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

Table of Contents

Modern Processors

Stored-program computer architecture

General-purpose cache-based microprocessor architecture

Memory hierarchies

Multicore processors

Multithreaded processors

Vector processors

Basic Optimization Techniques for Serial Code

Scalar profiling

Common sense optimizations

Simple measures, large impact

The role of compilers

C++ optimizations

Data Access Optimization

Balance analysis and lightspeed estimates

Storage order

Case study: The Jacobi algorithm

Case study: Dense matrix transpose

Algorithm classification and access optimizations

Case study: Sparse matrix-vector multiply

Parallel Computers

Taxonomy of parallel computing paradigms

Shared-memory computers

Distributed-memory computers

Hierarchical (hybrid) systems

Networks

Basics of Parallelization

Why parallelize?

Parallelism

Parallel scalability

Shared-Memory Parallel Programming with OpenMP

Short introduction to OpenMP

Case study: OpenMP-parallel Jacobi algorithm

Advanced OpenMP: Wavefront parallelization

Efficient OpenMP Programming

Profiling OpenMP programs

Performance pitfalls

Case study: Parallel sparse matrix-vector multiply

Locality Optimizations on ccNUMA Architectures

Locality of access on ccNUMA

Case study: ccNUMA optimization of sparse MVM

Placement pitfalls

ccNUMA issues with C++

Distributed-Memory Parallel Programming with MPI

Message passing

A short introduction to MPI

Example: MPI parallelization of a Jacobi solver

Efficient MPI Programming

MPI performance tools

Communication parameters

Synchronization, serialization, contention

Reducing communication overhead

Understanding intranode point-to-point communication

Hybrid Parallelization with MPI and OpenMP

Basic MPI/OpenMP programming models

MPI taxonomy of thread interoperability

Hybrid decomposition and mapping

Potential benefits and drawbacks of hybrid programming

Appendix A: Topology and Affinity in Multicore Environments

Appendix B: Solutions to the Problems

Bibliography

Index

Responding to the developments of the past twenty years, Les Kirkup has thoroughly updated his popular book on experimental methods, while retaining the extensive coverage and practical advice from the first edition. Many topics from that edition remain, including keeping a record of work, how to deal with measurement uncertainties, understanding the statistical basis of data analysis and reporting the results of experiments. However, with new technologies influencing how experiments are devised, carried out, analyzed, presented and reported, this new edition reflects the digital changes which have taken place and the increased emphasis on the importance of communication skills in reporting results. Bringing together key elements of experimental methods into one coherent book, it is perfect for students seeking guidance with their experimental work, including how to acquire, analyse and present data. Exercises, worked examples and end-of-chapter problems are provided throughout the book to reinforce fundamental principles.

The definitive guide to the principles and practice of experimental organic chemistry - fully updated and now featuring more than 100 experiments The latest edition of this popular guide to experimental organic chemistry takes students from their first day in the laboratory right through to complex research procedures. All sections have been updated to reflect new techniques, equipment and technologies, and the text has been revised with an even sharper focus on practical skills and procedures. The first half of the book is devoted to safe laboratory practice as well as purification and analytical techniques; particularly spectroscopic analysis. The second half contains step-by-step experimental procedures, each one illustrating a basic principle, or important reaction type. Tried and tested over almost three decades, over 100 validated experiments are graded according to their complexity and all are chosen to highlight important chemical transformations and to teach key experimental skills. New sections cover updated health and safety guidelines, additional spectroscopic techniques, electronic notebooks and record keeping, and techniques, such as semi-automated chromatography and enabling technologies such as the use of microwave and flow chemistry. New experiments include transition metal-catalysed cross-coupling, organocatalysis, asymmetric synthesis, flow chemistry, and microwave-assisted synthesis. Key aspects of this third edition include: * Detailed descriptions of the correct use of common apparatus used in the organic laboratory * Outlines of practical skills that all chemistry students must learn * Highlights of aspects of health and safety in the laboratory, both in the first section and throughout the experimental procedures * Four new sections reflecting advances in techniques and technologies, from electronic databases and information retrieval to semi-automated chromatography * More than 100 validated experiments of graded complexity from introductory to research level * A user-friendly experiment directory * An instructor manual and PowerPoint slides of the figures in the book available on a companion website A comprehensive guide to contemporary organic chemistry laboratory principles, procedures, protocols, tools and techniques, Experimental Organic Chemistry, Third Edition is both an essential laboratory textbook for students of chemistry at all levels, and a handy bench reference for experienced chemists.

Since the first recognition of outbreaks of cerebrospinal or spotted fever at the end of the nineteenth and the beginning of the twentieth centuries, the menace of the meningococcus has been high on the list of public health prio- ties. Few if any pathogens surpass the meningococcus in the rapidity and sev- ity with which it devastates previously healthy individuals. The challenge of understanding the biology of this fascinating microbe is immense, but few will doubt that successful control of meningococcal meningitis and septicemia will only transpire through the application of a body of extraordinary detailed inf- mation, including key minutiae of its molecular biology. In the first of two companion volumes, Meningococcal Vaccines, the team of experts gathered by Andy Pollard and Martin Maiden converge to p- vide an impressive accumulation of molecular tools with which to lay bare the secrets of the meningococcus. The results of this ambitious and welcome v- ume represent an exciting and much needed resource for all of us in the field.

Million-copy bestselling author of The Elements, Molecules, and Reactions Theodore Gray applies his trademark mix of engaging stories, real-time experiments, and stunning photography to the inner workings of machines, big and small, revealing the extraordinary science, beauty, and rich history of everyday things. Theodore Gray has become a household name among fans, both young and old, of popular science and mechanics. He's an incorrigible tinkerer with a constant curiosity for how things work. Gray's readers love how he always brings the perfect combination of know-how, humour and daring-do to every project or demonstration, be it scientific or mechanical. In How Things Work he explores the mechanical underpinnings of dozens of types of machines and mechanisms, from the cotton gin to the wristwatch to an industrial loom. Filled with stunning original photographs in Gray's inimitable style, How Things Work is a must-have exploration of stuff - large and small - for any builder, maker or lover of mechanical things.

The evolution of observational instruments, simulation techniques, and computing power has given aquatic scientists a new understanding of biological and physical processes that span temporal and spatial scales. This has created a need for a single volume that addresses concepts of scale in a manner that builds bridges between experimentalists and theoreticians in aquatic ecology. Handbook of Scaling Methods in Aquatic Ecology: Measurement, Analysis, Simulation is the first comprehensive compilation of modern scaling methods used in marine and freshwater ecological research. Written by leading researchers, it presents a systematic approach to dealing with space and time in aquatic ecology. This is a compendium that analyzes themes related to the response or behavior of organisms to processes occurring over multiple spatial and temporal scales. This book covers: novel techniques for data collection, focusing on processes over a broad range of scales (from bacteria to ocean basins); newly-developed concepts and data analysis algorithms; and innovative computer models and simulations to mimic complex biological processes. The Handbook serves as a reference volume for investigators seeking insight into new experimental approaches and data analysis, as well as the sensor design required for optimal sampling. Many of the algorithms and models provided are directly applicable to your experimental data. This comprehensive treatment of scaling methods and applications can help foster a unified understanding of subject matter among the modeling, experimental, and field research communities.

Dealing with the volume, complexity, and diversity of data currently being generated by scientific experiments and simulations often causes scientists to waste productive time. Scientific Data Management: Challenges, Technology, and Deployment describes cutting-edge technologies and solutions for managing and analyzing vast amounts of data, helping scientists focus on their scientific goals. The book begins with coverage of efficient storage systems, discussing how to write and read large volumes of data without slowing the simulation, analysis, or visualization processes. It then focuses on the efficient data movement and management of storage spaces and explores emerging database systems for scientific data. The book also addresses how to best organize data for analysis purposes, how to effectively conduct searches over large datasets, how to successfully automate multistep scientific process workflows, and how to automatically collect metadata and lineage information. This book provides a comprehensive understanding of the latest techniques for managing data during scientific exploration processes, from data generation to data analysis. Enhanced by numerous detailed color images, it includes real-world examples of applications drawn from biology, ecology, geology, climatology, and more. Check out Dr. Shoshani discuss the book during an interview with International Science Grid This Week (iSGTW): http://www.isgtw.org/?pid=1002259

Bestselling author Theodore Gray has spent more than a decade dreaming up, executing, photographing, and writing about extreme scientific experiments, which he then published between 2009 and 2014 in his monthly Popular Science column "Gray Matter." Previously published in book form by Black Dog in two separate volumes (Mad Science and Mad Science 2), these experiments, plus 5 more all-new ones, will now be combined in one complete book. Packaged in a smaller, chunkier format Completely Mad Science is 432 pages of dazzling chemical demonstrations, illustrated in spectacular full-color photographs. Some of the completely mad experiments in the book include: Casting a model fish out of mercury (demonstrating how this element behaves very differently depending upon temperature); the famous Flaming Bacon Lance that can cut through steel (demonstrating the amount of energy contained in fatty foods like bacon); creating nylon thread out of pure liquid by combining molecules of hexamethylenediamine and sebacoyl chloride; making homemade ice cream using a fire extinguisher and a pillow case; powering your iPhone using 150 pennies and an apple, and many, many more. It's the ultimate collection for Gray's millions of fans.

Passive acoustic monitoring is increasingly used by the scientific community to study, survey and census marine mammals, especially cetaceans, many of which are easier to hear than to see. PAM is also used to support efforts to mitigate potential negative effects of human activities such as ship traffic, military and civilian sonar and offshore exploration. Walter Zimmer provides an integrated approach to PAM, combining physical principles, discussion of technical tools and application-oriented concepts of operations. Additionally, relevant information and tools necessary to assess existing and future PAM systems are presented, with Matlab code used to generate figures and results so readers can reproduce data and modify code to analyse the impact of changes. This allows the principles to be studied whilst discovering potential difficulties and side effects. Aimed at graduate students and researchers, the book provides all information and tools necessary to gain a comprehensive understanding of this interdisciplinary subject.

Originally published in 1941, this book seeks to inform the scientific community of the possible uses of photography in research or teaching. Lawrence gives an account of the possibilities and limitations of the medium for the scientific reader as well as for the 'serious amateur', explains the various mechanisms of the camera and gives some suggestions for scientific applications, such as high-speed photography. This book will be of value to anyone with an interest in photography or the history of science.

Written for animal researchers, this book provides a comprehensive guide to the design and statistical analysis of animal experiments. It has long been recognised that the proper implementation of these techniques helps reduce the number of animals needed. By using real-life examples to make them more accessible, this book explains the statistical tools employed by practitioners. A wide range of design types are considered, including block, factorial, nested, cross-over, dose-escalation and repeated measures and techniques are introduced to analyse the experimental data generated. Each analysis technique is described in non-mathematical terms, helping readers without a statistical background to understand key techniques such as t-tests, ANOVA, repeated measures, analysis of covariance, multiple comparison tests, non-parametric and survival analysis. This is also the first text to describe technical aspects of InVivoStat, a powerful open-source software package developed by the authors to enable animal researchers to analyse their data and obtain informative results.

The use of thermal and calorimetric methods has shown rapid growth over the past few decades, in an increasingly wide range of applications. The original text was published in 2001; since then there have been significant advances in various analytical techniques and their applications. This second edition supplies an up to date, concise and readable account of the principles, experimental apparatus and practical procedures used in thermal analysis and calorimetric methods of analysis. Written by experts in their field, brief accounts of the basic theory are reinforced with detailed technical advances and contemporary developments. Where appropriate, applications are used to highlight particular operating principles or methods of interpretation. As an important source of information for many levels of readership in a variety of areas, this book will be an aid for students and lecturers through to industrial and laboratory staff and consultants.

Proceedings of a Seminar in the CEC Programme of the Coordination of Research on Plant Protein Improvement, held in Gembloux, Belgium, Sept. 3-5, 1985

This book was first published in 2006. The standard model brings together two theories of particle physics in order to describe the interactions of subatomic particles, except those due to gravity. This book uses the standard model as a vehicle for introducing quantum field theory. In doing this the book also introduces much of the phenomenology on which this model is based. The book uses a modern approach, emphasizing effective field theory techniques, and contains brief discussions of some of the main proposals for going beyond the standard model, such as seesaw neutrino masses, supersymmetry, and grand unification. Requiring only a minimum of background material, this book is ideal for graduate students in theoretical and experimental particle physics. It concentrates on getting students to the level of being able to use this theory by doing real calculations with the minimum of formal development, and contains several problems.

This volume contains the proceedings of the Eighth Conference on Vacuum Microbalance Techniques held at Wakefield, Massachusetts on June 12 and 13, 1969. The tenth anniversary of the first confer ence will be registered as this volume passes through the typeset ting and proofreading stages. The eight volumes that have spawned from this continuing series of conferences now contain a total of 125 papers. Thus, these volumes serve as a major repository of the world's literature on vacuum microbalance techniques. The Ninth and Tenth Conferences will be held in West Germany in June 1970 and in Texas in 1971. Each of the eight meetings has served as a forum where new developments in this rapidly advancing field can be presented and discussed constructively within a conference atmosphere of cordial informality. The interaction of the participants at the conferences has led to the first treatise on ultra mlcrogravtmetry;' edited by S. P. Wolsky and E. J. Zdanuk, with most of the fourteen chapters written by steady contributors to the volumes on Vacuum Micro balance Techniques. The number of research investigations and published works in which a vacuum microbalance is utilized con tinues to expandr apldly. f This is a direct result of several types of automatic recording balances that are now available commercial ly. 3 The Eighth Conference was held to bring together again re search scientists and engineers who exploit the measurement of mass as a means of studying physical and chemical phenomena.

Earlier efforts in the field of thermal analysis were concerned with the demonstration of the applicability of techniques to a broad spectrum of materials and to establish the relationship of such techniques with other more accepted methods. While such efforts will and should continue, the Third International Conference was unique in that the first standards were disclosed for differential thermal analysis. This was the culmination of the international, cooperative effort of the ICTA's Standardization Committee. The standards currently are available from the United State's National Bureau of Standards. Thus, thermal analysis can be considered to have attained its majority. Reali zation of full maturity can be expected in the near future. Inclusion of plenary lectures in these volumes represents a significant departure from previous Conferences. This change is the result of the ICTA's recognition of its educational responsibilities. In the Foreword of the Proceedings of the Second International Confer ence, Professor L. Berg expressed the hope that thermal methods of analysis would find wider application in science and technology. The citation above, together with the papers presented, indicate the fulfillment of this hope. Xerox Corporation C. B. Murphy Rochester, N.Y., U.S.A. President, ICTA 1968-1971 X Ill PREFACE For the past two decades thermoanalytical methods have reached a stage of considerable importance, which is particularly due to the developments in the area of instrumentation."

Organic Synthesis: State of the Art 2011-2013 is a convenient, concise reference that summarizes the most important current developments in organic synthesis, from functional group transformations to complex natural product synthesis. The fifth volume in the esteemed State of the Art series, the book compiles two years' worth of Douglass Taber's popular weekly column Organic Chemistry Highlights. The series is an invaluable resource, leading chemists quickly and easily to the most significant developments in the field. The book is logically divided into two sections: the first section focuses on specific topics in organic synthesis, such as C-N Ring Construction and Carbon-Carbon Bond Formation. Each topic is presented using the most significant publications within those areas of research. The journal references are included in the text. The second section focuses on benchmark total syntheses, with an analysis of the strategy for each, and discussions of pivotal transformations. Synthetic organic chemistry is a complex and rapidly growing field, with additional new journals appearing almost every year. Staying abreast of recent research is a daunting undertaking. This book is an ideal tool for both practicing chemists and students, offering a rich source of information and suggesting fruitful pathways for future investigation.

This immensely practical guide to PIV provides a condensed, yet exhaustive guide to most of the information needed for experiments employing the technique. This second edition has updated chapters on the principles and extra information on microscopic, high-speed and three component measurements as well as a description of advanced evaluation techniques. What's more, the huge increase in the range of possible applications has been taken into account as the chapter describing these applications of the PIV technique has been expanded.

Thomas Hankins and Robert Silverman investigate an array of instruments from the seventeenth through the nineteenth century that seem at first to be marginal to science--magnetic clocks that were said to operate by the movements of sunflower seeds, magic lanterns, ocular harpsichords (machines that played different colored lights in harmonious mixtures), Aeolian harps (a form of wind chime), and other instruments of "natural magic" designed to produce wondrous effects. By looking at these and the first recording instruments, the stereoscope, and speaking machines, the authors show that "scientific instruments" first made their appearance as devices used to evoke wonder in the beholder, as in works of magic and the theater.

The authors also demonstrate that these instruments, even though they were often "tricks," were seen by their inventors as more than trickery. In the view of Athanasius Kircher, for instance, the sunflower clock was not merely a hoax, but an effort to demonstrate, however fraudulently, his truly held belief that the ability of a flower to follow the sun was due to the same cosmic magnetic influence as that which moved the planets and caused the rotation of the earth. The marvels revealed in this work raise and answer questions about the connections between natural science and natural magic, the meaning of demonstration, the role of language and the senses in science, and the connections among art, music, literature, and natural science.

Originally published in 1999.

The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These paperback editions preserve the original texts of these important books while presenting them in durable paperback editions. The goal of the Princeton Legacy Library is to vastly increase access to the rich scholarly heritage found in the thousands of books published by Princeton University Press since its founding in 1905.

Passive acoustic monitoring is increasingly used by the scientific community to study, survey and census marine mammals, especially cetaceans, many of which are easier to hear than to see. PAM is also used to support efforts to mitigate potential negative effects of human activities such as ship traffic, military and civilian sonar and offshore exploration. Walter Zimmer provides an integrated approach to PAM, combining physical principles, discussion of technical tools and application-oriented concepts of operations. Additionally, relevant information and tools necessary to assess existing and future PAM systems are presented, with Matlab code used to generate figures and results so readers can reproduce data and modify code to analyse the impact of changes. This allows the principles to be studied whilst discovering potential difficulties and side effects. Aimed at graduate students and researchers, the book provides all information and tools necessary to gain a comprehensive understanding of this interdisciplinary subject.

In addition to the traditional cytogenetics still used as the basic methodology for everyday clinical diagnosis, new molecular cytogenetic techniques provide a useful basis for routine diagnosis. Flourescence in situ hybridization (FISH) has become a standard technique, and comparative genomic hybridization (CGH), spectral karyotyping (SKY), and multi-color FISH have shown their potential for diagnostic purposes. Following a section on tissue culture, chromosome staining and basic information about karyotyping, nomenclature and quality standards, protocols of relevance for comprehensive cytogenetic diagnostics are presented.