SRSG UNIVERSE-HPC Training

There are seven available sparse matrix types in scipy.sparse:

csc_matrix: Compressed Sparse Column format
csr_matrix: Compressed Sparse Row format
bsr_matrix: Block Sparse Row format
lil_matrix: List of Lists format
dok_matrix: Dictionary of Keys format
coo_matrix: COOrdinate format (aka IJV, triplet format)
dia_matrix: DIAgonal format

As indicated by the excellent documentation, the dok_matrix or lil_matrix formats are preferable to construct matrices as they support basic slicing and indexing similar to a standard NumPy array.

You will notice that the FD matrix we have constructed for the Poisson problem is composed entirely of diagonal elements, as is often the case. If you were constructing a similar matrix in MATLAB, you would use the spdiags function, and scipy.sparse has its own equivalent. However, all the scipy.sparse formats also have special methods setdiag which provide a more object-orientated method of doing the same thing.

Scipy has a few different direct solvers for sparse matrics, given below:

spsolve: This solves $Ax=b$ where $A$ is converted into CSC or CSR form

spsolve_triangular: Solves $Ax=b$ , where $A$ is assumed to be triangular.

factorized: This computes the $LU$ decomposition of the input matrix $A$ , returning a Python function that can be called to solve $Ax = b$

splu: This computes the $LU$ decomposition of the input matrix $A$ using the popular SuperLU library. It returns a Python object of class SuperLU, that has a solve method you can use to solve $Ax = b$

Note, scipy.sparse.linalg also has many iterative solvers, which we will investigate further in the next chapter.

Problems

Your goal for this problem is to construct the FD matrix $A$ given above, using scipy.sparse, and:

Visualise Poisson Matrix

Visualise the matrix $A$ using the Matplotlib spy plot

Solve Poisson problem

Solve the Poisson problem using:

$f(x) = 2 \cos(x) / e^x$ , with boundary conditions $g(0) = 0$ and $g(2 \pi)=0$ . The analytical solution is $u_{a}(x) = -\sin(x) / e^x$ .
$f(x) = 2 \sin(x) / e^x$ , with boundary conditions $g(0) = 1$ and $g(2 \pi)=1 / e^{2 \pi}$ . The analytical solution is $u_{a}(x) = \cos(x) / e^x$

L = 2*np.pi
x = np.linspace(0, L, N+2)
h = x[1] - x[0]
fcos = 2 * np.cos(x) / np.exp(x)
analytical_cos = -np.sin(x) / np.exp(x)
fsin = 2 * np.sin(x) / np.exp(x)
analytical_sin = np.cos(x) / np.exp(x)

# Use sparse lu decomposition, matrix is tridiagonal so no fill-in
splu = sp.linalg.splu(A / h**2)
fig, axs = plt.subplots(1, 2)
axs[0].spy(splu.L)
axs[0].set_title('L')
axs[1].spy(splu.U)
axs[1].set_title('U')
plt.show()

# Use decomposition to solve both problems
for f, a in zip([fcos, fsin], [analytical_cos, analytical_sin]):
    b = f[1:-1]
    b[0] -= a[0] / h**2
    b[-1] -= a[-1] / h**2
    v = splu.solve(b)
    plt.plot(x[1:-1], v, label='solution')
    plt.plot(x, a, label='analytical')
    plt.legend()
    plt.show()

Sparse versus dense: matrix multiplication

Vary the number of discretisation points $N$ and calculate $AA$ using both sparse and dense matrices. For each $N$ calculate the time to calculate the matix multiplicatiion using Python's time.perf_counter, and plot execution time versus $N$ for dense and sparse matrix multiplication. Comment on how the time varies with $N$ .

import time

num = 100
times = np.empty(num, dtype=float)
times_dense = np.empty(num, dtype=float)
times_dense[:] = np.nan
Ns = np.logspace(0.5, 6, num=num, dtype=int)
for i, N in enumerate(Ns):
    e = np.ones(N, dtype=float)
    A = sp.spdiags([e, -2*e, e], [-1, 0, 1], N, N, format='csc')

    t0 = time.perf_counter()
    AA = A @ A
    t1 = time.perf_counter()
    times[i] = t1 - t0

    if N < 2000:
        Adense = A.toarray()
        t0 = time.perf_counter()
        AA = Adense @ Adense
        t1 = time.perf_counter()
        times_dense[i] = t1 - t0

plt.clf()
plt.loglog(Ns, times, label='sparse')
plt.loglog(Ns, times_dense, label='dense')
plt.xlabel('N')
plt.ylabel('time taken')
plt.legend()
plt.show()

Sparse versus dense: solving Poisson problem

Vary the number of discretisation points $N$ and solve the Poisson problem with varying $N$ , and with using both the sparse and direct $LU$ solvers. For each $N$ record the time taken for both the dense and sparse solvers, and record the numerical error $||\mathbf{v} - \mathbf{v}_a||_2$ . Generate plots of both error and time versus $N$ , and comment on how they vary with $N$

times = np.empty(num, dtype=float)
times_dense = np.empty(num, dtype=float)
times_dense[:] = np.nan

for i, N in enumerate(Ns):
    e = np.ones(N, dtype=float)
    A = sp.spdiags([e, -2*e, e], [-1, 0, 1], N, N, format='csc')

    x = np.linspace(0, L, N+2)
    h = x[1] - x[0]
    fcos = 2 * np.cos(x) / np.exp(x)
    analytical_cos = -np.sin(x) / np.exp(x)

    A /= h**2

    b = fcos[1:-1]
    b[0] -= analytical_cos[0] / h**2
    b[-1] -= analytical_cos[-1] / h**2

    t0 = time.perf_counter()
    splu = sp.linalg.splu(A)
    v = splu.solve(b)
    t1 = time.perf_counter()
    times[i] = t1 - t0
    if N < 2000:
        Adense = A.toarray()
        t0 = time.perf_counter()
        lu = scipy.linalg.lu_factor(Adense)
        v = scipy.linalg.lu_solve(lu, b)
        t1 = time.perf_counter()
        times_dense[i] = t1 - t0

plt.clf()
plt.loglog(Ns, times, label='sparse LU')
plt.loglog(Ns, times_dense, label='dense LU')
plt.xlabel('N')
plt.ylabel('time taken')
plt.legend()
plt.show()

Scipy.sparse and problems

Problems

Visualise Poisson Matrix

Solve Poisson problem

Sparse versus dense: matrix multiplication

Sparse versus dense: solving Poisson problem