Gundolf Haase

Bio: Gundolf Haase is an academic researcher from University of Graz. The author has contributed to research in topics: Multigrid method & Domain decomposition methods. The author has an hindex of 19, co-authored 79 publications receiving 1139 citations. Previous affiliations of Gundolf Haase include Chemnitz University of Technology & Johannes Kepler University of Linz.

Algebraic Multigrid Preconditioner for the Cardiac Bidomain Model

Abstract: The bidomain equations are considered to be one of the most complete descriptions of the electrical activity in cardiac tissue, but large scale simulations, as resulting from discretization of an entire heart, remain a computational challenge due to the elliptic portion of the problem, the part associated with solving the extracellular potential. In such cases, the use of iterative solvers and parallel computing environments are mandatory to make parameter studies feasible. The preconditioned conjugate gradient (PCG) method is a standard choice for this problem. Although robust, its efficiency greatly depends on the choice of preconditioner. On structured grids, it has been demonstrated that a geometric multigrid preconditioner performs significantly better than an incomplete LU (ILU) preconditioner. However, unstructured grids are often preferred to better represent organ boundaries and allow for coarser discretization in the bath far from cardiac surfaces. Under these circumstances, algebraic multigrid (AMG) methods are advantageous since they compute coarser levels directly from the system matrix itself, thus avoiding the complexity of explicitly generating coarser, geometric grids. In this paper, the performance of an AMG preconditioner (BoomerAMG) is compared with that of the standard ILU preconditioner and a direct solver. BoomerAMG is used in two different ways, as a preconditioner and as a standalone solver. Two 3-D simulation examples modeling the induction of arrhythmias in rabbit ventricles were used to measure performance in both sequential and parallel simulations. It is shown that the AMG preconditioner is very well suited for the solution of the bidomain equation, being clearly superior to ILU preconditioning in all regards, with speedups by factors in the range 5.9-7.7

A parallel algebraic multigrid solver on graphics processing units

Abstract: The paper presents a multi-GPU implementation of the preconditioned conjugate gradient algorithm with an algebraic multigrid preconditioner (PCG-AMG) for an elliptic model problem on a 3D unstructured grid. An efficient parallel sparse matrix-vector multiplication scheme underlying the PCG-AMG algorithm is presented for the many-core GPU architecture. A performance comparison of the parallel solver shows that a singe Nvidia Tesla C1060 GPU board delivers the performance of a sixteen node Infiniband cluster and a multi-GPU configuration with eight GPUs is about 100 times faster than a typical server CPU core.

Adaptive Domain Decomposition Methods for Finite and Boundary Element Equations

Abstract: The use of the FEM and BEM in different subdomains of a non-overlapping Domain Decomposition (DD) and their coupling over the coupling boundaries (interfaces) brings about several advantages in many practical applications. The paper presents parallel solvers for large-scaled coupled FE-BE-DD equations approximating linear and nonlinear plane magnetic field problems as well as plane linear elasticity problems. The parallel algorithms presented are of asymptotically optimal, or, at least, almost optimal complexity and of high parallel efficiency.

A Tutorial on Elliptic Pde Solvers and Their Parallelization

Abstract: From the Publisher: This compact yet thorough tutorial is the perfect introduction to the basic concepts of solving partial differential equations (PDEs) using parallel numerical methods. In just eight short chapters, the authors provide readers with enough basic knowledge of PDEs, discretization methods, solution techniques, parallel computers, parallel programming, and the run-time behavior of parallel algorithms to allow them to understand, develop, and implement parallel PDE solvers. Examples throughout the book are intentionally kept simple so that the parallelization strategies are not dominated by technical details. A Tutorial on Elliptic PDE Solvers and Their Parallelization is a valuable aid for learning about the possible errors and bottlenecks in parallel computing. One of the highlights of the tutorial is that the course material can run on a laptop, not just on a parallel computer or cluster of PCs, thus allowing readers to experience their first successes in parallel computing in a relatively short amount of time. This tutorial is intended for advanced undergraduate and graduate students in computational sciences and engineering; however, it may also be helpful to professionals who use PDE-based parallel computer simulations in the field.

The Ensemble Kalman Filter: Theoretical formulation and practical implementation

Abstract: The purpose of this paper is to provide a comprehensive presentation and interpretation of the Ensemble Kalman Filter (EnKF) and its numerical implementation. The EnKF has a large user group, and numerous publications have discussed applications and theoretical aspects of it. This paper reviews the important results from these studies and also presents new ideas and alternative interpretations which further explain the success of the EnKF. In addition to providing the theoretical framework needed for using the EnKF, there is also a focus on the algorithmic formulation and optimal numerical implementation. A program listing is given for some of the key subroutines. The paper also touches upon specific issues such as the use of nonlinear measurements, in situ profiles of temperature and salinity, and data which are available with high frequency in time. An ensemble based optimal interpolation (EnOI) scheme is presented as a cost-effective approach which may serve as an alternative to the EnKF in some applications. A fairly extensive discussion is devoted to the use of time correlated model errors and the estimation of model bias.

Automatic differentiation in machine learning: a survey

Abstract: Derivatives, mostly in the form of gradients and Hessians, are ubiquitous in machine learning. Automatic differentiation (AD), also called algorithmic differentiation or simply "auto-diff", is a family of techniques similar to but more general than backpropagation for efficiently and accurately evaluating derivatives of numeric functions expressed as computer programs. AD is a small but established field with applications in areas including computational uid dynamics, atmospheric sciences, and engineering design optimization. Until very recently, the fields of machine learning and AD have largely been unaware of each other and, in some cases, have independently discovered each other's results. Despite its relevance, general-purpose AD has been missing from the machine learning toolbox, a situation slowly changing with its ongoing adoption under the names "dynamic computational graphs" and "differentiable programming". We survey the intersection of AD and machine learning, cover applications where AD has direct relevance, and address the main implementation techniques. By precisely defining the main differentiation techniques and their interrelationships, we aim to bring clarity to the usage of the terms "autodiff", "automatic differentiation", and "symbolic differentiation" as these are encountered more and more in machine learning settings.