Questions tagged [sparse-matrix]

Questions related to storage, assembly, operations, and other aspects of dealing with sparse matrices, for which only non-zero elements are stored. Questions that do not with sparse matrices directly, but other means of using sparsity should be tagged with [sparse-operator].

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What guidelines should I follow when choosing a sparse linear system solver?

Sparse linear systems turn up with increasing frequency in applications. One has a lot of routines to choose from for solving these systems. At the highest level, there is a watershed between direct (...
J. M.'s user avatar
  • 3,155
18 votes
6 answers
2k views

How to reorder variables to produce a banded matrix of minimum bandwidth?

I'm trying to solve a 2D Poisson equation by finite differences. In the process, I obtain a sparse matrix with only $5$ variables in each equation. For example, if the variables were $U$, then the ...
Paul's user avatar
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35 votes
6 answers
33k views

What is the fastest way to calculate the largest eigenvalue of a general matrix?

EDIT: I am testing if any eigenvalues have a magnitude of one or greater. I need to find the largest absolute eigenvalue of a large sparse, non-symmetric matrix. I have been using R's ...
power's user avatar
  • 521
11 votes
2 answers
6k views

How to efficiently implement Dirichlet boundary conditions in global sparse finite element stiffnes matrices

I am wondering how Dirichlet boundary conditions in global sparse finite element matrices are actually implemented efficiently. For example lets say that our global finite element matrix was: $$K = \...
James's user avatar
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10 votes
2 answers
611 views

Which novel data structures are used in adaptive FEM?

A lot of adaptive FEM libraries use more advanced mesh data structures to handle adding/removing nodes, edges, triangles, tetrahedra, etc. For example, the p4est library uses octree data structures ...
Daniel Shapero's user avatar
8 votes
2 answers
312 views

calculating eigenvector components of a given vector

I have some vector $V$ which can be decomposed into the eigenspace of the hermitian sparse operator $M$: $V = \sum_i v_i \hat{m}_i$ Is there a way to find the $\hat{m}_i$ (the eigenvector itself) ...
Andrew Spott's user avatar
  • 1,155
7 votes
5 answers
12k views

How to solve block tridiagonal matrix using Thomas algorithm

Thomas algorithm can be used to solve a tridiagonal matrix: $$ \begin{bmatrix} {b_ 1} & {c_ 1} & { } & { } & { 0 } \\ {a_ 2} & {b_ 2} & {c_ 2} & { } & { }...
xslittlegrass's user avatar
4 votes
4 answers
8k views

Efficient assembly of finite element matrix in MATLAB

Question What is the most efficient algorithm for finding a row of a matrix which matches a given row? This is the same as a table lookup based on multiple criteria. Context Finite Element Matrices ...
Daryl's user avatar
  • 178
18 votes
5 answers
8k views

What is the best way to determine the number of non zeros in sparse matrix multiplication?

I was wondering whether there is a fast and efficient method to find the number of non zeros in advance for sparse matrix multiplication operation assuming both matrices are in CSC or CSR format. I ...
Recker's user avatar
  • 333
12 votes
3 answers
3k views

Sparse linear solver for many right-hand sides

I need to solve the same sparse linear system (300x300 to 1000x1000) with many right hand sides (300 to 1000). In addition to this first problem, I would also like to solve different systems, but with ...
nat chouf's user avatar
  • 353
10 votes
4 answers
573 views

Are there any quad-double arithmetic sparse matrix package?

I am working on some ill-conditioned large sparse linear system of equations. I want to use double-double arithmetic or quad-double arithmetic to solve them. I know that there is a package named MPACK ...
Hanyu Ye's user avatar
  • 191
10 votes
3 answers
4k views

Calculating the log-determinant of a large sparse matrix

I need to calculate $\log(\det (\mathbf M_i))$ where the $\mathbf M_i$'s are large sparse matrices, which are real, symmetric and positive semi-definite. I hope to have between $10$ and $100$ of ...
yohbs's user avatar
  • 267
9 votes
1 answer
508 views

Solving a system with a small rank diagonal update

Suppose I have the original large, sparse linear system: $A\textbf{x}_0=\textbf{b}_0$. Now, I do not have $A^{-1}$ as A is too large to factor or any sort of decomposition of $A$, but assume that I ...
Costis's user avatar
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9 votes
2 answers
2k views

Solving Lx = b for big sparse Laplacian matrices

What algorithm is more practically suited in terms of performance for solving the $\mathbf{Lx=b}$ equation, where $\mathbf{L}$ is a generic Laplacian matrix (associated to a strongly connected graph, ...
teodron's user avatar
  • 193
8 votes
3 answers
895 views

Solving shifted linear systems with LU factorization

I am interested in solving a sequence of shifted linear systems $(A+\sigma I)x = b$ for various values of $\sigma$. The matrix $A$ is sparse and not too large, so I have its LU factorization available....
Victor Liu's user avatar
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7 votes
1 answer
1k views

Sparse hermitian eigensystems: are there better techniques than Arpack or TRLan?

As a part of other work I need to solve relatively large (~1E5x1E5) and sparse (~100 non-zero elements in each raw in few blocks) hermitian eigensystems. Usually only few eigenvalues+vectors are ...
Misha's user avatar
  • 240
7 votes
2 answers
3k views

Sparse Incomplete Cholesky

I'm looking for an efficient, multicore, library to do incomplete cholesky (possibly modified). Many ILU code exists, but I can't find much about IC except in PETSC or Pastix. Could some of you drop ...
Tom's user avatar
  • 465
6 votes
2 answers
572 views

Large-scale generalized eigenvalue problem with low rank LHS matrix

Assume that we have generalized eigenvalue problem: $B^HB\textbf{x} = \lambda A\textbf{x}$ where $A$ is an nxn Hermitian sparse matrix (n is very large, so we do not have $A^{-1}$ but can solve ...
Costis's user avatar
  • 1,320
6 votes
2 answers
341 views

Is it possible to ignore/discard part of a matrix when finding eigenvalues?

I have have multiple large matrices for which I need to find the largest absolute eigenvalue. I know that there is a large submatrix that does not vary. Is it possible to ignore/discard the submatrix? ...
power's user avatar
  • 521
6 votes
1 answer
1k views

Supernodal vs. Multifrontal Matrix Decompositions

Reading through Tim Davis' book Direct Methods For Sparse Linear Systems, he says that matlab can use a supernodal Cholesky decomposition but never uses a multifrontal Cholesky decomposition. At least ...
cjordan1's user avatar
  • 805
5 votes
0 answers
1k views

Symmetric sparse direct solvers in scipy

scipy.linalg.solve, in its newer versions, has a parameter assume_a that can be used to specify that the matrix $A$ is symmetric ...
Federico Poloni's user avatar
5 votes
2 answers
657 views

How "sparse" should a sparse matrix be to see benefits?

I have a matrix, whose size scales as $2^N$ (assume even $N$). In each row of the matrix, only about $2^{N/2}$ of the entries are filled ($N$ can be somewhere between 10 and 40, depending on what's ...
Henry Shackleton's user avatar
5 votes
3 answers
2k views

What is the best solver for solving a large sparse indefinite system

What's the best solver that can solve a large sparse but indefinite matrix?
Hao Yu's user avatar
  • 51
5 votes
1 answer
110 views

Is the bandwidth of indefinite A equal to its factor L in LDL^T?

In George, Liu, and Ng's book Computer Solutions of Sparse Linear Systems, it has been shown that bandwidth of $A$ is equal to bandwidth of its factors in $LL^T$.(section 4.3) However, I guess this is ...
Armut's user avatar
  • 245
4 votes
1 answer
4k views

Iteratively solving 3D Poisson equation in MATLAB

I have written a function that sets up a sparse matrix A and RHS b for the 3D Poisson equation in a relatively efficient way. The set-up is nothing fancy: I have extended the 2D 5-point stencil to an ...
slvrbld's user avatar
  • 143
4 votes
1 answer
427 views

Test matrices for large sparse overdetermined system of linear equations

I'm working on some c++ code to solve (conjugate gradient, least squares conjugate gradient, LSQR,..) large sparse overdetermined systems of linear equations. There is a twist to my matrices and the ...
Dominic Hofer's user avatar
4 votes
2 answers
3k views

Reordering sparse matrices in computational science

On page 3 of this document, there are some matrix forms for sparse matrices. I wonder if there are other forms used in computational problems encountered in physics, chemistry, etc., so that ...
Kadir's user avatar
  • 273
4 votes
2 answers
694 views

Poisson-Nernst-Planck equations with ill-conditioned sparse matrix

I am trying to solve Poisson-Nernst-Planck system of equations for ions diffusion problem using finite volume method. Nernst-Planck equation for mass transport and Poisson equation for electrostatic ...
Ben's user avatar
  • 41
4 votes
1 answer
320 views

Choosing preconditioner for unsymmetric pressure-velocity coupled system

I'm working with pressure-velocity coupled systems. It means that instead of solving 4 different linear systems in segregated approach (1 for pressure and 3 for Ux, Uy, Uz), we can solve only one ...
soh's user avatar
  • 41
3 votes
2 answers
444 views

Knapsack problem with fixed number of elements?

I am looking at an optimization problem that looks like this: $$ \text{minimize}\;\; \mathbf{x}^TQ\mathbf x \;\;, \; \mathbf x \in \mathbb R^n, x_i \in \lbrace 0, 1 \rbrace\\ \text{subject to}\;\; ||...
Slug Pue's user avatar
  • 189
3 votes
2 answers
1k views

Dirichlet boundary condition for sparse matrix - Solving Ax=b only for free nodes?

I am solving Biot equation with sparse matrix in MATLAB. I have no problem with global sparse matrices assembly, but when I assign Dirichlet boundary condition, it is so slow. From this topic, How to ...
Phạm Hùng's user avatar
3 votes
2 answers
684 views

Why iterative method: AMG preconditioned PCG is slower than Matlab direct method 'A\b'?

Recently, I have met a question that a saying goes that for large linear system: iterative methods are required because of memory problem of direct methods. But when I implement some experiments ...
Happy's user avatar
  • 961
2 votes
1 answer
3k views

Ways to solve $Ax=b$ for a sparse (banded) $A$ with updates

I want to solve the time-dependent Schrodinger Equation using the Crank-Nicolson scheme. I end up with the following matrix equation ...
Physicist's user avatar
  • 227
1 vote
1 answer
563 views

Linear solve using CHLOMOD in C

I am using the open-source CHLOMOD (as here http://faculty.cse.tamu.edu/davis/suitesparse.html) in order to solve a linear system Ax=b (performing A/b=x) in my domain decomposition code but I am ...
user20973's user avatar
1 vote
1 answer
67 views

Is there an upper bound for fill-ins for indefinite triangular factorization?

For $A=LU$, or $A=LDL^T$ factorization, bandwidth is preserved when there is no pivoting. This is true even for indefinite A, see question. However, when there is pivoting band structure is destroyed, ...
Armut's user avatar
  • 245