I want to use Eigen to compute L_1^{-1}L_2, where both L_1 and L_2 are lower triangular matrices and are stored as column oriented sparse matrices in Eigen.
I tried the Eigen triangular solver. However, that requires L_2 to be dense.
The solve method in fact is not overloaded for sparse rhs, however you can use the solveInPlace method like so (I did not actually try this):
Eigen::SparseMatrix<double> foo(Eigen::SparseMatrix<double> const& L1, Eigen::SparseMatrix<double> const& L2)
{
Eigen::SparseMatrix<double> res = L2;
L1.triangularView<Eigen::Lower>().solveInPlace(res);
return res;
}
Still you should consider if you actually need the full matrix.
Related
I am working with square matrices of type std::complex<double>. In particular, a sparse matrix S and a self-adjoint, dense matrix H, and I would like to compute the product of the form S*H*S.adjoint() and add it to another dense, self-adjoint matrix J. So a straight-forward way to do this in Eigen would be:
#include <Eigen/Dense>
#include <Eigen/Sparse>
#include <complex>
Eigen::Matrix<std::complex<double>, Eigen::Dynamic, Eigen::Dynamic> J, H;
Eigen::SparseMatrix<std::complex<double>> S;
// ...
// Set H, and J to be some self-adjoint matrices of the same size, and S also same
// size, but not necessarily self-adjoint.
// ...
J += S*H*S.adjoint();
But because H and J are self-adjoint and by the form of the product S*H*S.adjoint(), we know that J will remain self-adjoint after the operation. So there is really no need to compute the entire dense matrix result S*H*S.adjoint() and we could probably save some computation time by only computing the lower- or upper-triangular part of the result and adding that to the corresponding part of the matrix J. Eigen provides an API for this sort of optimization, but I'm not able to use it in this case. For example if instead of the sparse matrix S we had a dense matrix D, then doing
J += D*H*D.adjoint();
should be less efficient than
J.triangularView<Eigen::Lower>() = D*H*D.adjoint();
or
J.triangularView<Eigen::Lower>() = D*H.selfadjointView<Eigen::Lower>()*H.adjoint();
but the API doesn't seem to provide this level of optimization when computing the former product with a sparse matrix S instead of the dense matrix D. That is,
J.triangularView<Eigen::Lower>() = S*H*S.adjoint();
doesn't compile. So my question is: is there a way to tell Eigen to only compute the lower- (or upper-) triangular part of the matrix S*H*S.adjoint() and add it to the lower- (or upper-) triangular part of the self-adjoint matrix J to improve performance?
Perhaps even better would be an overload of a rank 1 update that looked something like
J.selfadjointView<Eigen::Lower>().rankUpdate(S,H);
Of course the current API doesn't support this form and to get the desired result would require taking the square root of H, call it G and do
J.selfadjointView<Eigen::Lower>().rankUpdate(S*G);
but although this should give the correct result, taking the square root is probably super expensive compared to the rest, so this would probably be slower.
The best performance I've found so far is
J.noalias() += S*H*S.adjoint();
The following code works as expected:
matrix.cpp
// [[Rcpp::depends(RcppEigen)]]
#include <RcppEigen.h>
// [[Rcpp::export]]
SEXP eigenMatTrans(Eigen::MatrixXd A){
Eigen::MatrixXd C = A.transpose();
return Rcpp::wrap(C);
}
// [[Rcpp::export]]
SEXP eigenMatMult(Eigen::MatrixXd A, Eigen::MatrixXd B){
Eigen::MatrixXd C = A * B;
return Rcpp::wrap(C);
}
// [[Rcpp::export]]
SEXP eigenMapMatMult(const Eigen::Map<Eigen::MatrixXd> A, Eigen::Map<Eigen::MatrixXd> B){
Eigen::MatrixXd C = A * B;
return Rcpp::wrap(C);
}
This is using the C++ eigen class for matrices, See https://eigen.tuxfamily.org/dox
In R, I can access those functions.
library(Rcpp);
Rcpp::sourceCpp('matrix.cpp');
A <- matrix(rnorm(10000), 100, 100);
B <- matrix(rnorm(10000), 100, 100);
library(microbenchmark);
microbenchmark(eigenMatTrans(A), t(A), A%*%B, eigenMatMult(A, B), eigenMapMatMult(A, B))
This shows that R performs pretty well on resorting (transpose). Multiplying has some advantages with eigen.
Using the Matrix library, I can convert a normal matrix to a sparse matrix.
Example from https://cmdlinetips.com/2019/05/introduction-to-sparse-matrices-in-r/
library(Matrix);
data<- rnorm(1e6)
zero_index <- sample(1e6)[1:9e5]
data[zero_index] <- 0
A = matrix(data, ncol=1000)
A.csr = as(A, "dgRMatrix");
B.csr = t(A.csr);
A.csc = as(A, "dgCMatrix");
B.csc = t(A.csc);
So if I wanted to multiply A.csr times B.csr using eigen, how to do that in C++? I do not want to have to convert types if I don't have to. It is a memory size thing.
The A.csr %*% B.csr is not-yet-implemented.
The A.csc %*% B.csc is working.
I would like to microbenchmark the different options, and see how matrix size will be most efficient. In the end, I will have a matrix that is about 1% sparse and have 5 million rows and cols ...
There's a reason that dgRMatrix crossproduct functions are not yet implemented, in fact, they should not be implemented because otherwise they would enable bad practice.
There are a few performance considerations when working with sparse matrices:
Accessing marginal views against the major marginal orientation is highly inefficient. For instance, a column iterator in a dgRMatrix and a row iterator in a dgCMatrix need to loop through almost all elements of the matrix to find the ones in just that column or row. See this Rcpp gallery post for additional enlightenment.
A matrix cross-product is simply a dot product between all combinations of columns. This means the penalty of using a column iterator in a dgRMatrix (vs. a column iterator in a dgCMatrix) is multiplied by the number of column combinations.
Cross-product functions in R are highly optimized, and are not (in my experience) significantly faster than Eigen, Armadillo, equivalent STL variants. They are parallelized, and the Matrix package takes wonderful advantage of these optimized algorithms. I have written C++ parallelized STL cross-product variants using Rcpp structures and I don't see any increase in performance.
If you're really going this route, check out my Rcpp gallery post on Sparse Matrix structures in Rcpp. This is to be preferred to Eigen and Armadillo Sparse Matrices if memory is a concern, as Eigen and Armadillo perform a deep copy rather than a reference to an R object already existing in memory.
At 1% density, the inefficiencies of row iterators will be greater than at say 5 or 10% density. I do most of my tests at 5% density and generally binary operations take 5-10x longer for row iterators than for column iterators.
There may be applications where row-major ordering shines (i.e. see the work by Dmitry Selivanov on CSR matrices and irlba svd), but this is absolutely not one of them, in fact, so much so you are better off doing in-place conversion to get to a CSC matrix.
tl;dr: column-wise cross-product in row-major matrices is the ultimatum of inefficiency.
I'm using the Armadillo Cpp code for matrix algebra. I have an Eigenvector matrix E that I want to sort by its eigenvalues in a vector d.
mat E;
vec d;
eig_sym(d,E,Rxx);
// Sort indices of eignen values / vectors
// based on decreasing real part of eigen values.
uvec order = sort_index(-d);
// Extract top eigen vectors.
E = E(span::all,order(1,nb_sources));
I couldn't find anything related to this kind of indexing in the documentation. Indexing using a vector is such a common requirement that I'd be surprised if it isn't present in Armadillo.
What is the proper way to do this in Armadillo?
One way to do it is
E = E.cols(order(span(0,nb_sources-1)));
I'm a new to Eigen and I'm working with sparse LU problem.
I found that if I create a vector b(n), Eigen could compute the x(n) for the Ax=b equation.
Questions:
How to display the L & U, which is the factorization result of the original matrix A?
How to insert non-zeros in Eigen? Right now I just test with some small sparse matrix so I insert non-zeros one by one, but if I have a large-scale matrix, how can I input the matrix in my program?
I realize that this question was asked a long time ago. Apparently, referring to Eigen documentation:
an expression of the matrix L, internally stored as supernodes The only operation available with this expression is the triangular solve
So there is no way to actually convert this to an actual sparse matrix to display it. Eigen::FullPivLU performs dense decomposition and is of no use to us here. Using it on a large sparse matrix, we would quickly run out of memory while trying to convert it to dense, and the time required to compute the factorization would increase several orders of magnitude.
An alternative solution is using the CSparse library from the Suite Sparse as:
extern "C" { // we are in C++ now, since you are using Eigen
#include <csparse/cs.h>
}
const cs *p_matrix = ...; // perhaps possible to use Eigen::internal::viewAsCholmod()
css *p_symbolic_decomposition;
csn *p_factor;
p_symbolic_decomposition = cs_sqr(2, p_matrix, 0); // 1 = ordering A + AT, 2 = ATA
p_factor = cs_lu(p_matrix, m_p_symbolic_decomposition, 1.0); // tol = 1.0 for ATA ordering, or use A + AT with a small tol if the matrix has amostly symmetric nonzero pattern and large enough entries on its diagonal
// calculate ordering, symbolic decomposition and numerical decomposition
cs *L = p_factor->L, *U = p_factor->U;
// there they are (perhaps can use Eigen::internal::viewAsEigen())
cs_sfree(p_symbolic_decomposition); cs_nfree(p_factor);
// clean up (deletes the L and U matrices)
Note that although this does not use expliit vectorization as some Eigen functions do, it is still fairly fast. CSparse is also very compact, it is just a single header and about thirty .c files with no external dependencies. Easy to incorporate in any C++ project. There is no need to actually include all of Suite Sparse.
If you'll use Eigen::FullPivLU::matrixLU() to the original matrix, you'll receive LU decomposition matrix. To display L and U separately, you can use method triangularView<mode>. In Eigen wiki you can find good example of it. Inserting nonzeros into matrices depends on numbers, which you wan't to put. Eigen has convenient syntax, so you can easily insert values in loop:
for(int i=0;i<size;i++)
{
for(int j=size;j>someNumber;j--)
{
matrix(i,j)=yourClass.getNextNumber();
}
}
I need to convert a MATLAB code into C++, and I'm stuck with this instruction:
a = K\F
, where K is a sparse matrix of size n x n, and F is a column vector of size n.
I know it's easy to solve that using the Eigen library - I have tried the fullPivLu() method, and I've been able to built a working snippet, using a Matrix and a Vector.
However, my K is a SparseMatrix<double> (while F is a VectorXd). My declarations:
SparseMatrix<double> K(nec, nec);
VectorXd F(nec);
and it seems that SparseMatrix doesn't have the fullPivLu() method, nor the lu() one.
I've tried, in fact, these two different approaches, taken from the documentation:
//1.
MatrixXd x = K.fullPivLu().solve(F);
//2.
VectorXf x;
K.lu().solve(F, &x);
They don't work, because fullPivLu() and lu() are not members of 'Eigen::SparseMatrix<_Scalar>'
So, I am asking: is there a way to solve a system of linear equations (the MATLAB's mldivide, or '\'), using Eigen for C++, with K being a sparse matrix?
Thank you for any help.
Would Eigen::SparseLU work for you?