title: Fast Sparse Cholesky Decomposition and Inversion using Nested Dissection Matrix Reordering.
abstract: Here we present an efficient, yet nonlinear scaling, algorithm for the computation of Cholesky factors of sparse symmetric positive definite matrices and their inverses. The key feature of this implementation is the separation of the task into an algebraic and a numeric part. The algebraic part of the algorithm attempts to find a reordering of the rows and columns which preserves at least some degree of sparsity and afterward determines the exact nonzero structure of both the Cholesky factor and its corresponding inverse. It is based on graph theory and does not involve any kind of numerical thresholding. This preprocessing then allows for a very efficient implementation of the numerical factorization step. Furthermore this approach even allows use of highly optimized dense linear algebra kernels which leads to yet another performance boost. We will show some illustrative timings of our sparse code and compare it to the standard library implementation and a recent sparse implementation using thresholding. We conclude with some comments on how to deal with positive semidefinite matrices.
authors.affiliation: Department of Chemistry, University of California, Berkeley, California 94720, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States.
authors.forename: Kai
authors.initials: K
authors.lastname: Brandhorst
authors.affiliation: Department of Chemistry, University of California, Berkeley, California 94720, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States.
authors.forename: Martin
authors.initials: M
authors.lastname: Head-Gordon