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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73 views

Givens rotation algorithm without matrix-matrix multiplication

I would like to implement a givenRotation algorithm without having matrix-matrix multiplication. Matrix-vector is fine or just for looping. I am to decompose a rectangular (m+1)xm Hessenberg matrix. I ...
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1answer
91 views

What is the difference between Adittive Schwarz as a preprocessor and a solver?

As we all know, the Additive Schwarz approach can be used as either solver or preconditioner, however, my question is, what is the difference between the two? In other words, how to use AS as solver, ...
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1answer
77 views

What is the conventional approach for sparse matrix multiplication?

When you're multiplying sparse matrices against other sparse matrices or dense matrices, what is the conventional approach for each? How are the sparse matrices stored? What does matrix multiplication ...
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1answer
81 views

Bounds for the optimal bandwidth of 2D/3D FEM stiffness matrices

is anyone here aware of whether there exist bounds on the optimal bandwidths of 2D/3D FEM stiffness matrices? Edit: more specifically, I would like to have bounds on the minimum bandwidth after ...
6
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1answer
192 views

Algorithm for solving systems which are nearly symmetric/adjoint?

I am familiar with Cholesky decomposition and LU factorization for solving systems of linear equations. I have a problem where I have large sparse matrices (say, 1000x1000 or larger) where only one or ...
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1answer
36 views

Best search algorithm for optimal weight factor in SOR method

I had written an algorithm that searches for the optimal weight parameter to be implemented in the successive-over relaxation (SOR) method which worked cleanly by vectorizing the interval and for ...
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1answer
71 views

Efficiency of scipy.sparse.linalg.expm_multiply with sparse vs unsparse vectors

From the package scipy.sparse.linalg in Python, calling expm_multiply(X, v) allows you to compute the vector ...
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0answers
111 views

Invert a huge sparse operator;

please help me with this question, I want to invert a huge sparse (non-circulant) this below in a $Ax=y$ equation: $$(\lambda I+ \beta D+ \sigma C)x=y$$ where I is an Identity Matrix,D is a Diagonal ...
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0answers
35 views

Tolerance is not satisfied in eigsh function

I am diagonalizing a sparse matrix of size $153600\times 153600$ via eigsh function. I did not set the tolerance to specific value, so it would be the default value ...
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0answers
49 views

Viable algorithms for efficiently solving a block matrix system with non-uniform sparsity structure

I am trying to use Newton's method to get a stationary solution for a system of equations of the following form: $$ \begin{Bmatrix} \frac{\partial x}{\partial t} \\ 0 \end{Bmatrix} = \begin{Bmatrix} f(...
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1answer
118 views

How can I extract the banded or block diagonal part of a sparse matrix in MATLAB?

Given a large sparse (square) matrix in MATLAB, how can I extract the banded or the block-diagonal parts (of fixed size) of it efficiently? These are useful operations when prototyping and testing ...
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0answers
72 views

Solving PDEs: What is the best way to deal with non-banded/dense jacobians?

I have a system of PDEs describing atmospheric chemistry and transport. I use finite-differences to make my system of PDEs into a system of ~10,000 ODEs. I then integrate the ODEs forward in time with ...
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1answer
93 views

`eigsh` (Lanczos algorithm) slows down for degenerate eigenvalues

I have a complex Hermitian matrix of size about $70000\times 70000$. I want about 100 eigenvalues near 0. However, I know that every eigenvalues are two-fold degenerate. I found out that the running ...
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1answer
86 views

RCM better than Nested dissection? (For FEM discretizations in 2D and 3D)

I realize this might be a too general question but here goes nothing: I am trying different re-ordering strategies and checking the fill-in of $A=LU$. I have 2D ($p=1$, $h=1/40$ on $\Omega = [-1,1]^2$)...
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63 views

Does shift-invert method has invertibility issue?

Please note that I have nearly zero background on numerical methods. I understand the shift invert method as described in SciPy Tutorial The main argument of the above link is as follows. Suppose we ...
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0answers
59 views

Software for solving large systems of linear equations over gf(2)

What available solvers are there for linear equation solver over GF(2) (Boolean), capable of dealing with large sparse systems (in the 10k - 100k variables range)?
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3answers
215 views

How to apply the boundary condition when global stiffness matrix is stored in csr format? [duplicate]

I am solving the poisson equation and I constructed the global stiffness matrix in compressed row storage format. Then I wrote the preconditioned conjugate gradient solver for solving the system of ...
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0answers
81 views

C.S.R method in finite element matrix assembly

I have solved the 2D Poisson equation using finite element method with simplex triangular element in MATLAB. First, I generated the triangular mesh using pdetool in ...
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0answers
51 views

Nonsymmetric permutations for LU factorisation of symmetric matrix

Let $A$ be a symmetric matrix. It is then well known that computing the LU factorisation of $PAP^T$ instead of $A$ for a suitably chosen permutation matrix $P$ can greatly reduce fill-in. My question ...
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1answer
100 views

Nonlinear root solving libraries which accept a Jacobian in band-storage

I'm in search for a library for solving large systems of non-linear equations, similar to MINPACK, but unlike MINPACK, can accept a Jacobian in band-storage. My Jacobian is sometimes not invertible, ...
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2answers
132 views

Solving a specific sparse linear system without dense materialization

I need to (computationally) solve a system of equations, for the purposes of an interior point method, of the form $$ \left[\begin{array}{cc}B & A^T \\ A & 0\end{array}\right] \left[\begin{...
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1answer
2k views

How to compute Singular value decomposition of a large matrix with Python

Language: Python3 Problem: I have a matrix Q of shape [51200 rows x 51200 cols] stored in a binary file, each of the element in this matrix has a data type of complex64. To load the data into memory I ...
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1answer
257 views

Efficiently computing $e^{tX}$ for many different values of $t$

Given an anti-Hermitian and sparse matrix $X$, I am using Python (NumPy and SciPy) to compute the matrix exponential $f(t) := e^{tX}$ for many values of $t$. The method I am currently using is to ...
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1answer
118 views

Complexity of solving an image differential linear system

Define an "image differential linear system" as a linear system $A\mathbf{x}=\mathbf{b}$ wherein $\mathbf{x}$ contains the ($\mathbb{R}$) pixels of an image and each row of $A$ constrains ...
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1answer
285 views

Parallelize Scipy iterative methods for linear equation systems(bicgstab) in Python

I need to solve linear equations system Ax = b, where A is a sparse CSR matrix with size 500 000 x 500 000. I'am using scipy.bicgstab and it takes almost 10min to solve this system on my PC and I need ...
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0answers
88 views

performance comparison between PETSc and SLATE

We want to start a new project to solve a large-scale inverse problem (O(10^6) number of parameters) to invert for subsurface wave speeds. We will use FEM to solve forward and adjoint PDEs. In our ...
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78 views

How to make a directed graph symmetric?

Say I have a directed graph given as an adjacency matrix $A$ in CSR format represented by the arrays ia (row indexes) and ja (...
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1answer
34 views

In Eigen, can a sparse matrix contain vectors/objects instead of simple scalar values?

I need to have a sparse matrix whose elements are not simple numbers, but objects, e.g. a couple of floating point values and a bunch of integer indices. I am wondering if Eigen has something similar, ...
3
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1answer
103 views

Choice of iterative solver for a sparse asymmetric matrix with symmetric structure

I have a sparse $nxn$ matrix A with pretty interesting structure. It has a block structure with symmetric structure but asymmetric blocks. Expressed mathematically the block $A_{jk} = A_{kj}$ but $A_{...
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3answers
116 views

Create a sparse matrix

I am writing a FE program which calculates the displacements under a uniform load. I want to store the stiffness matrix in sparse form(COO) without using an external library.Assume an upper-bound for ...
2
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2answers
142 views

L1 least squares minimization with a sparse matrix

I have the following problem: $$\min_{x\in \mathbb{R}^n}\|Ax-b\|_1$$ where the matrix $A$ is large and sparse. I am looking for methods/code that can minimize this efficiently. References are very ...
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2answers
779 views

When is it easy to invert a sparse matrix?

(Crossposted on cstheory.SE) When is it easy to invert a sparse matrix? Specifically, I'm wondering about the cases in which matrix inversion has similar cost to sparse matrix multiplication, hence ...
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3answers
392 views

On the reordering of sparse matrices

I have been reading on different techniques used to reorder sparse matrices to achieve better performance, the most popular being the Cuthill-McKee or Reverse Cuthill-McKee algorithm. Most of those ...
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0answers
74 views

Derivative-free ill-conditioned non-linear least squares

I am looking for a package which can solve (non-linear) least squares problems without the use of derivatives (because of an expensive model), but which also deals with ill-conditioning well (such as ...
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1answer
218 views

Implementation of sparse matrix SVD for GPU

I have a sparse matrix $W$ which is almost-squared ($N+1 \times N$) and I would like to know the eigenvalues of $A = W^T W$. $A$ is Hermitian so the eigenvalues are real-positive valued. The usual ...
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1answer
171 views

Solving large sparse system

I am working on a problem with very large sparse matrices. I'd like to compute $A^{-1} B$, that is a crucial part of converting DAE to ODE (and there is no workaround). Here size of $A$ is 2E+5 x 2E+5 ...
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1answer
159 views

Efficient way to solve a set of linear equations $Ax=b$ when $A$ is sparse and some elements of $b$ are equal to zero

I have a set of linear equations, $Ax=b$. And about half of the elements in the right-hand side (vector $b$) are equal to zero. My system matrix $A$ is a sparse complex matrix. And $A$ is in the size ...
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2answers
338 views

Is there an iterative solver for dense matrices with possible zero diagonal entries?

Is there an iterative solver that can handle potentially zero entries on the central diagonal? I am implementing a polynomial fitting algorithm (up to $10^{th}$-order) and my matrix is a "...
3
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0answers
216 views

Compute Nullspace of Sparse Matrix

I am computing the nullspace of a sparse rectangular $m$ x $n$ matrix $A$, where $m$ << $n$. I do this by computing the QR decomposition of $A^T$ and extract the $n-m$ right-most columns of the ...
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1answer
173 views

Solving a sparse linear system using transpose of lower triangular matrix without copying

I have a sparse lower-triangular matrix $L$, and a right-hand side $b$, and I'd like to solve the linear system $$L^T x = b$$ but without explicitly creating $L^T$. Ideally, I could write something ...
2
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1answer
128 views

Fast way to build stiffness directly as CSC matrix

I have been working on finite element code in Fortran 2008, and have implemented my own sparse matrix types. I have found that mapping local stiffness matrices (real type) to a global COO sparse type ...
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1answer
109 views

How to delete $n^{th}$ row and $n^{th}$ column of a matrix K in Petsc and restructure it?

I have a matrix K in Petsc. I want to delete the $n^{th}$ row and $n^{th}$ column of this matrix and restructure it. I am a beginner in Petsc. Can you suggest how to do it? Example: I have matrix K ...
3
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1answer
436 views

Why is 'scipy.sparse.linalg.spilu' less efficient than 'scipy.linalg.lu' for sparse matrix?

I have a matrix B which is sparse and try to utilize a function scipy.sparse.linalg.spilu specialized for sparse matrix to ...
2
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1answer
60 views

what does `cusparse<t>csrsv2_analysis()` do?

In cuSPARSE, you can solve a sparse triangular linear system by calling cusparse<t>csrsv2_solve(). However, you need to call ...
3
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1answer
301 views

Fast nonzero indices per row/column for (sparse) 2D numpy array

I am looking for the fastest way to obtain a list of the nonzero indices of a 2D array per row and per column. The following is a working piece of code: ...
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1answer
102 views

How to fill matrix entries for two-dimensional implicit finite-difference for the general case

If I have derived a finite-difference formula for a 2D problem, for example something like: $af_{i,j}+bf_{i-1,j}+cf_{i,j-1}+df_{i-1,j-1}=g_{i,j}$ where f is the unknown function on a grid and ...
2
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1answer
107 views

Best way to convert a sparse (containing zeros) covariance matrix into a correlation matrix?

I have a $100$x$100$ covariance matrix that looks like this. Some rows/cols are all-zero because those corresponding elements are not present in the sample from which covariance is calculated. I'm ...
3
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0answers
307 views

What is the algorithm to convert an adjacency matrix to a block diagonal structure?

I'm a little at loss as to what my supervisor meant by the "hierarchical block decomposition" of a matrix, but the goal is to put a sparse symmetric adjacency matrix into a block diagonal structure to ...
2
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0answers
84 views

How to determine the finite difference coefficient matrix in 2D with periodic BC?

I'm solving a PDE in matlab using ode15s, and since the spatial dimension is 2, and number of variables grow large very quickly, I need to supply the structure of ...
3
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1answer
614 views

Sparse Matrix Matrix multiplication using Intel MKL

Let $D$ be a sparse matrix. I want to compute $D\times D^T$. As $D$ is fairly large, so I am row-slicing $D$. That means for a range $(i,j)$, I am computing $C = D(i:j,:) \times D^T$ and performing ...

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