framework. In the second part, the book focuses on high-performance data analytics. Flat and hierarchical clustering algorithms are introduced for data exploration along with how to program these algorithms on computer clusters, followed by machine learning classification, and an introduction to graph analytics. This part closes with a concise introduction to data core-sets that let big data problems be amenable to tiny data problems. Exercises are included at the end of each chapter in order for students to practice the concepts learned, and a final section contains an overall exam which allows them to evaluate how well they have assimilated the material covered in the book.

Petascale Computing

Author: David A. Bader
Publisher: CRC Press
ISBN: 9781584889106
Format: PDF, ePub, Mobi
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Although the highly anticipated petascale computers of the near future will perform at an order of magnitude faster than today’s quickest supercomputer, the scaling up of algorithms and applications for this class of computers remains a tough challenge. From scalable algorithm design for massive concurrency toperformance analyses and scientific visualization, Petascale Computing: Algorithms and Applications captures the state of the art in high-performance computing algorithms and applications. Featuring contributions from the world’s leading experts in computational science, this edited collection explores the use of petascale computers for solving the most difficult scientific and engineering problems of the current century. Covering a wide range of important topics, the book illustrates how petascale computing can be applied to space and Earth science missions, biological systems, weather prediction, climate science, disasters, black holes, and gamma ray bursts. It details the simulation of multiphysics, cosmological evolution, molecular dynamics, and biomolecules. The book also discusses computational aspects that include the Uintah framework, Enzo code, multithreaded algorithms, petaflops, performance analysis tools, multilevel finite element solvers, finite element code development, Charm++, and the Cactus framework. Supplying petascale tools, programming methodologies, and an eight-page color insert, this volume addresses the challenging problems of developing application codes that can take advantage of the architectural features of the new petascale systems in advance of their first deployment.

The R Book

Author: Michael J. Crawley
Publisher: John Wiley & Sons
ISBN: 1118448960
Format: PDF, ePub, Mobi
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Hugely successful and popular text presenting an extensive and comprehensive guide for all R users The R language is recognized as one of the most powerful and flexible statistical software packages, enabling users to apply many statistical techniques that would be impossible without such software to help implement such large data sets. R has become an essential tool for understanding and carrying out research. This edition: Features full colour text and extensive graphics throughout. Introduces a clear structure with numbered section headings to help readers locate information more efficiently. Looks at the evolution of R over the past five years. Features a new chapter on Bayesian Analysis and Meta-Analysis. Presents a fully revised and updated bibliography and reference section. Is supported by an accompanying website allowing examples from the text to be run by the user. Praise for the first edition: ‘…if you are an R user or wannabe R user, this text is the one that should be on your shelf. The breadth of topics covered is unsurpassed when it comes to texts on data analysis in R.’ (The American Statistician, August 2008) ‘The High-level software language of R is setting standards in quantitative analysis. And now anybody can get to grips with it thanks to The R Book…’ (Professional Pensions, July 2007)