Supercomputing For Molecular Dynamics Simulations
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Supercomputing For Molecular Dynamics Simulations
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Author : Alexander Heinecke
language : en
Publisher: Springer
Release Date : 2015-03-30
Supercomputing For Molecular Dynamics Simulations written by Alexander Heinecke and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-03-30 with Computers categories.
This work presents modern implementations of relevant molecular dynamics algorithms using ls1 mardyn, a simulation program for engineering applications. The text focuses strictly on HPC-related aspects, covering implementation on HPC architectures, taking Intel Xeon and Intel Xeon Phi clusters as representatives of current platforms. The work describes distributed and shared-memory parallelization on these platforms, including load balancing, with a particular focus on the efficient implementation of the compute kernels. The text also discusses the software-architecture of the resulting code.
Special Purpose Computers
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Author : Berni J. Alder
language : en
Publisher: Academic Press
Release Date : 2014-05-10
Special Purpose Computers written by Berni J. Alder and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-05-10 with Computers categories.
Special Purpose Computers describes special-purpose computers and compares them to general-purpose computers in terms of speed and cost. Examples of computers that were designed for the efficient solution of long established algorithms are given, including Navier-Stokes hydrodynamic solvers, classical molecular dynamic machines, and Ising model computers. Comprised of seven chapters, this volume begins by documenting the progress of the CalTech Concurrent Computation Program and its evolution from computational high-energy physics to a supercomputer initiative, with emphasis on the lessons learned including computer architecture issues and the trade-offs between in-house and commercial development. The reader is then introduced to the QCD Machine, a special-purpose parallel supercomputer that was designed and built to solve the lattice quantum chromodynamics problem. Subsequent chapters focus on the Geometry-Defining Processors and their application to the solution of partial differential equations; the Navier-Stokes computer; parallel processing using the Loosely Coupled Array of Processors (LCAP) system; and the Delft Ising system processor. The design and implementation of the Delft molecular-dynamics processor are also described. This book will be of interest to computer engineers and designers.
Supercomputing
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Author : Vladimir Voevodin
language : en
Publisher: Springer Nature
Release Date : 2022-12-15
Supercomputing written by Vladimir Voevodin and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-12-15 with Computers categories.
This book constitutes the refereed proceedings of the 8th Russian Supercomputing Days on Supercomputing, RuSCDays 2022, which took place in Moscow, Russia, in September 2022. The 49 full papers and 1 short paper presented in this volume were carefully reviewed and selected from 94 submissions. The papers are organized in the following topical sections: Supercomputer Simulation; HPC, BigData, AI: Architectures, Technologies, Tools; Distributed and Cloud Computing.
Computer Simulation Of Biomolecular Systems
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Author : W.F. van Gunsteren
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-11-27
Computer Simulation Of Biomolecular Systems written by W.F. van Gunsteren and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-11-27 with Technology & Engineering categories.
The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...
Supercomputing
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Author : Julian M. Kunkel
language : en
Publisher: Springer
Release Date : 2013-06-12
Supercomputing written by Julian M. Kunkel and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-06-12 with Computers categories.
This book constitutes the refereed proceedings of the 28th International Supercomputing Conference, ISC 2013, held in Leipzig, Germany, in June 2013. The 35 revised full papers presented together were carefully reviewed and selected from 89 submissions. The papers cover the following topics: scalable applications with 50K+ cores; performance improvements in algorithms; accelerators; performance analysis and optimization; library development; administration and management of supercomputers; energy efficiency; parallel I/O; grid and cloud.
Report Of The Committee On Proposal Evaluation For Allocation Of Supercomputing Time For The Study Of Molecular Dynamics
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Author : National Research Council
language : en
Publisher: National Academies Press
Release Date : 2013-09-25
Report Of The Committee On Proposal Evaluation For Allocation Of Supercomputing Time For The Study Of Molecular Dynamics written by National Research Council and has been published by National Academies Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-09-25 with Science categories.
This letter report evaluates proposals for allocation of time to the non-commercial research community on Anton, a supercomputer specially designed and built by D.E. Shaw Research (DESRES) that allows for dramatically increased molecular dynamics simulations compared to other currently available resources. Over the past three years (October 1, 2010 ââ'¬" September 30, 2013), DESRES has made available to the non-commercial research community node-hours on an Anton system housed at the Pittsburgh Supercomputing Center (PSC), based on the advice of previous National Research Council committees convened in 2010, 2011, and 2012.
Molecular Dynamics Simulation
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Author : J. M. Haile
language : en
Publisher: Wiley-Interscience
Release Date : 1992-06-05
Molecular Dynamics Simulation written by J. M. Haile and has been published by Wiley-Interscience this book supported file pdf, txt, epub, kindle and other format this book has been release on 1992-06-05 with Technology & Engineering categories.
"Provides a lot of reading pleasure and many new insights." -Journal of Molecular Structure "This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." -Contemporary Physics "A very useful introduction . . . more interesting to read than the often dry equation-based texts." -Journal of the American Chemical Society Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics. Stresses easy-to-use molecules * Provides sample calculations and figures * Includes four complete FORTRAN codes
Supercomputing
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Author : Toshiko Matsuda
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
Supercomputing written by Toshiko Matsuda and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-06 with Computers categories.
As the technology of Supercomputing processes, methodologies for approaching problems have also been developed. The main object of this symposium was the interdisciplinary participation of experts in related fields and passionate discussion to work toward the solution of problems. An executive committee especially arranged for this symposium selected speakers and other participants who submitted papers which are included in this volume. Also included are selected extracts from the two sessions of panel discussion, the "Needs and Seeds of Supercomputing", and "The Future of Supercomputing", which arose during a wide-ranging exchange of viewpoints.
Report Of The Committee On Proposal Evaluation For Allocation Of Supercomputing Time For The Study Of Molecular Dynamics
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Author : National Academies of Sciences, Engineering, and Medicine
language : en
Publisher: National Academies Press
Release Date : 2018-10-18
Report Of The Committee On Proposal Evaluation For Allocation Of Supercomputing Time For The Study Of Molecular Dynamics written by National Academies of Sciences, Engineering, and Medicine and has been published by National Academies Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-10-18 with Computers categories.
This report describes the work of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Ninth Round. The committee evaluated submissions received in response to a Request for Proposals (RFP) for biomolecular simulation time on Anton 2, a supercomputer specially designed and built by D.E. Shaw Research (DESRES). Over the past 8 years, DESRES has made an Anton or Anton 2 system housed at the Pittsburgh Supercomputing Center (PSC) available to the non-commercial research community, based on the advice of previous National Research Council committees. As in prior rounds, the goal of the ninth RFP for simulation time on Anton 2 is to continue to facilitate breakthrough research in the study of biomolecular systems by providing a massively parallel system specially designed for molecular dynamics simulations. The program seeks to continue to support research that addresses important and high impact questions demonstrating a clear need for Anton's special capabilities. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Ninth Round is the final report of the committee's evaluation of proposals based on scientific merit, justification for requested time allocation, and investigator qualifications and past accomplishments. This report identifies the proposals that best met the selection criteria.
Parallel Computing
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Author : Roman Trobec
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-06-18
Parallel Computing written by Roman Trobec and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-06-18 with Computers categories.
The use of parallel programming and architectures is essential for simulating and solving problems in modern computational practice. There has been rapid progress in microprocessor architecture, interconnection technology and software devel- ment, which are in?uencing directly the rapid growth of parallel and distributed computing. However, in order to make these bene?ts usable in practice, this dev- opment must be accompanied by progress in the design, analysis and application aspects of parallel algorithms. In particular, new approaches from parallel num- ics are important for solving complex computational problems on parallel and/or distributed systems. The contributions to this book are focused on topics most concerned in the trends of today’s parallel computing. These range from parallel algorithmics, progr- ming, tools, network computing to future parallel computing. Particular attention is paid to parallel numerics: linear algebra, differential equations, numerical integ- tion, number theory and their applications in computer simulations, which together form the kernel of the monograph. We expect that the book will be of interest to scientists working on parallel computing, doctoral students, teachers, engineers and mathematicians dealing with numerical applications and computer simulations of natural phenomena.