Varying the s in Your s-step GMRES

International audienceKrylov subspace methods are commonly used iterative methods for solving large sparse linear systems, however they suffer from communication bottlenecks on parallel computers.Therefore, $s$-step methods have been developed where the Krylov subspace is built block by block, so that $s$ matrix-vector multiplications can be done before orthonormalizing the block. Then Communication-Avoiding algorithms can be used for both kernels.This paper introduces a new variation on $s$-step GMRES in order to reduce the number of iterations necessary to ensure convergence, with a small overhead in the number of communications. Namely, we develop a $s$-step GMRES algorithm, where the block size is variable and increases gradually. Our numerical experiments show a good agreement with our analysis of condition numbers and demonstrate the efficiency of our variable $s$-step approach

An Efficient Numerical Method for Simulating Electrochemically Driven Enzymatic Reactions

We consider systems in which electroactive enzymes are immobilised on an electrode surface through physical adsorption or covalent attachment on an electrode surface and substrate(s), product(s) and inhibitor(s) are present in the bulk solution. We solve the governing equations numerically by fully implicit finite differences (FIFD). Our numerical method relies on the formation of a sparse matrix from matrix blocks, which we call the kinetic block, containing kinetic terms for the enzyme reactions, and mass transport block(s) which contain the terms for the mass transport of substrate(s), product(s) and inhibitor(s). The resultant non-linear sparse matrix equation is solved using the sparse matrix solver in the MATHEMATICA kernel which in turn uses UMFPACK multifrontal direct solver methods and Krylov iterative methods preconditioned by an incomplete LU factorization. Due to the non-linear nature of the problem the solution is iterated at each time step until the desired degree of precision is obtained. Adaptation to a variety of mechanisms is performed by changing the terms in the kinetic block and the boundary conditions in the mass transport blocks. Adaptation to a number of different voltammetric methods is achieved by changing one or two lines of code describing the how applied potential changes with time

A block Krylov subspace time-exact solution method for linear ODE systems

We propose a time-exact Krylov-subspace-based method for solving linear ODE (ordinary differential equation) systems of the form $y'=-Ay + g(t)$ and $y''=-Ay + g(t)$, where $y(t)$ is the unknown function. The method consists of two stages. The first stage is an accurate piecewise polynomial approximation of the source term $g(t)$, constructed with the help of the truncated SVD (singular value decomposition). The second stage is a special residual-based block Krylov subspace method. The accuracy of the method is only restricted by the accuracy of the piecewise polynomial approximation and by the error of the block Krylov process. Since both errors can, in principle, be made arbitrarily small, this yields, at some costs, a time-exact method. Numerical experiments are presented to demonstrate efficiency of the new method, as compared to an exponential time integrator with Krylov subspace matrix function evaluations

A global method for coupling transport with chemistry in heterogeneous porous media

Modeling reactive transport in porous media, using a local chemical equilibrium assumption, leads to a system of advection-diffusion PDE's coupled with algebraic equations. When solving this coupled system, the algebraic equations have to be solved at each grid point for each chemical species and at each time step. This leads to a coupled non-linear system. In this paper a global solution approach that enables to keep the software codes for transport and chemistry distinct is proposed. The method applies the Newton-Krylov framework to the formulation for reactive transport used in operator splitting. The method is formulated in terms of total mobile and total fixed concentrations and uses the chemical solver as a black box, as it only requires that on be able to solve chemical equilibrium problems (and compute derivatives), without having to know the solution method. An additional advantage of the Newton-Krylov method is that the Jacobian is only needed as an operator in a Jacobian matrix times vector product. The proposed method is tested on the MoMaS reactive transport benchmark.Comment: Computational Geosciences (2009) http://www.springerlink.com/content/933p55085742m203/?p=db14bb8c399b49979ba8389a3cae1b0f&pi=1

Composing Scalable Nonlinear Algebraic Solvers

Most efficient linear solvers use composable algorithmic components, with the most common model being the combination of a Krylov accelerator and one or more preconditioners. A similar set of concepts may be used for nonlinear algebraic systems, where nonlinear composition of different nonlinear solvers may significantly improve the time to solution. We describe the basic concepts of nonlinear composition and preconditioning and present a number of solvers applicable to nonlinear partial differential equations. We have developed a software framework in order to easily explore the possible combinations of solvers. We show that the performance gains from using composed solvers can be substantial compared with gains from standard Newton-Krylov methods.Comment: 29 pages, 14 figures, 13 table