I want to ask a question about fast solver to the Poisson equation with Homogenous boundary conditions as follows: $$-\Delta u = f.$$ After centered difference using $n+2$ equidistance points in all directions, we get a SPD system: $$ Ax=b. $$ Let $T = \begin{bmatrix} 2 & -1 & & \\ -1 & 2 & {\ddots} & \\ & {\ddots} & {\ddots} & -1 \\ & & -1 & 2 \\ \end{bmatrix}\in \mathbb{R}^{n\times n}$, then we have

  1. in 1D case, $A=T\in \mathbb{R}^{n\times n}$;
  2. in 2D case, $A = T\otimes I +I\otimes T\in \mathbb{R}^{n^2\times n^2}$;
  3. in 3D case, $A = T\otimes I\otimes I+I\otimes T\otimes I+I\otimes I\otimes T\in \mathbb{R}^{n^3\times n^3},$ where $\otimes$ denotes the kroneck product.

I have known that in 1D and 2D, matlab command A\b is very fast and I have tested in matlab. But in 3D 'A\b' tends to be slow for large sparse matrix $A$. I have heard that in matlab, there is a function 'fft' (fast fourier transformation) can solve Ax=b quickly, but I can not understand that. Can someone give me the matlab impelementation codes that I can easily understand how matlab use 'fft' to solve this Ax=b quickly? Thanks very much.

Below is my matlab code for n=50 such that A\b fails in my matlab2018b (CPU 8G memory):

T = spdiags(ones(n,1).*[-1 2 -1], [-1 0 1],n,n);
I = speye(n);
A = kron(kron(T,I),I)+kron(I,kron(T,I))+kron(I,kron(I,T));
N = length(A);
b = rand(N,1);
  • $\begingroup$ If you just want to solve x=A\B faster, try iterative methods such as pcg. (Matlab has already included the function pcg.) $\endgroup$
    – Xi Zou
    Oct 30, 2019 at 12:16
  • $\begingroup$ Thanks Prof Zou, I want to know that in PCG command, if we give it parameters matrix $A$ and $b$, then matlab will compute matrix-vector Ax automatically the optimal way? (老师您好,如果选择使用PCG命令,我们给他一个参数矩阵A和右端项b,pcg(A,b) matlab内部会自动最佳的方式计算Ax把?不需要我们人为再去设置A*x的算法了把?谢谢老师) $\endgroup$
    – Happy
    Oct 30, 2019 at 13:30
  • $\begingroup$ Input: x = pcg(A,b,1e-8,1000); you can obtain the approximate solution. Or you can use the incomplete Cholesky factorization preconditioner, as $\endgroup$ Oct 30, 2019 at 13:58
  • $\begingroup$ @Hsien-MingKu thanks Prof Ku, but pcg indeed computes the approximate solution instead of exact solution from direct methods. Then in 3D case for very large scale, we cannot obtain the exact solution like direct methods, right? What's more, does pcg automatically choose the optimal way to compute the matrix-vector operations when we use pcg(A,b,1e-8,100)? $\endgroup$
    – Happy
    Oct 30, 2019 at 14:20
  • $\begingroup$ Sure for computing A*x in the sparse format. In fact, the multigrid is the best choice for such problems. $\endgroup$ Oct 30, 2019 at 14:24

1 Answer 1


Let $T \in \mathbb{R}^{n \times n}$ be defined as in your question, $$ T = \begin{pmatrix} 2 & -1 & & \\ -1 & 2 & {\ddots} & \\ & {\ddots} & {\ddots} & -1 \\ & & -1 & 2 \\ \end{pmatrix}. $$ Then, it is well known that the eigenvalue decomposition of $T$ is given by $$ T = Z \Lambda Z, $$ where $\Lambda$ is diagonal with $$ \Lambda_{jj} = 2\left(1-\cos\left( \frac{\pi j}{n+1} \right)\right) $$ and $Z$ is given by $$ Z_{jk} = \sqrt{\frac{2}{n+1}}\sin\left(\frac{\pi j k}{n+1}\right). $$ Notice that $Z = Z^T = Z^{-1}$.

Then, e.g. for the two-dimensional Laplacian, we have \begin{align*} A &= I \otimes T + T \otimes I \\ & = I \otimes (Z\Lambda Z) + (Z\Lambda Z) \otimes I \\ &= (Z \otimes Z) (I \otimes \Lambda + \Lambda \otimes I) (Z \otimes Z). \end{align*}

So, we can solve $A u = b$ according to the following algorithm:

  1. Let $b' = (Z \otimes Z) b$.
  2. Solve $u' = (I \otimes \Lambda + \Lambda \otimes I)^{-1} b'$ (notice that this matrix is diagonal, and the values of $\Lambda$ are known using the above formula).
  3. Compute $u = (Z \otimes Z) u'$.

The algorithm for the $d$-dimensional Laplacian is obtained analogously.

FFT Poisson solvers are based on using the FFT to quickly compute products of the form $(Z \otimes \cdots \otimes Z) b$. The idea is as follows.

The discrete Fourier transform (DFT) of a vector $v \in \mathbb{R}^m$ is given by the matrix-vector product $\Phi v$ where the matrix $\Phi \in \mathbb{R}^{m \times m}$ is defined by $$ \Phi_{jk} = \exp\left( \frac{- 2 \pi i j k }{m} \right). $$

Then, notice that multiplying a vector $b \in \mathbb{R}^n$ by $Z$ to compute the product $Z b$ corresponds to taking a subvector of the imaginary part of the DFT of a padded vector. In particular, define $\tilde{b} = (0, b, 0, \ldots, 0) \in \mathbb{R}^{2n+2}$ (i.e. padding $b$ on the left with one zero, and on the right with $n+1$ zeros). Then, $Zb$ is equal to $\sqrt{2/(n+1)}$ times the second through $(n+1)$st entries of the imaginary part of the size-$(2n+2)$ DFT of $\tilde{b}$. We use the FFT to compute the DFT of $\tilde{b}$ efficiently.

This idea generalizes to arbitrary dimensions, by considering the vector $b$ to be a $d$-tensor, and then constructing $\tilde{b}$ by padding with zeros along each dimension, and then applying the FFT in succession along each dimension.

See below for a proof-of-concept for the two-dimensional Laplacian. It should be possible to extend this to 3D with a bit of book-keeping.

n = 50;
T = spdiags(ones(n,1).*[-1 2 -1],[-1 0 1],n,n);
I = speye(n);
A = kron(T,I) + kron(I,T);

lambda = zeros(n,1);
for i=1:n
   lambda(i) = 2*(1-cos(pi*i/(n+1)));
L = lambda + lambda';

% random right-hand side
b = rand(n*n,1);
B = reshape(b,n,n);

% pad with zeros
B_ext = [zeros(1,n) ; B ; zeros(n+1,n)];
B_ext = [zeros(2*n+2,1) B_ext zeros(2*n+2, n+1)];

% compute (Z \otimes Z) B
c = -sqrt(2/(n+1));
B_prime = imag(fft(B_ext, [], 2));
B_prime = imag(fft(B_prime(:,2:n+1), [], 1));
B_prime = c^2*B_prime(2:n+1,:);

% solve diagonal system
U_prime = B_prime ./ L;

% pad with zeros
U_prime_ext = [zeros(1,n) ; U_prime ; zeros(n+1,n)];
U_prime_ext = [zeros(2*n+2,1) U_prime_ext zeros(2*n+2, n+1)];

% compute (Z \otimes Z) U_prime
U = imag(fft(U_prime_ext, [], 2));
U = imag(fft(U(:,2:n+1), [], 1));
U = c^2*U(2:n+1,:);
  • $\begingroup$ Thanks Professor. Since fft method is so fast and less computational operations, then fft is the best method for Poisson equations, right? How about AMG method and PCG methods compared with fft method for Poisson equations? thanks. $\endgroup$
    – Happy
    Nov 1, 2019 at 0:13
  • 1
    $\begingroup$ Multigrid methods (such as AMG) are optimal $\mathcal{O}(N)$ methods for the Poisson problem. FFT, while fast, is suboptimal, requiring $\mathcal{O}(N\log(N))$ operations. Multigrid is an iterative method whereas FFT is direct. Generally speaking, multigrid methods are also more flexible than FFT solvers. Multigrid methods will typically be harder to implement than FFT methods (which, as you can see, require only a couple dozen lines of code for simple cases). $\endgroup$
    – Will P.
    Nov 1, 2019 at 23:23
  • $\begingroup$ Get it! Thanks Professor for your reply. I have learned a lot. $\endgroup$
    – Happy
    Nov 2, 2019 at 7:24

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