Many applications in computational science rely on algorithms for largescale sparse. In many applications measured data can be represented in a matrix x m. You take the matrix, k to d, you take the permutation that comes from approximate minimum degree, that gives you this reordered matrix. I wonder if there are other forms used in computational problems encountered in physics, chemistry, etc. Sparse matrices are used in specific ways in computer science, and have different data analysis and storage protocols and techniques related to. Preconditioning sparse matrices for computing eigenvalues and solving linear systems of equations by tzuyi chen b. University of california, berkeley 1998 a dissertation submitted in partial satisfaction of the requirements for the degree of. This paper has been followed by a lot of algorithms, one. Feb 19, 2014 a seminar given at stanford in june 20. We then do elimination, which factors in l times u probably l. Sparse matrix computations is a collection of papers presented at the 1975 symposium by the same title, held at argonne national laboratory. Algorithms for reordering sparse matrices play a vital role in our ability to. Improving the locality of the sparse matrixvector product on shared.
In this paper we examine the cuthillmckee algorithm for ordering the. Preconditioning sparse matrices for computing eigenvalues and. From this, a simple algorithm can be constructed which loops over the indices i from 1 through n and j from. The implementation is based closely on the sparspak implementation described by george and liu. You can then use the reverse cuthillmckee ordering to get the permutations you want, and apply these permutations to ab. The basic algorithms, such as matrix multiplication are simple enough to invite total comprehension, yet. All algorithms in this paper have been shown to be the fastest possible in terms of bilinear complexity. Preprocessing overhead for matrix reordering should be amortizable via the gain in computation step.
Then use the identifiers to create the ordered block matrix aperm from abperm and youll have the desired result, i believe. Comparative analysis of the cuthillmckee and the reverse cuthill. Reordering was originally developed for direct methods but it has recen. A permutation vector p, which is a full vector containing a permutation of 1. A permutation matrix p acts on the rows of s as ps or on the columns as sp. Algorithm 5 toeplitzplushankel matrix vector product 1. Sparse matrix algorithms stanford, june 20, tim davis. Second, a parallel ordering of a is computed from the filled graph that results from symbolically factoring a using the. This thorough, concise, and superbly written volume is the first in a selfcontained fivevolume series devoted to matrix algorithms, and focuses on the computation of matrix decompositions. Siam journal on scientific and statistical computing. If most of the elements of the matrix have 0 value, then it is called a sparse matrix. Graph working on the adjacency graph directly and provides some ordering algorithms, like the mentioned cuthillmckee, and minimumdegree ordering ptscotch for graphpartitioning and sparse matrix reordering. We consider the problem of finding equivalent reorderings of a sparse matrix so.
We have also performed a comparison with other reordering algorithms. This is in contrast to a dense matrix, where many or most of the elements have a nonzero value. The algorithm first finds a pseudoperipheral vertex of the graph of the matrix. The book contains an introduction to matrix analysis, and to the basic algorithms of numerical linear algebra. Section 2 discusses the shortcomings of current sparse matrix data structures and proposes new alternatives.
Permutation and reordering sparse matrices mathematics. A permutation of the rows and columns of a sparse matrix s can be represented in two ways. A survey of direct methods for sparse linear systems tamu. Sparse matrix reordering consists of swapping the matrix rows and columns in order to reduce the fillin orand the matrix bandwidth. What is the fastest algorithm for computing the inverse. Parallelization of reordering algorithms for bandwidth and.
Sparse matrix computation is a key kernel of many applications. Algorithms for structured matrixvector product of optimal. The paper examines techniques for solving linear systems represented by dense matrices. This makes the algorithms prohibitive for large scale computations. Computing a compressed approximate matrix decomposition, by p. Matrix reordering is not only useful for speedup but often mandatory in order to obtain a code which runs in a reasonable amount of time, especially for sparse direct solvers. A fast algorithm for reordering sparse matrices for. Improving performance of sparse matrixvector multiplication. This paper investigates the performance of sparse matrix multiplication kernels on two leading highperformance computing architectures intels knights landing processor and nvidias pascal gpu.
The main benefits of reordering are calculation speedup and memory storage reduction. Algorithm 5 toeplitzplushankel matrixvector product 1. Create a matrix of processes of size p12 12 x p so that each process can maintain a block of a matrix and a block of b matrix. Step 1take the middle n2,m2 of the matrix and compare it to the value step 2 if the value equals mi,j return i,j step 3 if the value is higher you can get rid from the first quarter step 4 if the value is lower you can get rid from the forth quarter step 5 split the 3 other quarters to 2, a rectangle and a box, send those both. A comparison of vertex ordering algorithms for large graph. Reordering the reorderable matrix as an algorithmic problem erkkim. The full restriction operation of order 8 applied to a scale 23 rmat matrix. The problem is to complete the matrix based on the observed entries, and has been dubbed the matrix completion problem ccs08, cr08, rfp07, ct09, kom09, rs05. The book of horn and johnson hj85 is an excellent reference for theoretical results about matrix analysis. The gibbspoolestockmeyer and gibbsking algorithms for reordering sparse matrices. Course home syllabus calendar readings assignments projects study materials video.
First, the matrix a is ordered by some fillreducing ordering. Algorithms of levinsontype and of schurtype are discussed. The dissect function uses graphtheoretic techniques to produce fillreducing orderings. Bring machine intelligence to your app with our algorithmic functions as a service api. Matrixvector multiplication, triangular solvers, matrix reordering. We propose several parallel algorithms for such applications based on ideas from cyclic reduction, dynamic programming, and nested dissection.
A sparse matrix is a matrix in which many or most of the elements have a value of zero. Then ab is a simple sparse matrix size 3x3 in the example. The result should consist of three sparse matrices, one obtained by adding the two input matrices, one by multiplying the two matrices and. The remainder of this paper is organized as follows. Preconditioning sparse matrices for computing eigenvalues. Matrix block structure in sparse matrixvector multiplication. From this, a simple algorithm can be constructed which loops over the indices i from 1 through n and j from 1 through p, computing the above using a nested loop. Reordering matrices for optimal sparse matrix bipartitioning. In numerical linear algebra, the cuthillmckee algorithm cm, named for elizabeth cuthill and james mckee, is an algorithm to permute a sparse matrix that has a symmetric sparsity pattern into a band matrix form with a small bandwidth. On page 3 of this document, there are some matrix forms for sparse matrices. Sparse matrix and its representations set 1 using arrays and linked lists a matrix is a twodimensional data object made of m rows and n columns, therefore having total m x n values. Matrix methods have important applications in many scienti. These aim to keep the number of extra entries that are filled in during lufactorization small.
The vector representation is slightly more compact and efficient, so the various sparse matrix permutation routines all return full row vectors with the exception of the pivoting permutation in lu triangular factorization, which returns a matrix. Parallel algorithms for sparse matrix product, indexing, and. We describe a data placement method and a chunkingbased algorithm for our kernels that exploits the existence of the multiple memory spaces in each. Except for the c 2 105 case, the rmat matrix has more nonzeros than the righthand matrix. Given two sparse matrices sparse matrix and its representations set 1 using arrays and linked lists, perform operations such as add, multiply or transpose of the matrices in their sparse form itself. The number of zerovalued elements divided by the total number of elements e. A 6 6 sparse matrix a on the left and its corresponding hypergraph for the sparsematrix partitioning problem. Each block is sent to each process, and the copied sub blocks are multiplied together and the results added to the partial results in the c subblocks. Computing inverse elements for a large matrix requires a lot of memory and is very timeconsuming even using our e cient algorithm with optimization. Special topics in sparse matrix algorithms department of computer science and engineering spring 2015 syllabus tim davis last modi ed september 23, 2014 1 catalog description csce 689. Toledo 7 proposed identifying 1 2 blocks of a matrix and writing the matrix as the sum of two matrices, the. The thorough explanations has necessarily restricted the scope of the series, but topic selection gives the reader a sound basis for further study.
In numerical analysis and scientific computing, a sparse matrix or sparse array is a matrix in which most of the elements are zero. Many sparse matrix computations can be speeded up if the matrix is first reordered. Sparse matrix and its representations set 1 using arrays. Parmetis a library for graphpartitioning, but provides matrix reordering algorithms as well. Fast algorithms for toeplitz and hankel matrices georg heinig and karla rost abstract the paper gives a selfcontained survey of fast algorithms for solving linear systems of equations with toeplitz or hankel coe cient matrices. Spectral regularization algorithms for learning large. Sparse reverse cuthillmckee ordering matlab symrcm. The reordering algorithms were tested for a broad set of matrices. All content, all journals, all books, all proceedings, this journal. So if you pick an ordering, like approximate minimum degree and you pick a matrix like this one and you run ive been very interested in that. We consider three general classes of algorithms for generating orderings. Your matrices are probably too small for sparse algorithms to be worthwhile, so the only other opportunities for faster algorithms would require additional matrix structure e. The a subblocks are rolled one step to the left and the b. Here youll find current best sellers in books, new releases in books, deals in books, kindle ebooks, audible audiobooks, and so much more.
Many algorithms can be used to reorder sparse matrices. If p is a sparse matrix, then both representations use storage proportional to n and you can apply either to s in time proportional to nnzs. In proceedings of the 27th acm on symposium on parallelism. 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. We propose alternative data structures, as well as reordering algorithms to increase the effectiveness of those data structures, to reduce the number of memory indirections in spmxv. This page contains the documents abstract and table of contents. 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. Reordering sparse matrices for parallel elimination sciencedirect. By contrast, if most of the elements are nonzero, then the matrix is considered dense. The books homepage helps you explore earths biggest bookstore without ever leaving the comfort of your couch. The new reordering algorithm using rotation is shown to produce trees with.
Sparse matrix algorithms solve lx b with l unit lower triangular. In proceedings of the 27th acm on symposium on parallelism in algorithms and architectures, spaa 15, pages 8688. The definition of matrix multiplication is that if c ab for an n. The proofs may be found in 14 and involve determining the tensor ranks of these structured matrixvector products. Reordering the reorderable matrix as an algorithmic problem. Performance analysis rows of alltoall broadcasts, each is among a group of processes. A spectral algorithm for envelope reduction of sparse matrices. Implementing sparse matrices for graph algorithms author. A preliminary version of parts of this paper, in particular the main algorithm and main theorem of section 3, appeared as. Sparse matrix computations paperback september 23, 2014 by james r. This library provides first sparse matrix computation kernels including spmv and spgemm. Routines to read and write sparse matrices using a simple file format with one line per nonzero, specifying the row, column, and value. It then generates a level structure by breadthfirst search and orders the vertices by decreasing distance from the pseudoperipheral vertex.
137 569 1281 504 1405 790 1386 1238 1239 961 1049 257 768 1413 1237 972 85 1246 466 1370 446 1081 568 1395 1360 1197 1120 34 1139 22 752 1025 241 649 1150 665 335 339 999