Matrix multiplication very slow in Eigen

Question

I have implemented a Gauss-Newton optimization process which involves calculating the increment by solving a linearized system Hx = b. The H matrx is calculated by H = J.transpose() * W * J and b is calculated from b = J.transpose() * (W * e) where e is the error vector. Jacobian here is a n-by-6 matrix where n is in thousands and stays unchanged across iterations and W is a n-by-n diagonal weight matrix which will change across iterations (some diagonal elements will be set to zero). However I encountered a speed issue.

When I do not add the weight matrix W, namely H = J.transpose()*J and b = J.transpose()*e, my Gauss-Newton process can run very fast in 0.02 sec for 30 iterations. However when I add the W matrix which is defined outside the iteration loop, it becomes so slow (0.3~0.7 sec for 30 iterations) and I don't understand if it is my coding problem or it normally takes this long.

Everything here are Eigen matrices and vectors.

I defined my W matrix using .asDiagonal() function in Eigen library from a vector of inverse variances. then just used it in the calculation for H ad b. Then it gets very slow. I wish to get some hints about the potential reasons for this huge slowdown.

EDIT:

There are only two matrices. Jacobian is definitely dense. Weight matrix is generated from a vector by the function vec.asDiagonal() which comes from the dense library so I assume it is also dense.

The code is really simple and the only difference that's causing the time change is the addition of the weight matrix. Here is a code snippet:

for (int iter=0; iter<max_iter; ++iter) {
    // obtain error vector
    error = ...  
    // calculate H and b - the fast one
    Eigen::MatrixXf H = J.transpose() * J;
    Eigen::VectorXf b = J.transpose() * error;
    // calculate H and b - the slow one
    Eigen::MatrixXf H = J.transpose() * weight_ * J;
    Eigen::VectorXf b = J.transpose() * (weight_ * error);
    // obtain delta and update state
    del = H.ldlt().solve(b);
    T <- T(del)   // this is pseudo code, meaning update T with del
}

It is in a function in a class, and weight matrix now for debug purposes is defined as a class variable that can be accessed by the function and is defined before the function is called.

Answer 1

I guess that weight_ is declared as a dense MatrixXf? If so, then replace it by w.asDiagonal() everywhere you use weight_, or make the later an alias to the asDiagonal expression:

auto weight = w.asDiagonal();

This way Eigen will knows that weight is a diagonal matrix and computations will be optimized as expected.