Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Numerical Optimization presents a comprehensive and up-to-date description of the most effective methods in continuous optimization. It responds to the growing interest in optimization in engineering, science, and business by focusing on the methods that are best suited to practical problems. For this new edition the book has been thoroughly updated throughout. There are new chapters on nonlinear interior methods and derivative-free methods for optimization, both of which are used widely in practice and the focus of much current research. Because of the emphasis on practical methods, as well as the extensive illustrations and exercises, the book is accessible to a wide audience. It can be used as a graduate text in engineering, operations research, mathematics, computer science, and business. It also serves as a handbook for researchers and practitioners in the field. The authors have strived to produce a text that is pleasant to read, informative, and rigorous - one that reveals both the beautiful nature of the discipline and its practical side.

Numerical Optimization

SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments.

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SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python

We present a primal-dual interior-point algorithm with a filter line-search method for nonlinear programming. Local and global convergence properties of this method were analyzed in previous work. Here we provide a comprehensive description of the algorithm, including the feasibility restoration phase for the filter method, second-order corrections, and inertia correction of the KKT matrix. Heuristics are also considered that allow faster performance. This method has been implemented in the IPOPT code, which we demonstrate in a detailed numerical study based on 954 problems from the CUTEr test set. An evaluation is made of several line-search options, and a comparison is provided with two state-of-the-art interior-point codes for nonlinear programming.

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On the implementation of an interior-point filter line-search algorithm for large-scale nonlinear programming

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

/pdf/scipy-1-0-fundamental-algorithms-for-scientific-computing-in-45othhotbu.pdf

SciPy 1.0: fundamental algorithms for scientific computing in Python.

Preface 1. Introduction Part I. Preliminaries: 2. Basic Concepts 3. Basic Analysis and Optimality Conditions 4. Basic Linear Algebra 5. Krylov Subspace Methods Part II. Trust-Region Methods for Unconstrained Optimization: 6. Global Convergence of the Basic Algorithm 7.The Trust-Region Subproblem 8. Further Convergence Theory Issues 9. Conditional Models 10. Algorithmic Extensions 11. Nonsmooth Problems Part III. Trust-Region Methods for Constrained Optimization with Convex Constraints: 12. Projection Methods for Convex Constraints 13. Barrier Methods for Inequality Constraints Part IV. Trust-Region Mewthods for General Constained Optimization and Systems of Nonlinear Equations: 14. Penalty-Function Methods 15. Sequential Quadratic Programming Methods 16. Nonlinear Equations and Nonlinear Fitting Part V. Final Considerations: Practicalities Afterword Appendix: A Summary of Assumptions Annotated Bibliography Subject and Notation Index Author Index.

Trust Region Methods

The purpose of this article is to discuss the scope and functionality of a versatile environment for testing small- and large-scale nonlinear optimization algorithms. Although many of these facilities were originally produced by the authors in conjunction with the software package LANCELOT, we believe that they will be useful in their own right and should be available to researchers for their development of optimization software. The tools can be obtained by anonymous ftp from a number of sources and may, in many cases, be installed automatically. The scope of a major collection of test problems written in the standard input format (SIF) used by the LANCELOT software package is described. Recognizing that most software was not written with the SIF in mind, we provide tools to assist in building an interface between this input format and other optimization packages. These tools provide a link between the SIF and a number of existing packages, including MINOS and OSL. Additionally, as each problem includes a specific classification that is designed to be useful in identifying particular classes of problems, facilities are provided to build and manage a database of this information. There is a Unix and C shell bias to many of the descriptions in the article, since, for the sake of simplicity, we do not illustrate everything in its fullest generality. We trust that the majority of potential users are sufficiently familiar with Unix that these examples will not lead to undue confusion.

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CUTE: constrained and unconstrained testing environment

The global and local convergence properties of a class of augmented Lagrangian methods for solving nonlinear programming problems are considered. In such methods, simple bound constraints are treated separately from more general constraints and the stopping rules for the inner minimization algorithm have this in mind. Global convergence is proved, and it is established that a potentially troublesome penalty parameter is bounded away from zero.

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A globally convergent augmented Lagrangian algorithm for optimization with general constraints and simple bounds

This book, which is concerned with algorithms for solving large-scale non-linear optimization problems, is the only complete source of documentation for the software package Lancelot and will mainly be used as a manual in conjunction with the software package. However, it is not only a reference to the input format but also to the underlying algorithms. It is the first publication of this kind for large-scale general non-linear problems. Numerous figures and tables enhance its usefulness to both novices and experts. In addition, it also gives valuable guidance to future designers of related software.

Lancelot: A FORTRAN Package for Large-Scale Nonlinear Optimization (Release A)

The initial release of CUTE, a widely used testing environment for optimization software, was described by Bongartz, et al. [1995]. A new version, now known as CUTEr, is presented. Features include reorganisation of the environment to allow simultaneous multi-platform installation, new tools for, and interfaces to, optimization packages, and a considerably simplified and entirely automated installation procedure for unix systems. The environment is fully backward compatible with its predecessor, and offers support for Fortran 90/95 and a general C/C++ Application Programming Interface. The SIF decoder, formerly a part of CUTE, has become a separate tool, easily callable by various packages. It features simple extensions to the SIF test problem format and the generation of files suited to automatic differentiation packages.

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Nicholas I. M. Gould

Papers

Trust Region Methods

CUTE: constrained and unconstrained testing environment

A globally convergent augmented Lagrangian algorithm for optimization with general constraints and simple bounds

Lancelot: A FORTRAN Package for Large-Scale Nonlinear Optimization (Release A)

CUTEr and SifDec: A constrained and unconstrained testing environment, revisited