Sparse multifrontal rank revealing qr factorization siam. Computing row and column counts for sparse qr and lu. In linear algebra, a qr decomposition, also known as a qr factorization or qu factorization is a decomposition of a matrix a into a product a qr of an orthogonal matrix q and an upper triangular matrix r. The computational complexity of sparse operations is proportional to nnz, the number of nonzero elements in the matrix. Sparse qr factorization in matlab in the recently presented sparse matrix extension of matlab, there is no routine for sparse qr factorization. We present a sparse multifrontal qr factorization method that meets. For example for a matrix with nonzeros only along the first row, first column, and diagonal the cholesky factors have 100% fillin the lower and upper triangles are 100% dense. Sparse least squares and qless qr cornell university. Second, in sparse factorizations, the ordering of the equations can have a dramatic effect on the amount of fillin and computation time during factorization. Sparse nonnegative matrix factorization for clustering. Sparse nonnegative matrix factorization for clustering jingu kim and haesun park. In the recently presented sparse matrix extension of matlab, there is no routine for.
Acm transactions on mathematical softwareaugust 2017. In the recently presented sparse matrix extension of matlab, there is no routine for sparse qr factorization. His primary scholarly contribution is the creation of widelyused sparse matrix algorithms and software. A sparse implementation of each of these algorithms is introduced. I am using pardiso to solve a sparse linear of equations, and at least it is what i understand pardiso is for. Sparse qr factorization on a massively parallel computer. Our method factorizes many frontal matrices in parallel and keeps all the data transmitted between frontal matrices on the gpu. Parallel sparse qr factorization on shared memory architectures. We describe a multifrontal method for sparse qr factorization and its.
The sparse qr routines provide a multifrontal sparse qr factorization method for solving a sparse system of linear equations. The permuted qr factorization q, r, p qr a factorization allows the construction of an orthogonal basis of span a if the matrix a is sparse, then the sparse qr factorization of a is computed using csparse. Its utility arises from the numerical stability offered by orthogonal transformations. Introduction sparse qr factorization is one of the key direct methods for solving large sparse linear systems and leastsquares problems. If pivoting, compute the decomposition a p q r as above, but where p is chosen such that the diagonal of r is nonincreasing.
As the matrix q is in general a full matrix, this function returns the qless factorization r of a, such that r chol a a. We present a sparse multifrontal qr factorization method that meets this challenge and is significantly faster than a highly optimized method on a multicore cpu. We describe an algorithm to compute an approximate rank revealing sparse qr factorization. Multifrontal multithreaded rankrevealing sparse qr factorization. Qr factorization, leastsquare problems, sparse matrices. Computational complexity also depends linearly on the row size m and column size n of the matrix, but is independent of the product mn, the total number of zero and nonzero elements. Fillin reduction in sparse matrix factorizations using. This research domain lies in the intersection of graph algorithms, combinatorics, robust software design, and matrix computations. Davis, geophysical journal international 205 2, 830836, 2016 for tech report, click here and here. Algorithms, experimentation, performance additional key words and phrases. The algorithms were originally introduced by trevor hastie et al. This is true even for qr and lu factorizations where pivoting takes place to insure numerical stability. Sparse factorization qr provides a sparse counterpart to the dense qr routine.
Suitesparseqr is a sparse qr factorization package based on the multifrontal method. The permuted qr factorization q, r, p qr a factorization allows the construction of an orthogonal basis of span a. Construct the matrices l and u if possible solve lyb for y using forward substitution solve uxy for x using back substitution. Even though it is qualified as rankrevealing, this strategy might fail. The qr factorization of ais given by a qr, where q. The following software packages are provided by sol under the terms of the mit license mit. Use qr to factorize the matrix into the factors r and c qb. Although there is good software for sparse qr factorization, there is little support for updating and downdating, something that is absolutely essential in some linear programming algorithms, for example. Suitesparseqr, a multifrontal multithreaded sparse qr factorization. Qr factorization, leastsquare problems, sparse matrices 1. How to compute the rank of a large sparse matrix in matlab. This means that any element of a matrix above this value would be considered. This is just a copy included with suitesparse via the opensource license provided by george karypis rbio readwrite sparse matrices in rutherfordboeing format author. Sparse matrix algorithms stanford, june 20, tim davis.
Multifrontal multithreaded rankrevealing sparse qr. Parallelism across different frontal matrices is handled with intels. Sparse linear leastsquares problems are instead solved by the augmented system method. For sparse qr factorization, nding a good column ordering of the matrix to. The problem im having is that the cholesky factors are not necessarily sparse just like the product of two sparse matrices is not necessarily sparse. Create a random 500by20 sparse matrix with 10% density and a vector of ones. Computing rankrevealing qr factorizations of dense. Request pdf a software package for sparse orthogonal factorization and updating although there is good software for sparse qr factorization, there is little support for updating and downdating. Qr decomposition is often used to solve the linear least squares problem and is the basis for a particular eigenvalue algorithm, the qr algorithm. Suitesparseqr is a sparse multifrontal qr factorization algorithm. Qr decomposition of a large sparse matrix is used to solve the linear least squares ls problem arising in power system state estimation. Sparse linear least squares problems are instead solved. Citeseerx document details isaac councill, lee giles, pradeep teregowda. The problem is cast as a dataflow graph, whose nodes are mapped to a virtual dataflow machine in such a way that only nearestneighbor communication is required.
The accuracy in computed solutions is strongly dependent on a scaling parameter. This article describes an implementation of sparse lq factorization, including block triangularization, approximate minimum degree ordering, symbolic factorization, multifrontal factorization. The ordering from colamd is also suitable for sparse qr factorization, and the factorization of matrices of the form a t a and aa t, such as this work was supported in part by the national. The column exchange strategy used in the initial qr factorization will exploit the fact that certain column exchanges do not change the sparsity structure, and compute a sparse qr factorization that is a good approximation of the soughtafter rrqr factorization. This chapter describes functions for solving linear systems. In that case, the computation avoids the construction of q and returns r such that r chol a a if an additional matrix b is supplied and two return values are requested, then qr returns c.
Sparse qr factorization in matlab acm transactions on. Compute q tbas r ta b, since the latter computation involves only a sparse multiply and a sparse triangular solve. Whether or not factorization should include pivoting for rankrevealing qr decomposition. The accuracy in computed solutions is strongly dependent on a scaling parameter its optimal value is expensive to compute, and it must therefore be approximated.
As the matrix q is in general a full matrix, it is recommended to request only one return value, which is the qless factorization r of a, such that r chol a a. An effective strategy in sparse qr factorizations is to first reorder the columns. The software may alternatively be used under the terms of a bsd license bsdlicense. Even if the 2 functions can do other things, at least they can both be used to solve a linear system with. Sparse matrix operations efficiency of operations computational complexity. This repo introduces two sparse matrix factorization algorithms. Multifrontal multithreaded rankrevealing sparse qr factorization suitesparseqr is a sparse qr factorization package based on the multifrontal method. Software including sparse qr and hardware that complies with ieee754 format for the floating point numbers use the smallest denormalized number as the zero threshold, which is 4. If the matrix a is sparse, then compute the sparse qr factorization of a, using csparse. If the input matrix a is sparse then the sparse qr factorization is computed using csparse.
The sparse matrix is shipped to the gpu and the final factors are retreived when it completes. A software package for sparse orthogonal factorization and. A novel scheduling algorithm for communicationavoiding dense qr. Sparse matrix factorization involves a mix of regular and irregular computation, which is a particular challenge when trying to obtain highperformance on the highly parallel generalpurpose computing cores available on graphics processing units gpus. Unfortunately, it handles only sparse matrix times dense matrix multiplica. Dense matrix methods within each frontal matrix enable the method to obtain high performance on multicore architectures. Therefore, one must impose conditions on the sparse and lowrank components in order to guarantee their identi. Description details objects from the class slots methods see also examples.
Fortran, matlab, and python software for sparse symmetric linear equations \ax b\, where \a\ is definite or indefinite. Doolittle factorization l has 1s on its diagonal crout factorization u has 1s on its diagonal cholesky factorization ul t or lu t solution to axb is found as follows. Solve a sparse linear system and use the results to see how much of vector b lies in the column space of s. It can also be used to estimate rank of matrix rank revealing qr decomposition. Multifrontal multithreaded rankrevealing sparse qr factorization, acm trans. Finding good column orderings for sparse qr factorization. A structure that contains options that affect the numerical stage of a sparse factorization. Qr, lq, or svd you have the problem that because some of the columns of the orthogonal matrix have to span a particular subspace, and because the remaining columns have to form an orthogonal basis for the complement to this subspace, and because these spaces can be completely arbitrary, the orthogonal matrix wont be sparse. In such cases, these components may be confused for each other, and thus the desired decomposition of y may not be identi. To this end, the paper proposes to compute an initial qr factorization using amore. Calculates the solution of a sparse system of linear equations using qr factorization.
Sparse qr factorization in matlab, acm transactions on. Mathematical softwarealgorithm analysis, efficiency. This class follows the sparse solver concept the numerical pivoting strategy and default threshold are the same as in suitesparse qr, and detailed in the following paper. Sparse linear least squares problems are instead solved by the augmented system method. This paper shows that qr factorization of large, sparse matrices can be performed efficiently on massively parallel simd single instruction streammultiple data stream computers such as the connection machine cm2. Appears as qr and xa\b in matlab, with cuda acceleration. Within each frontal matrix, lapack and the multithreaded blas enable the method to obtain high performance on multicore architectures. Parallelism across different frontal matrices is handled with intels threading building blocks library. Because the matrix q is, in general, a full matrix, it is recommended to request only one return value r. Qtbimplicitly at the same time it does the qr factorization. Computing the cholesky factorization of sparse matrices.
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