Low-rank updates and a divide-and-conquer method for linear matrix equations

Linear matrix equations, such as the Sylvester and Lyapunov equations, play an important role in various applications, including the stability analysis and dimensionality reduction of linear dynamical control systems and the solution of partial differential equations. In this work, we present and analyze a new algorithm, based on tensorized Krylov subspaces, for quickly updating the solution of such a matrix equation when its coefficients undergo low-rank changes. We demonstrate how our algorithm can be utilized to accelerate the Newton method for solving continuous-time algebraic Riccati equations. Our algorithm also forms the basis of a new divide-and-conquer approach for linear matrix equations with coefficients that feature hierarchical low-rank structure, such as HODLR, HSS, and banded matrices. Numerical experiments demonstrate the advantages of divide-and-conquer over existing approaches, in terms of computational time and memory consumption

TMB: Automatic Differentiation and Laplace Approximation

TMB is an open source R package that enables quick implementation of complex nonlinear random effect (latent variable) models in a manner similar to the established AD Model Builder package (ADMB, admb-project.org). In addition, it offers easy access to parallel computations. The user defines the joint likelihood for the data and the random effects as a C++ template function, while all the other operations are done in R; e.g., reading in the data. The package evaluates and maximizes the Laplace approximation of the marginal likelihood where the random effects are automatically integrated out. This approximation, and its derivatives, are obtained using automatic differentiation (up to order three) of the joint likelihood. The computations are designed to be fast for problems with many random effects (~10^6) and parameters (~10^3). Computation times using ADMB and TMB are compared on a suite of examples ranging from simple models to large spatial models where the random effects are a Gaussian random field. Speedups ranging from 1.5 to about 100 are obtained with increasing gains for large problems. The package and examples are available at http://tmb-project.org

Efficient approximation of functions of some large matrices by partial fraction expansions

Some important applicative problems require the evaluation of functions $\Psi$ of large and sparse and/or \emph{localized} matrices $A$. Popular and interesting techniques for computing $\Psi(A)$ and $\Psi(A)\mathbf{v}$, where $\mathbf{v}$ is a vector, are based on partial fraction expansions. However, some of these techniques require solving several linear systems whose matrices differ from $A$ by a complex multiple of the identity matrix $I$ for computing $\Psi(A)\mathbf{v}$ or require inverting sequences of matrices with the same characteristics for computing $\Psi(A)$. Here we study the use and the convergence of a recent technique for generating sequences of incomplete factorizations of matrices in order to face with both these issues. The solution of the sequences of linear systems and approximate matrix inversions above can be computed efficiently provided that $A^{-1}$ shows certain decay properties. These strategies have good parallel potentialities. Our claims are confirmed by numerical tests

Solving rank structured Sylvester and Lyapunov equations

We consider the problem of efficiently solving Sylvester and Lyapunov equations of medium and large scale, in case of rank-structured data, i.e., when the coefficient matrices and the right-hand side have low-rank off-diagonal blocks. This comprises problems with banded data, recently studied by Haber and Verhaegen in "Sparse solution of the Lyapunov equation for large-scale interconnected systems", Automatica, 2016, and by Palitta and Simoncini in "Numerical methods for large-scale Lyapunov equations with symmetric banded data", SISC, 2018, which often arise in the discretization of elliptic PDEs. We show that, under suitable assumptions, the quasiseparable structure is guaranteed to be numerically present in the solution, and explicit novel estimates of the numerical rank of the off-diagonal blocks are provided. Efficient solution schemes that rely on the technology of hierarchical matrices are described, and several numerical experiments confirm the applicability and efficiency of the approaches. We develop a MATLAB toolbox that allows easy replication of the experiments and a ready-to-use interface for the solvers. The performances of the different approaches are compared, and we show that the new methods described are efficient on several classes of relevant problems

SlabLU: A Two-Level Sparse Direct Solver for Elliptic PDEs

The paper describes a sparse direct solver for the linear systems that arise from the discretization of an elliptic PDE on a two dimensional domain. The solver is designed to reduce communication costs and perform well on GPUs; it uses a two-level framework, which is easier to implement and optimize than traditional multi-frontal schemes based on hierarchical nested dissection orderings. The scheme decomposes the domain into thin subdomains, or "slabs". Within each slab, a local factorization is executed that exploits the geometry of the local domain. A global factorization is then obtained through the LU factorization of a block-tridiagonal reduced coefficient matrix. The solver has complexity $O(N^{5/3})$ for the factorization step, and $O(N^{7/6})$ for each solve once the factorization is completed. The solver described is compatible with a range of different local discretizations, and numerical experiments demonstrate its performance for regular discretizations of rectangular and curved geometries. The technique becomes particularly efficient when combined with very high-order convergent multi-domain spectral collocation schemes. With this discretization, a Helmholtz problem on a domain of size $1000 \lambda \times 1000 \lambda$ (for which N=100 \mbox{M}) is solved in 15 minutes to 6 correct digits on a high-powered desktop with GPU acceleration

Integrated Nested Laplace Approximations for Large-Scale Spatial-Temporal Bayesian Modeling

Bayesian inference tasks continue to pose a computational challenge. This especially holds for spatial-temporal modeling where high-dimensional latent parameter spaces are ubiquitous. The methodology of integrated nested Laplace approximations (INLA) provides a framework for performing Bayesian inference applicable to a large subclass of additive Bayesian hierarchical models. In combination with the stochastic partial differential equations (SPDE) approach it gives rise to an efficient method for spatial-temporal modeling. In this work we build on the INLA-SPDE approach, by putting forward a performant distributed memory variant, INLA-DIST, for large-scale applications. To perform the arising computational kernel operations, consisting of Cholesky factorizations, solving linear systems, and selected matrix inversions, we present two numerical solver options, a sparse CPU-based library and a novel blocked GPU-accelerated approach which we propose. We leverage the recurring nonzero block structure in the arising precision (inverse covariance) matrices, which allows us to employ dense subroutines within a sparse setting. Both versions of INLA-DIST are highly scalable, capable of performing inference on models with millions of latent parameters. We demonstrate their accuracy and performance on synthetic as well as real-world climate dataset applications.Comment: 22 pages, 14 figure

Solution of partial differential equations on vector and parallel computers

The present status of numerical methods for partial differential equations on vector and parallel computers was reviewed. The relevant aspects of these computers are discussed and a brief review of their development is included, with particular attention paid to those characteristics that influence algorithm selection. Both direct and iterative methods are given for elliptic equations as well as explicit and implicit methods for initial boundary value problems. The intent is to point out attractive methods as well as areas where this class of computer architecture cannot be fully utilized because of either hardware restrictions or the lack of adequate algorithms. Application areas utilizing these computers are briefly discussed

The automatic solution of partial differential equations using a global spectral method

A spectral method for solving linear partial differential equations (PDEs) with variable coefficients and general boundary conditions defined on rectangular domains is described, based on separable representations of partial differential operators and the one-dimensional ultraspherical spectral method. If a partial differential operator is of splitting rank $2$, such as the operator associated with Poisson or Helmholtz, the corresponding PDE is solved via a generalized Sylvester matrix equation, and a bivariate polynomial approximation of the solution of degree $(n_x,n_y)$ is computed in $\mathcal{O}((n_x n_y)^{3/2})$ operations. Partial differential operators of splitting rank $\geq 3$ are solved via a linear system involving a block-banded matrix in $\mathcal{O}(\min(n_x^{3} n_y,n_x n_y^{3}))$ operations. Numerical examples demonstrate the applicability of our 2D spectral method to a broad class of PDEs, which includes elliptic and dispersive time-evolution equations. The resulting PDE solver is written in MATLAB and is publicly available as part of CHEBFUN. It can resolve solutions requiring over a million degrees of freedom in under $60$ seconds. An experimental implementation in the Julia language can currently perform the same solve in $10$ seconds.Comment: 22 page