Questions tagged [sparse-arrays]
Questions on the construction and manipulation of sparse arrays in Mathematica, with functions like SparseArray[] and Band[].
321
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3
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Why does using a sparse matrix for least squares instead slow down the speed?
Here is the code. The matrix appears to be relatively sparse in terms of its visual representation, but why does using least squares result in significantly slower speed compared to the previously ...
- 113
2
votes
0
answers
66
views
Performance of multiplying two identity matrices
I am running Mathematica 13.3.1.0 on a M1 Mac, and I ran the following codes to check on the time spent on matrix multiplication.
...
- 513
0
votes
0
answers
28
views
Sparse Kronecker Product of Pauli Matricies
Suppose I have a list of Pauli matrices (X, Z and I type)
paulis = {x,z,z,i,z,x,i,z};
I would like to compute a sparse array equivalent to
$$x \otimes z\otimes z \...
- 829
1
vote
1
answer
31
views
Best way to Simplify (or applying other functions to) a SymmetrizedArray
I wanted to perform an element-wise Simplify[] on a SymmetrizedArray, but I couldn't find an efficient way to do so without converting it to a "Normal" ...
- 13
8
votes
1
answer
309
views
How can I prevent conversion of a SparseArray to a DenseArray?
The Problem
I'm trying to implement an efficient Whitker-Eliers smoother in Mathematica. In Matlab, this is a few lines of code (taken from the SI of the above paper):
...
- 490
5
votes
2
answers
192
views
Reshaping sparse arrays to have extra index
I have an $n \times m \times p$ array, let's call it $r$.
I want to obtain an $n \times m \times p \times 5$ array (let's call it $q$) where $q$ is the same as $r$ except that every non-zero component ...
- 175
6
votes
1
answer
105
views
DeleteDuplicates without destroying SparseArray
When I use DeleteDuplicates to delete equal rows of a sparse array, the output is not a sparse array anymore. In my application, the sparse arrays are huge but very ...
- 1,470
0
votes
2
answers
54
views
Transformation invariant subspace of three-component array
I have a large sparse array A with dimensions $m \times n \times q $. I also have two transformation matrices, B ($n \times n$) ...
- 175
9
votes
7
answers
772
views
How to quickly make a rectangular array of continous 1 and 0 given the start position of 1
I would like to make a rectangular array of 1 and 0 with continuous columns of 1.
We are ...
4
votes
1
answer
147
views
Third party libraries in LibraryLink
I am trying to use third-party libraries in LibraryLink, but the kernel crashes when I call their functions.
In particular, I want to make available some functions of SuiteSparse to manipulate ...
- 966
8
votes
1
answer
145
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Rank of singular, large, sparse matrices
I need to find the rank (and eventually do the Gaussian elimination) of a large, sparse, non-square matrix of integers. There are a few methods in Mathematica to find the rank of a non-square matrix (...
- 966
6
votes
2
answers
267
views
Efficient way to compose a SparseArray from system of linear equations [closed]
I have several relations between some variables, e.g. id[1] - id[2] = 0, id[2] = 0. I need to compose a SparseArray that contains the coefficients. In that example,<...
- 966
6
votes
1
answer
136
views
Minimizing computational time for a quantum walk problem
Any suggestions as to how to speed up the computational time for this quantum walk problem which is coded using a normalized SparseArray coin operator as follows:
...
- 3,198
1
vote
0
answers
54
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Method for MinimumBandwidthOrdering [closed]
MinimumBandwidthOrdering[m, Method -> "RCMD"]
What method is 'RCMD' in Mathematica?
Reverse Cuthill-McKee,
Reduced Canonical Matrix Diagram,
Restricted Minimum Column Degree,
other?
- 53
5
votes
1
answer
131
views
How could I see the memory use on sparse array and constant array matrices? What is the advantage? [duplicate]
I have a huge matrix defined using constant array function and it allocates so much memory preventing the calculation. Therefore, I would like to change the constant array matrix into sparse matrix ...
3
votes
1
answer
201
views
Efficient memory usage while building a large sparse matrix
I am sure the following problem has been solved already, but I am unable to find any solution... Any help appreciated!
So I am building a pretty huge matrix (or tensor, actually) using
...
- 115
2
votes
0
answers
64
views
Dot product of arrays that are members of the same list
Lets say I have a list of n arrays:
n=3;
list = Table[RandomInteger[{-10, 10}, {2, 2}], n];
I would like to calculate the matrix corresponding to:
...
7
votes
1
answer
124
views
Fast Sparse Tensor Addition
How can one do a fast sparse tensor addition?
Below, I have the following code: We first generate 3 random sparse 1000x1000x1000 tensors with 10^6 entries each.
Then, I want to add them. But the usual ...
2
votes
1
answer
112
views
How do I create a banded matrix using values from a given function [closed]
I would like to create a matrix were values of the function P make up the diagonals. I tried using the For loop but did not get it right.
...
- 21
4
votes
1
answer
209
views
Speeding Up Sparse Matrix Generalized Eigenvalues
I have a generalized eigenvalue problem
$$
{\mathbf A}\vec v = \lambda {\mathbf B} \vec v
$$
for which I am trying to find the smallest eigenvalue $\lambda$ and the associated eigenvector $\vec v$. ...
- 285
2
votes
1
answer
119
views
Reconstruction on large sparse array
I'm struggling with a reconstruction of a large sparse array. What I'm trying to do is to rearrange a 2 dimensional array (respresenting a system matrix for a given system of equations) such that I ...
- 45
6
votes
4
answers
1k
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Implementation of MATLAB's "numgrid" function [closed]
I am looking for an implementation of MATLAB's numgrid function, in particular the "B" mode.
For example, I want to get the matrix corresponding to the ...
- 8,051
3
votes
3
answers
169
views
Insert a dynamic vector into a matrix
If I have the following dynamic vector
Cs[NN_] :=
Table[{Sin[(2*i - 1) τ], Sin[(2*i - 1) τ]}, {i, 1, NN}] //
Flatten
The size of Cs depends on the integer ...
- 1,329
1
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1
answer
83
views
1
vote
0
answers
57
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Erratic behavior retrieving large data (several tens of gigabytes) that has been serialized by Mathematica
Hardware: PC with 256GB RAM
OS: Windows 10
Mathematica: Version 13.0.1
One of my projects has led to the creation of a SparseArray whose ByteCount is ~ 35GB in RAM. At the time of creation the ...
- 2,114
2
votes
1
answer
100
views
Define a function with sparsearray
I am trying to define a function using SparseArray, but the entries were defined before. How can I avoid this error?
Code is:
...
- 121
1
vote
0
answers
29
views
Why does Sparsearray diagonalization by Krylov technique become slower for very large sizes?
Here is an example sparse matrix, taken from example Hamiltonian, which was a question I asked before in this forum.
...
- 613
2
votes
0
answers
27
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Threshold on triangular SparseArray
I am confused by the behavior of Threshold on sparse UpperTringularize (and LowerTringularize...
- 7,663
3
votes
0
answers
74
views
Fastest Way to make rows and columns zero and corresponding (i,i) element 1 of a large Sparse Matrix
I have a 5552 by 5552 sparse matrix:
...
4
votes
3
answers
499
views
Generating signed permutation matrices
As most people (on here at least) know a permutation matrix is a square binary matrix that has exactly one entry of 1 in each row and each column and 0s elsewhere. For the $n \times n$ case there are $...
- 747
8
votes
0
answers
171
views
Defining a SparseArray functions in Mathematica 13
I am defining a sparse array as a function of argument x, i.e.
f[x_] = SparseArray[{1->x}, {3}]
In Mathematica 12 this works perfectly, I can pass arguments and ...
- 81
0
votes
0
answers
710
views
How to convert an SparseArray into a Matrix?
I have the following sparse array and I want to change it to a matrix. Could you please tell me how to do that?
...
2
votes
1
answer
112
views
How to create a 3D matrix from different blocks?
I would like to generate a $3D$ matrix of dimension $(n1\times n1\times n1)$ compose of $216$ matrix blocks $(n2\times n2\times n2)$. All 216 matrix blocks are subdivided into 4 groups, each one with ...
- 1,335
9
votes
2
answers
195
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SparseArray Input
How to create a SparseArray without using lists of rule in MMA?
In MMA we can define a SparseArray using lists of rule
...
- 1,816
7
votes
0
answers
54
views
Is there a way to make SparseArray distinguish between background values of different precision that are numerically equal?
To illustrate what I mean, consider the following:
SparseArray[{{1} -> 1, {5} -> 1.}, Automatic, 0] // Normal
{1, 0, 0, 0, 1.}
As you can see, the ...
- 21.9k
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0
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33
views
2
votes
0
answers
176
views
Building a Matrix as a piecewise-function of the indices without for loops [closed]
I'm very new to Mathematica and this site. I've read that building matrices with For loops is slow, and I have experienced this myself on the current project. I'm trying to wrap my head around ...
- 21
4
votes
0
answers
98
views
How to efficiently build a large sparse matrix and overloading a compiled function?
I would like to construct a large sparse matrix folding from rank-4 tensor given by the following:
$\mathcal{L}_{1L}^{00}(i,j)=\mathcal{L}_{1L}^{00}(m_1,m_2;M_1,M_2)$
The indices of matrix $(i,j)$ are ...
- 445
6
votes
2
answers
436
views
Speedup the production of a sparse symmetric matrix with a dense vector
The optimization of the production of a sparse symmetric matrix with a dense vector has existed for a long time. Someone once compared the matrix operations of Mathematica with MATLAB, and then came ...
- 141
1
vote
2
answers
130
views
1
vote
1
answer
155
views
Why does generating a list of elements for SparseArray crash the kernel?
I am trying to create a sparse matrix by the SparseArray command. For a set of index pairs $(i,j)$ I want to calculate the $A_{i,j}$ element and then use this ...
- 243
2
votes
0
answers
52
views
Implementing array with partial cyclic data?
I'd like to construct an array where some columns are cyclic. As an illustrative example, take
Table[Mod[k, 2^i], {k, 2^10}, {i, 0, 10}] //Grid,
where the vast ...
- 763
2
votes
1
answer
322
views
Diagonal matrix command in Mathematica
How to find the corresponding Mathematica commands for diagonal matrix operation in Matlab, e.g.
AA=rand(3,3);
Step 1.) finding the diagonal elements, and export ...
- 1,816
3
votes
1
answer
126
views
How to write correctly some arguments in SparseArray
I am struggling to put an argument in SparseArray. Let's consider the following example
...
- 45
1
vote
0
answers
64
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Parallelizing construction of sparsearray
I'm constructing sparse arrays where blocks of each array are results of the integral defined in integralList
...
- 63
1
vote
2
answers
177
views
Improving large array manipulation
I am doing an iterative program, which uses large arrays/vectors and where the output of one round is used as an input for the next steps but works slowly when dimensions are bigger.
In brief, we ...
- 45
0
votes
0
answers
83
views
sparse matrix multiplication
Say I have a sparse matrix $M$ with $\sim 50.000 .000$ non zero elements.
What is the fastest way to make operations such as :
$$M^k X$$
where $X$ is a given vector.
Is the operation $MX$ ...
- 964
1
vote
1
answer
68
views
Fastest way to convert two associations into a sparse matrix
I have two association $N$ and $C$
$N$ has this form :
$N=<|x_1\rightarrow \{x_{1,1},...x_{1,p_1}\},x_2\rightarrow \{x_{2,1},...x_{2,p_2}\}...,x_D\rightarrow \{x_{D1},...x_{Dp_D}\} |>$
$C$ has ...
- 964
9
votes
1
answer
194
views
Efficiently populate a Sparsearray for a set of rules for a constrained basis
I want to populate quite a large SparseArray(10^6 x10^6) efficiently. It is basically a spin system Hamiltonian with a constrained Hilbert space. Unlike the examples I have looked at in this forum ...
- 613
1
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0
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88
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