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Massively parallel

About: Massively parallel is a research topic. Over the lifetime, 10562 publications have been published within this topic receiving 225877 citations. The topic is also known as: massively parallel processor & passively parallel processing.


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Journal ArticleDOI
TL;DR: A range of new simulation algorithms and features developed during the past 4 years are presented, leading up to the GROMACS 4.5 software package, which provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
Abstract: Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. Availability: GROMACS is an open source and free software available from http://www.gromacs.org. Contact: erik.lindahl@scilifelab.se Supplementary information:Supplementary data are available at Bioinformatics online.

6,029 citations

Journal ArticleDOI
TL;DR: The main purpose is to update the designers and users of parallel numerical algorithms with the latest research in the field and present the novel ideas, results and work in progress and advancing state-of-the-art techniques in the area of parallel and distributed computing for numerical and computational optimization problems in scientific and engineering application.
Abstract: Edited by Tianruo Yang Kluwer Academic Publisher, Dordrech, Netherlands, 1999, 248 pp. ISBN 0-7923-8588-8, $135.00 This book contains a selection of contributed and invited papers presented and the workshop Frontiers of Parallel Numerical Computations and Applications, in the IEEE 7th Symposium on the Frontiers on Massively Parallel Computers (Frontiers '99) at Annapolis, Maryland, February 20-25, 1999. Its main purpose is to update the designers and users of parallel numerical algorithms with the latest research in the field. A broad spectrum of topics on parallel numerical computations, with applications to some of the more challenging engineering problems, is covered. Parallel algorithm designers and engineers who use extensively parallel numerical computations, as well as graduate students in Computer Science, Scientific Computing, various engineering fields and applied mathematics should benefit from reading it. The first part is addressed to a larger audience and presents papers on parallel numerical algorithms. Two new libraries are presented: PSPASSES and PoLAPACK. PSPASSES is a collection of parallel direct solvers, for sparse symmetric positive definite linear systems, which are characterized by high performance and good scalability. PoLAPACK library contains LU and QR codes based on a new blocking strategy that guarantees good performance regardless of the physical block size. Next, an efficient approach to solving stiff ordinary differential equations by diagonal implicitly iterated Runge-Kutta (DIIRK) method is described. DIIRK renders a fast parallel implementation due to a reduced number of function evaluation and an automatic stepsize control mechanism. Finally, minimization of sufficiently smooth non-linear functionals is sought via parallel space decomposition. Here, a theoretical background of the problem and two equivalent algorithms are presented. New research directions for classical solvers are treated in the next three papers: first, reduction of the global synchronization in the biconjugate gradient method, second, a new more efficient Jacobi ordering for the multiple-port hypercubes, and finally, an analysis of the theoretical performance of an improved version of the Quasi-minimal residual method. Parallel numerical applications constitute the second part of the book, with results from fluid mechanics, material sciences, applications to signal and image processing, dynamic systems, semiconductor technology and electronic circuits and systems design. With one exception, the authors expose in detail parallel implementations of the algorithms and numerical results. First, a 3D-elasticity problem is solved using an additive overlapping domain decomposition algorithm. Second, an overlapping mesh technique is used in a parallel solver for the compressible flow problem. Then, a parallel version of a complex numerical algorithm to solve a lubrication problem studied in tribology is introduced. Next, a timid approach to parallel computing of the cavity flow by the finite element method is presented. The problem solved is rather small for today's needs and only up to 6 processors are used. This is also the only paper that does not present results from numerical experiments. The remaining applications discussed in the subsequent chapters are: large scale multidisciplinary design optimization problem with application to the design of a supersonic commercial aircraft, a report on progress in parallel solution of an electromagnetic scattering problem using boundary integral methods and an optimal solution to the convection-diffusion equation modeling the concentration of a pollutant in the air. The book is of definite interest to readers who keep up-to-date with the parallel numerical computation research. The main purpose, to present the novel ideas, results and work in progress and advancing state-of-the-art techniques in the area of parallel and distributed computing for numerical and computational optimization problems in scientific and engineering application is clearly achieved. However, due to its content it cannot serve as a textbook for a computer science or engineering class. Overall, is a reference type book to be kept by specialists and in a library rather than a book to be purchased for self-introduction to the field. Most of the papers presented are results of ongoing research and so they rely heavily on previous results. On the other hand, with only one exception, the results presented in the papers are a great source of information for the researchers currently involved in the field. Michelle Pal, Los Alamos National Laboratory

4,696 citations

Journal ArticleDOI
TL;DR: A general parallel search method is described, based on statistical mechanics, and it is shown how it leads to a general learning rule for modifying the connection strengths so as to incorporate knowledge about a task domain in an efficient way.

3,727 citations

Journal ArticleDOI
TL;DR: The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
Abstract: Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.

2,958 citations

Journal ArticleDOI
TL;DR: It is shown that a class of deterministic lattice gases with discrete Boolean elements simulates the Navier-Stokes equation, anc, and can be used to design simple, massively parallel computing machines.
Abstract: We show that a class of deterministic lattice gases with discrete Boolean elements simulates the Navier-Stokes equation, anc can be used to design simple, massively parallel computing machines.

2,288 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023147
2022302
2021216
2020269
2019319
2018364