Add Cython bindings for the PETSc API

[connorjward]

The ultimate aim is to move this file out of Firedrake and make it more widely available.

Why is this useful?

It can be useful to be able to access the C API of PETSc directly (instead of going through petsc4py) in cases where we need to call a function many many times (e.g. inside a loop that is the size of the mesh). I wrote a little demo that shows this:

import time

from petsc4py import PETSc


def slow():
    N = int(1e8)
    section = PETSc.Section().create()
    section.setChart(0, N)

    start = time.time()
    for i in range(N):
        if i % 2 == 0:
            section.setDof(i, 1)
    print(f"Time elapsed: {time.time() - start}")


slow()

vs

import time

import cython
from petsc4py import PETSc

from petsctools cimport cpetsc


def medium():
    N: cython.int = int(1e8)
    section: PETSc.Section = PETSc.Section().create()
    section.setChart(0, N)

    start = time.time()
    i: cython.int
    for i in range(N):
        if i % 2 == 0:
            section.setDof(i, 1)  # small amount of Python
    print(f"Time elapsed: {time.time() - start}")


def fast():
    N: cython.int = int(1e8)
    section: cpetsc.PetscSection_py = PETSc.Section().create()
    section.setChart(0, N)

    start = time.time()
    i: cython.int
    for i in range(N):
        if i % 2 == 0:
            cpetsc.CHKERR(cpetsc.PetscSectionSetDof(section.sec, i, 1))  # entirely C
    print(f"Time elapsed: {time.time() - start}")


medium()
fast()

The former takes 4.0s and the latter takes 1.8s and 0.78s each. The differences are admittedly much smaller than expected but still significant enough to care about.

But petsc4py have Cython headers too, why aren't those sufficient?

Basically 2 reasons:

• petsc4py is really complex and does not expose this information very clearly. By comparison what I have here is extremely straightforward to read and extend.
• They make some confusing choices regarding naming. For example the type representing a C Mat is called a PetscMat so all of the C API signatures look a bit odd. Here everything matches exactly, and a petsc4py Python Mat is called Mat_py.
• They use the older .pxi format (example) which literal-includes the text instead of importing via .pxd.

[JHopeCollins]

Looks like the cython build isn't finding the mpi compiler wrapper

[connorjward]

Looks like the cython build isn't finding the mpi compiler wrapper

Yeah. It passes locally which is strange. I'm investigating.

[connorjward]

All fixed now.

[JHopeCollins]

Just some naming questions if you're trying to be more consistent