mjcarley / libpetrbf

Automatically exported from code.google.com/p/petrbf

PetRBF library

This is a fork of the PetRBF code of Yokota, Barba, and Knepley, intended to compile using standard autoconf tools, to provide a library for integration in other codes. The original code is licensed by the Barba group under the MIT License. Further developments are covered by the GPL.

The prerequisite for installing the library is PETSc, which is available from https://www.petsc.org/ The installation process requires that the PETSc be visible as a package using pkg-config.

Original PetRBF description

Many applications in computational science need to approximate a function based on finite data. When the data are in a certain sense “scattered” in their domain, one very powerful technique is radial basis function (RBF) interpolation. For many years, the wide applicability of RBF interpolation was hindered by its numerical difficulty and expense. Indeed, in their mathematical expression, RBF methods produce an ill-conditioned linear system, for which a direct solution becomes prohibitive for more than a few thousand data points.

We have developed a parallel algorithm for RBF interpolation that exhibits O(N) complexity, requires O(N) storage, and scales excellently up to a thousand processes. The algorithm uses the GMRES iterative solver with a restricted additive Schwarz method (RASM) as a preconditioner and a fast matrix-vector algorithm. Previous fast RBF methods — achieving at most O(N log N) complexity — were developed using multiquadric and polyharmonic basis functions. In contrast, the present method uses Gaussians with a small variance. The fast decay of the Gaussian basis function allows rapid convergence of the iterative solver even when the subdomains in the RASM are very small. The method was implemented in parallel using the PETSc library (developer version). Numerical experiments demonstrate its capability in problems of RBF interpolation with more than 50 million data points, timing at 106 seconds (19 iterations for an error tolerance of 10e−15) on 1024 processors of a Blue Gene/L (700 MHz PowerPC processors).

See the paper PetRBF--A parallel O(N) algorithm for radial basis function interpolation by Rio Yokota, L A Barba, Matthew G Knepley, and visit The Barba Group page for more information. A summary of this project is also available among the Boston University research computing briefs.

We distribute this code under the MIT License, giving potential users the greatest freedom possible. We do, however, request fellow scientists that if they use our codes in research, they kindly include us in the acknowledgement of their papers. We do not request gratuitous citations; only cite our articles if you deem it warranted.