This book is a tutorial written by researchers and developers behind the FEniCS Project and explores an advanced, expressive approach to the development of mathematical software. The presentation spans mathematical background, software design and the use of FEniCS in applications. Theoretical aspects are complemented with computer code which is available as free/open source software. The book begins with a special introductory tutorial for beginners. Followingare chapters in Part I addressing fundamental aspects of the approach to automating the creation of finite element solvers. Chapters in Part II address the design and implementation of the FEnicS software. Chapters in Part III present the application of FEniCS to a wide range of applications, including fluid flow, solid mechanics, electromagnetics and geophysics.

Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book

In recent years, the SUite of Nonlinear and DIfferential/ALgebraic equation Solvers (SUNDIALS) has been redesigned to better enable the use of application-specific and third-party algebraic solvers and data structures. Throughout this work, we have adhered to specific guiding principles that minimized the impact to current users while providing maximum flexibility for later evolution of solvers and data structures. The redesign was done through creation of new classes for linear and nonlinear solvers, enhancements to the vector class, and the creation of modern Fortran interfaces that leverage interoperability features of the Fortran 2003 standard. The vast majority of this work has been performed "behind-the-scenes," with minimal changes to the user interface and no reduction in solver capabilities or performance. However, these changes now allow advanced users to create highly customized solvers that exploit their problem structure, enabling SUNDIALS use on extreme-scale, heterogeneous computational architectures.

Enabling New Flexibility in the SUNDIALS Suite of Nonlinear and Differential/Algebraic Equation Solvers.

http://www.mathcs.emory.edu/%7Ebenzi/Web_papers/survey.pdf

Preconditioning techniques for large linear systems: a survey

hypre is a software library for the solution of large, sparse linear systems on massively parallel computers. Its emphasis is on modern powerful and scalable preconditioners. hypre provides various conceptual interfaces to enable application users to access the library in the way they naturally think about their problems. This paper presents the conceptual interfaces in hypre. An overview of the preconditioners that are available in hypre is given, including some numerical results that show the efficiency of the library.

/pdf/hypre-a-library-of-high-performance-preconditioners-142t82tfp6.pdf

hypre: A Library of High Performance Preconditioners

https://ctflab.mae.cornell.edu/papers/Desjardins%20et%20al..%202008.%20High%20order%20conservative%20finite%20difference%20scheme%20for%20variable%20density%20low%20Mach%20number%20turbulent%20flows.pdf

High order conservative finite difference scheme for variable density low Mach number turbulent flows

BoomerAMG: a parallel algebraic multigrid solver and preconditioner

The hypre software library provides high performance preconditioners and solvers for the solution of large, sparse linear systems on massively parallel computers. One of its attractive features is the provision of conceptual interfaces. These interfaces give application users a more natural means for describing their linear systems, and provide access to methods such as geometric multigrid which require additional information beyond just the matrix. This chapter discusses the design of the conceptual interfaces in hypre and illustrates their use with various examples. We discuss the data structures and parallel implementation of these interfaces. A brief overview of the solvers and preconditioners available through the interfaces is also given.

/pdf/the-design-and-implementation-of-hypre-a-library-of-parallel-35ol472pjh.pdf

The Design and Implementation of hypre, a Library of Parallel High Performance Preconditioners

Algebraic multigrid (AMG) is a very efficient iterative solver and preconditioner for large unstructured sparse linear systems. Traditional coarsening schemes for AMG can, however, lead to computational complexity growth as problem size increases, resulting in increased memory use and execution time, and diminished scalability. Two new parallel AMG coarsening schemes are proposed that are based solely on enforcing a maximum independent set property, resulting in sparser coarse grids. The new coarsening techniques remedy memory and execution time complexity growth for various large three-dimensional (3D) problems. If used within AMG as a preconditioner for Krylov subspace methods, the resulting iterative methods tend to converge fast. This paper discusses complexity issues that can arise in AMG, describes the new coarsening schemes, and examines the performance of the new preconditioners for various large 3D problems.

/pdf/reducing-complexity-in-parallel-algebraic-multigrid-169qb3bpxs.pdf

Reducing Complexity in Parallel Algebraic Multigrid Preconditioners

This paper investigates the properties of smoothers in the context of algebraic multigrid (AMG) running on parallel computers with potentially millions of processors. The development of multigrid smoothers in this case is challenging, because some of the best relaxation schemes, such as the Gauss-Seidel (GS) algorithm, are inherently sequential. Based on the sharp two-grid multigrid theory from [R. D. Falgout and P. S. Vassilevski, SIAM J. Numer. Anal., 42 (2004), pp. 1669-1693] and [R. D. Falgout, P. S. Vassilevski, and L. T. Zikatanov, Numer. Linear Algebra Appl., 12 (2005), pp. 471-494] we characterize the smoothing properties of a number of practical candidates for parallel smoothers, including several $C$-$F$, polynomial, and hybrid schemes. We show, in particular, that the popular hybrid GS algorithm has multigrid smoothing properties which are independent of the number of processors in many practical applications, provided that the problem size per processor is large enough. This is encouraging news for the scalability of AMG on ultraparallel computers. We also introduce the more robust $\ell_1$ smoothers, which are always convergent and have already proven essential for the parallel solution of some electromagnetic problems [T. Kolev and P. Vassilevski, J. Comput. Math., 27 (2009), pp. 604-623].

/pdf/multigrid-smoothers-for-ultraparallel-computing-2zk7c7gm2s.pdf

Ulrike Meier Yang

Papers

hypre: A Library of High Performance Preconditioners

BoomerAMG: a parallel algebraic multigrid solver and preconditioner

The Design and Implementation of hypre, a Library of Parallel High Performance Preconditioners

Reducing Complexity in Parallel Algebraic Multigrid Preconditioners

Multigrid Smoothers for Ultraparallel Computing