Streamlining Development of a Multimillion-Line Computational Chemistry Code

被引：4

作者：

Betz, Robin M. ^{[1
]}

Walker, Ross C. ^{[2
]}

机构：

[1] San Diego Supercomp Ctr, Walker Mol Dynam Lab, La Jolla, CA 92093 USA

[2] San Diego Supercomp Ctr, Walker Mol Dynam Lab, La Jolla, CA USA

来源：

COMPUTING IN SCIENCE & ENGINEERING | 2014年 / 16卷 / 03期

基金：

美国国家科学基金会;

关键词：

AMBER;

D O I：

10.1109/MCSE.2014.9

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

Software engineering methodologies can be helpful in computational science and engineering projects. Here, a continuous integration software engineering strategy is applied to a multimillion-line molecular dynamics code; the implementation both streamlines the development and release process and unifies a team of widely distributed, academic developers.

引用

页码：10 / 17

页数：8

共 10 条

[1] OpenMP: An industry standard API for shared-memory programming [J].

Dagum, L ;

Menon, R .

IEEE COMPUTATIONAL SCIENCE & ENGINEERING, 1998, 5 (01) :46-55

[2]

Duvall P., 2007, Continuous Integration: Improving software quality and reducing risk

[3]

Fowler M., 2006, THOUGHT WORKS

[4] GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation [J].

Hess, Berk ;

Kutzner, Carsten ;

van der Spoel, David ;

Lindahl, Erik .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (03) :435-447

[5]

Humble J., 2010, Continuous Delivery: Reliable Software Releases through Build, Test, and Deployment Automation

[6]

Nvidia, 2007, COMP UN DEV ARCH PRO

[7] Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald [J].

Salomon-Ferrer, Romelia ;

Goetz, Andreas W. ;

Poole, Duncan ;

Le Grand, Scott ;

Walker, Ross C. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9 (09) :3878-3888

[8] An overview of the Amber biomolecular simulation package [J].

Salomon-Ferrer, Romelia ;

Case, David A. ;

Walker, Ross C. .

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2013, 3 (02) :198-210

[9]

Snir M., 1995, MPI: The Complete Reference

[10] AMBER - ASSISTED MODEL-BUILDING WITH ENERGY REFINEMENT - A GENERAL PROGRAM FOR MODELING MOLECULES AND THEIR INTERACTIONS [J].

WEINER, PK ;

KOLLMAN, PA .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1981, 2 (03) :287-303

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