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Author: Alexander Heinecke
Publisher: Springer
ISBN: 3319171488
Category : Computers
Languages : en
Pages : 83
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Book Description
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.
Author: Alexander Heinecke
Publisher: Springer
ISBN: 3319171488
Category : Computers
Languages : en
Pages : 83
Get Book Here
Book Description
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.
Author: Berni J. Alder
Publisher: Academic Press
ISBN: 1483266982
Category : Computers
Languages : en
Pages : 294
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Book Description
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.
Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
ISBN: 0309467527
Category : Computers
Languages : en
Pages : 24
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Book Description
This report describes the work of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Eighth 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 five 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 eighth 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, Eighth Round is the 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.
Author: Stefano Markidis
Publisher: Springer
ISBN: 3319159763
Category : Computers
Languages : en
Pages : 154
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Book Description
This volume contains the thoroughly refereed post-conference proceedings of the Second International Conference on Exascale Applications and Software, EASC 2014, held in Stockholm, Sweden, in April 2014. The 6 full papers presented together with 6 short papers were carefully reviewed and selected from 17 submissions. They are organized in two topical sections named: toward exascale scientific applications and development environment for exascale applications.
Author: Ivan Dimov
Publisher: Springer Nature
ISBN: 3030553477
Category : Technology & Engineering
Languages : en
Pages : 472
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Book Description
Every day we need to solve large problems for which supercomputers are needed. High performance computing (HPC) is a paradigm that allows to efficiently implement large-scale computational tasks on powerful supercomputers unthinkable without optimization. We try to minimize our effort and to maximize the achieved profit. Many challenging real world problems arising in engineering, economics, medicine and other areas can be formulated as large-scale computational tasks. The volume is a comprehensive collection of extended contributions from the High performance computing conference held in Borovets, Bulgaria, September 2019. This book presents recent advances in high performance computing. The topics of interest included into this volume are: HP software tools, Parallel Algorithms and Scalability, HPC in Big Data analytics, Modelling, Simulation & Optimization in a Data Rich Environment, Advanced numerical methods for HPC, Hybrid parallel or distributed algorithms. The volume is focused on important large-scale applications like Environmental and Climate Modeling, Computational Chemistry and Heuristic Algorithms.
Author: David A. Bader
Publisher: CRC Press
ISBN: 1584889101
Category : Computers
Languages : en
Pages : 584
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Book Description
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 vis
Author: W.F. van Gunsteren
Publisher: Springer Science & Business Media
ISBN: 9789072199256
Category : Science
Languages : en
Pages : 664
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Book Description
This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: simulation methodology the treatment of electrostatics protein structure refinement the combined experimental and theoretical approaches to the study of very large biological systems applications and methodology involved in the study of protein folding applications and methodology associated with structure-based design.
Author: Vladimir Voevodin
Publisher: Springer Nature
ISBN: 303122941X
Category : Computers
Languages : en
Pages : 713
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Book Description
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.
Author: Björn Engquist
Publisher: Springer
ISBN: 9783662528723
Category : Mathematics
Languages : en
Pages : 0
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Book Description
EACM is a comprehensive reference work covering the vast field of applied and computational mathematics. Applied mathematics itself accounts for at least 60 per cent of mathematics, and the emphasis on computation reflects the current and constantly growing importance of computational methods in all areas of applications. EACM emphasizes the strong links of applied mathematics with major areas of science, such as physics, chemistry, biology, and computer science, as well as specific fields like atmospheric ocean science. In addition, the mathematical input to modern engineering and technology form another core component of EACM.
Author: Roman Trobec
Publisher: Springer Science & Business Media
ISBN: 1848824092
Category : Computers
Languages : en
Pages : 531
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Book Description
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.
