Sparse matrix reordering algorithms book pdf

Matrix reordering methods for table and network visualization aviz. Matrix reordering using multilevel graph coarsening for ilu. This project aims the parallelization of some algorithms for the bandwidth and wavefront reduction problems. Parmetis a library for graphpartitioning, but provides matrix reordering algorithms as well. On evaluating parallel sparse cholesky factorizations. On optimal partitioning for sparse matrices in variable. Equivalent sparse matrix reordering by elimination tree. A fast reordering algorithm for parallel sparse triangular. Implementing sparse matrix vector multiplication on throughputoriented processors nathan bell and michael garland proceedings of supercomputing 09 efficient sparse matrix vector multiplication on cuda nathan bell and michael garland nvidia technical report nvr2008004, december 2008 iterative methods for sparse linear systems yousef saad. In fact, reordering rows and columns is one of the most.

I still, using sparsity can save large amounts of cpu time and also memory space. The algorithm treats the matrix as the adjacency matrix of a graph, coarsens the graph by collapsing vertices and edges, reorders the smaller graph, and then uses refinement steps to uncoarsen the small graph and produce a reordering of the original graph. A comparison of algorithms for sparse matrix factoring and variable reordering aimed at realtime multibodydynamic simulation joseluis torresmoreno, joseluis blanco, javier lopez martinez, 14 july, 20 zagreb croatia eccomas multibodydynamics 20 antonio gimenezfernandez. Steadystate genetic algorithm with duplicates elimination, where two. Many software libraries support sparse matrices, and provide solvers for sparse matrix equations. Sparse matrix computations is a collection of papers presented at the 1975 symposium by the same title, held at argonne national laboratory. Pdf morsya new tool for sparse matrix reordering researchgate. The dissect function uses graphtheoretic techniques to produce fillreducing orderings. At each step in the reordering process, choose the pivot that requires the. You can then use the reverse cuthillmckee ordering to get the permutations you want, and apply these permutations to ab. A comparison of algorithms for sparse matrix factoring and. Parallel algorithms for sparse matrix product, indexing, and.

The number of zerovalued elements divided by the total number of elements e. International journal for numerical methods in engineering 66. Section 3 states a new matrix reordering algorithm to permute the nonzeros of the matrix into contiguous locations. When oski tunes a sparse matrix to be cacheblocked, it creates a sparsematrixoftypeoski matcb t,whichcontainsalinkedlistof r x c cacheblock sparse matrices of type oski submatcb t that collectively represent the original sparse matrix.

Parallel sparse matrix matrix multiplication and indexing. Siam journal on scientific and statistical computing. Inputoutput for sparse matrices stored in harwellboeing format c more information. Moreover, some matrices that had not converged be fore reordering converged afterwards. Improving performance of sparse matrixvector multiplication. Then use the identifiers to create the ordered block matrix aperm from abperm and youll have the desired result, i believe. Implementing sparse matrices for graph algorithms author. Sparse matrix implementations, including the coordinate format, begin on page 85 pdf page 97. Variable reordering strategies for slam university of michigan. A permutation vector p, which is a full vector containing a permutation of 1.

First, the matrix a is ordered by some fillreducing ordering. Historically, matrix reordering was done manually, with the eye of the artist ber73 and. A permutation matrix p acts on the rows of s as ps or on the columns as sp. It is wellknown that reordering techniques applied to sparse matrices are common strategies to improve the performance of sparse matrix operations, and particularly, the sparse matrix vector. Reordering matrices for optimal sparse matrix bipartitioning. Parallel algorithms for matrix computations download. The only change to the outward appearance of the matlab language is a pair of commands to create full or sparse matrices. Recently, the algorithms that perform sparse matrix reordering are developed in graphtheoretical terms and efforts to build them have been based on objectoriented kumfert and pothen, 1998 the. Sparse matrix algorithms solve lx b with l unit lower triangular.

Pdf generic graph algorithms for sparse matrix ordering. Solving sparse linear systems is a problem that arises in many scientific applications, and sparse direct solvers are a time consuming and key kernel for those applications and for more advanced. Going back to sparse matrices, the adjacency graph of a sparse matrix is a graph. Effects of ordering strategies and programming paradigms on. Grey ballard, christopher siefert, and jonathan hu. Proceedings of the 1999 congress on evolutionary computationcec99 cat. Experimental results are presented in section 4, and. Second, a parallel ordering of a is computed from the filled graph that results from symbolically factoring a using the. Section iii describes the ordering algorithms we used and section iv introduces the machine learning method we employed. It is based on multilevel nested dissection algorithm with. Jul 31, 2006 the matrix computation language and environment matlab is extended to include sparse matrix storage and operations. On page 3 of this document, there are some matrix forms for sparse matrices.

I sparse matrix computations have alarger integer overhead associated with each oatingpoint operation. A permutation of the rows and columns of a sparse matrix s can be represented in two ways. Direct methods for sparse matrices univerzita karlova. Reducing communication costs for sparse matrix multiplication within algebraic multigrid. I need to sort this matrix rowbyrow and create another sparse matrix. In numerical analysis and scientific computing, a sparse matrix or sparse array is a matrix in which most of the elements are zero. A comparison of algorithms for sparse matrix factoring and variable reordering aimed at realtime multibody dynamic simulation. Mckee and kings algorithm george 1981 are the bandwidth minimization algorithms that we study here. In 24 a minimum discarded fill mdf algorithm is presented as a reordering. Iterative methods for sparse linear systems second edition. Parallel algorithms for sparse matrix product, indexing, and assignment ayd. Reverse cuthill mckee rcm bandwidth reduction sloan wavefront reduction dependencies. Click download or read online button to get parallel algorithms for matrix computations book now.

By contrast, if most of the elements are nonzero, then the matrix is considered dense. This book is composed of six parts encompassing 27 chapters that contain contributions in several areas of matrix computations and some of the most potential research in numerical linear algebra. Pdf reordering strategy for blocking optimization in. If all goes well, the matrix then decomposes into diagonal blocks and possibly some remains that can be easier examined for partial uniqueness of the solution.

The goal is to impart a working knowledge of the underlying theory and practice of sparse matrix algorithms, so that you will have the foundation to understand more complex but faster algorithms. Steps toward simplifying sparse matrix data structures. Permutation and reordering sparse matrices mathematics. Matlab and java interface to the suitesparse matrix collection. Feb 19, 2014 a seminar given at stanford in june 20. Raphael yuster y uri zwick z abstract let a and b two n. Suitesparse, a suite of sparse matrix algorithms, geared toward the direct solution of sparse linear systems. Use a standard sparse reordering of the equations and variables. Yousef saads iterative methods for sparse linear systems pdf, chapters of a textbook covering linear algebra and types of matrices. In numerical analysis the minimum degree algorithm is an algorithm used to permute the rows and columns of a symmetric sparse matrix before applying the cholesky decomposition, to reduce the number of nonzeros in the cholesky factor. We present morsy a new tool for reordering symmetric sparse matrices. Preprocessing overhead for matrix reordering should be amortizable via the gain in computation step. Pdf reordering strategy for blocking optimization in sparse. Sparse matrix data structures summary i sparse matrix algorithms aremore complicatedthan their dense equivalents, as we saw for sparse vector addition.

Sparse matrices reordering using evolutionary algorithms. The matlab codes presented in the book are tested with thousands of runs of matlab randomly generated matrices, and the notation in the book follows the matlab style to ensure a smooth transition from formulation to the code, with matlab codes discussed. Matrix algorithms in matlab focuses on the matlab code implementations of matrix algorithms. Suitesparse is a suite of sparse m atrix algorithms, including. Then ab is a simple sparse matrix size 3x3 in the example. Keywords, directed acyclic graph, elimination tree, massively parallel computers, reordering algorithm, sparse cholesky factorization, sparse triangular systems, transitive reduction. Nonspecultive datadriven parallelizations of irregular algorithms for sparse matrices reordering. We present a new algorithm that multiplies a and b using om0.

Parallel algorithms for matrix computations download ebook. I wonder if there are other forms used in computational problems encountered in physics, chemistry, etc. Petsc, a large c library, containing many different matrix solvers for a variety of matrix storage formats. Optimization of sparse matrixvector multiplication using. This site is like a library, use search box in the widget to get ebook that you want. Sparse matrix algorithms stanford, june 20, tim davis. In this paper, we introduce a class of fillpreserving equivalent reorderings for sparse cholesky factorization.