I want just to see example how to solve axb linear equation for sparse matrix. This example shows the usage of sparse matrices and demonstrates some template programming techniques. 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. The choice of the best matrix type depends on the access pattern. This is in contrast to a dense matrix, where many or most of the elements have a nonzero value. A scalable sparse matrixvector multiplication kernel for. Sparse matrixvector multiplication spmxv is a mathematical kernel that takes the form of. A list of authors and contributors can be found in the pdf manual. Sparse matrixmatrix multiplication or sparse matrix multiplication. Represent sparse matrices by some appropriate form of linked.
Sparse matrix operations efficiency of operations computational complexity. For example, a matrix vector product, where the matrix is stored as. Sparse matrices single linear list in rowmajor order. For a sparse matrix, s, the nnz function returns the number of nonzero elements in the matrix, and the nzmax function returns the amount of storage allocated for nonzero matrix elements. The boost ublas library 5 is one of the most widespread et math libraries since it is distributed together with the boost library 6. Unlike their densematrix counterpart routines, the underlying matrix storage format is not described by the interface. Therefore, it covers only the most classical results of a part of the. Mar 30, 2020 the intel mkl block compressed sparse row bsr format for sparse matrices is specified by four arrays. Also, if n is the number of grid points, we see that the size of the full matrix is n2. A more simple and efficient version is here lu matrix inversion. Looping over the nonzero elements of a ublas sparse matrix. I could write a brute force double loop to go over all the ent. Sparse matrices sparse many elements are zero dense few elements are zero example of sparse matrices diagonal tridiagonal lower triangular.
Represent sparse matrices by some appropriate form of linked lists. The most widely used format, namely the compressed sparse row. Sparse optimization methods stephen wright university of wisconsinmadison toulouse, feb 2009. Generate a sparse matrix of the given shape and density with. However, most publications deal with parallel sparse matrixvectormultiplication, 14, 15, since it is of pivotal importance in solving sparse linear systems and sparse eigenvalue problems. Applications, algorithms, and implementations organizers.
If you do want to apply a numpy function to these matrices, first check if scipy has its own implementation for the given sparse matrix class, or convert the sparse matrix to a numpy array e. Modelguided performance analysis of the sparse matrixmatrix. Modelguided performance analysis of the sparse matrixmatrix multiplication. The method that we perform, does a transition to the source matrix through steps to compute the value of elements of inverse matrix by using a unit matrix and a supplement matrix. The numer of iterations of the original cg, a diagonal preconditioner, a cholesky preconditioner and an incomplete cholesky preconditioner can be compared. While full or dense matrices store every single element in memory regardless of value, sparse matrices store only the nonzero elements and their row indices. Sparsematrix is implemented as an immutable object all operations create new matrix instead of changing the matrix the operation is called on. For a m xndimensional sparse matrix and 0 adjacency n, n. May be mapped into a 1d array so that a mapping function can be used to locate an element.
At the time of writing 092012 there are a lot of good matrix libraries available, e. I still, using sparsity can save large amounts of cpu time and also memory space. In the main function, we declare a list coefficients of triplets as a std vector and the right hand side vector which are. I sparse matrix computations have alarger integer overhead associated with each oatingpoint operation. Preprocessing of the model files to produce a cleaner and more usable matrix is a future phase of my project. Parallel sparse matrix matrix multiplication and indexing. Create sparse matrix matlab sparse mathworks nordic. Reducing communication costs for sparse matrix multiplication within algebraic multigrid. Feb 19, 2018 sparsematrix is implemented as an immutable object all operations create new matrix instead of changing the matrix the operation is called on.
The influence of different preconditioners can be seen. Represent sparse matrices by some appropriate form of. Modelguided performance analysis of the sparse matrix. In the example below, we define a 3 x 6 sparse matrix as a dense array, convert it to a csr sparse representation, and then convert it back to a dense array by calling the todense function. For this reason, using sparse matrices can significantly reduce the amount of memory required for data storage. Direct methods for sparse matrices univerzita karlova. Sparse matrix data structures summary i sparse matrix algorithms aremore complicatedthan their dense equivalents, as we saw for sparse vector addition. Note that sparse data representation does not only reduce the storage overhead, but is also the basis for more efficient algorithms. Therefore, a direct comparison of sparse and dense blas performance in gflops can be misleading as total time spend in sparse blas computations can be less than the total time spent in dense blas despite of higher gflops for dense blas functionality. Hi bill, it looks like you did not enable the ublas targets. Much work has been devoted to sparse matrix based algorithms and ef. Sparse matrix implementations, including the coordinate format, begin on page 85 pdf page 97.
For example, a matrixvector product, where the matrix is stored as. This class provides a base class for all sparse matrices. A sparse matrix is a matrix in which many or most of the elements have a value of zero. Implementing sparse matrixvector multiplication on throughputoriented processors nathan bell and michael garland proceedings of supercomputing 09 efficient sparse matrixvector multiplication on cuda nathan bell and michael garland nvidia technical report nvr2008004, december 2008 iterative methods for sparse linear systems yousef saad. All classes namespaces files functions variables typedefs enumerations enumerator friends macros pages. A gentle introduction to sparse matrices for machine learning.
Themajorapplication of sparse matrix techniques in optimization up to the present has been in the implementation of the simplex method for linear programming lp see, e. In fact, commercial codes for large lp problems seem to have predated codes for sparse linear equations even though solving a sparse lpproblem requires. In this example, we start by defining a columnmajor sparse matrix type of double sparsematrix, and a triplet list of the same scalar type triplet. Generate a sparse matrix of the given shape and density with uniformly distributed values. The contents of subsequent parts is indicated in the outline. Pdf on jan 1, 1984, sergio pissanetzky and others published sparse matrix technology find, read and cite all the research you need on researchgate.
Number of columns in the matrix has to be the same as the size of the. Contributions we map two fundamental computational kernels as generalpurpose sparse matrix building blocks onto the gpu. Number of columns in the matrix has to be the same as the size of the vector, otherwise invaliddimensionsexception is thrown. Then, the respective viennacl sparse matrix is created and initialized with data from the ublas matrix. Cc is a data directory which contains examples of files in the compressed column cc format for storing sparse matrices. This example computes the solution x of the system axb of linear equations using the iterative method of conjugate gradients. Each entry in the array represents an element a i,j of the matrix and is accessed by the two indices i and j. Sparse basic linear algebra subprograms blas library. The compressed sparse row csr sparse matrix storage format. For complex simulations with thousands of grid points, one cannot hope to solve these problems without taking advantage of sparsity.
Unstructured sparse matrices airline flight matrix. Sparse matrices provide efficient storage of double or logical data that has a large percentage of zeros. Sparse matrix implementations, including the coordinate format, begin on page 85 pdf. Sparse matrices are used in specific ways in computer science, and have different data analysis and storage protocols and techniques related to. Therefore, as n increases, the sparse matrix format becomes far more efficient than the full matrix format. The sparse compressed column data structure involves. The design and implementation unify mathematical notation via operator overloading and efficient code generation via expression templates.
For this reason, using sparse matrices can significantly reduce the amount of. By contrast, if most of the elements are nonzero, then the matrix is considered dense. Unlike their dense matrix counterpart routines, the underlying matrix storage format is not described by the interface. We setup a sparse matrix in ublas and populate it with values. A matrix is typically stored as a twodimensional array. I wrote a simple matrix inversion algorithm that uses ublas.
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. In numerical analysis and scientific computing, a sparse matrix or sparse array is a matrix in which most of the elements are zero. Conventionally, i is the row index, numbered from top to bottom, and j is the column index, numbered from left to right. Sparse blas bsr matrix storage format intel math kernel. The performance of sparse matrix algorithms tends to be much lower than that of dense matrices due to two key factors. Grey ballard, christopher siefert, and jonathan hu. M and n, the number of rows and columns of the matrix well often assume assume the matrix is square, in which case mn. After a direct manipulation of the viennacl matrix, matrix vector products are computed with both matrices.
The sample program below simulates the assembling of a fem stiffnes matrix by randomly adding small blocks to the global sparse matrix. Build a block diagonal sparse matrix from provided matrices. A triplet is a simple object representing a nonzero entry as the triplet. After a direct manipulation of the viennacl matrix, matrixvector products are computed with both matrices. From the lines for a and afull, we can see that the sparse matrix format requires far less memory that the full matrix format. The computational complexity of sparse operations is proportional to nnz, the number of nonzero elements in the matrix. If v is a vector or matrix, then one of the inputs i or j must also be a vector or matrix with the same number of elements any elements in v that are zero are ignored, as are the corresponding subscripts in i and j. If nnzs and nzmaxs return different results, then more storage might be allocated than is actually required. Yousef saads iterative methods for sparse linear systems pdf, chapters of a textbook covering linear algebra and types of matrices. Free opensource gpuaccelerated linear algebra and solver library. The structure of the matrix is chosen such that the incomplete cholesky is equivalent to the comlete cholesky decomposition. Numerical linear algebra in optimization most memory usage and computation time in optimization methods is. I could write a brute force double loop to go over all the entries in on2 time like below, but this is going to be too slow. For a m xndimensional sparse matrix and 0 sparse matrix that contains on elements.
853 608 723 159 821 259 1385 1100 185 116 1125 1469 577 965 1075 94 192 551 517 831 824 1237 784 1516 343 404 916 807 331 1357 585 913 1208 598