Supercomputing for Molecular Dynamics Simulations
Supercomputing for Molecular Dynamics Simulations

Author: Alexander Heinecke

Publisher: Springer

Published: 2015-03-30

Total Pages: 83

ISBN-13: 3319171488

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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
Special Purpose Computers

Author: Berni J. Alder

Publisher: Academic Press

Published: 2014-05-10

Total Pages: 294

ISBN-13: 1483266982

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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.

High Performance Computing - HiPC 2007
High Performance Computing - HiPC 2007

Author: Srinivas Aluru

Publisher: Springer

Published: 2008-01-22

Total Pages: 687

ISBN-13: 3540772200

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This book constitutes the refereed proceedings of the 14th International Conference on High-Performance Computing, HiPC 2007, held in Goa, India, in December 2007. The 53 revised full papers presented together with the abstracts of five keynote talks were carefully reviewed and selected from 253 submissions. The papers are organized in topical sections on a broad range of applications including I/O and FPGAs, and microarchitecture and multiprocessor architecture.

Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics
Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics

Author: National Academies of Sciences, Engineering, and Medicine

Publisher: National Academies Press

Published: 2017-10-27

Total Pages: 24

ISBN-13: 0309467527

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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.

Solving Software Challenges for Exascale
Solving Software Challenges for Exascale

Author: Stefano Markidis

Publisher: Springer

Published: 2015-02-18

Total Pages: 154

ISBN-13: 3319159763

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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.

Advances in High Performance Computing
Advances in High Performance Computing

Author: Ivan Dimov

Publisher: Springer Nature

Published: 2020-08-07

Total Pages: 464

ISBN-13: 3030553477

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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.

Supercomputing
Supercomputing

Author: Vladimir Voevodin

Publisher: Springer Nature

Published: 2022-12-15

Total Pages: 713

ISBN-13: 303122941X

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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.

Petascale Computing
Petascale Computing

Author: David A. Bader

Publisher: CRC Press

Published: 2007-12-22

Total Pages: 584

ISBN-13: 1584889101

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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 vis

Molecular Simulations and Biomembranes
Molecular Simulations and Biomembranes

Author: Mark S P Sansom

Publisher: Royal Society of Chemistry

Published: 2010-08-01

Total Pages: 331

ISBN-13: 1849732159

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The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.

Cardinal Spline Interpolation
Cardinal Spline Interpolation

Author: I. J. Schoenberg

Publisher: SIAM

Published: 1973-01-01

Total Pages: 127

ISBN-13: 089871009X

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In this book the author explains cardinal spline functions, the basic properties of B-splines and exponential Euler splines.