petsc4py not installing due to too old of cython

[lindsayad]

This seems to be the relevant excerpt from the install log. It looks like the cython version is deliberately pinned to this old version in the install script.
firedrake-install.log

Building wheels for collected packages: petsc4py
  Created temporary directory: /tmp/pip-wheel-p5emmi5v
  Destination directory: /tmp/pip-wheel-p5emmi5v
  Building wheel for petsc4py (pyproject.toml): started
  Running command Building wheel for petsc4py (pyproject.toml)
  running bdist_wheel
  running build
  running build_src
  removing Cython 0.29.36 from sys.modules
  fetching build requirement 'Cython >= 3.0.0'
  ********************************************************************************

    You need Cython >= 3.0.0 (you have version 0.29.36)

      $ /home/lindad/firedrake/bin/python -m pip install --upgrade cython

  ********************************************************************************
  error: unsatisfied build requirement 'Cython >= 3.0.0'
  error: subprocess-exited-with-error
  
  × Building wheel for petsc4py (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

[lindsayad]

I'm using my own PETSc. It looks like this is a well-known issue and should hopefully be solved soonish by #3290

[connorjward]

Yes we are trying to land support for Cython 3, numpy 2 and Python 3.12 all together. We have everything working and there is just a performance regression to track down. Definitely should be quite soon.

[connorjward]

numpy 2.0 is due to be released June 16th so once that happens we will get everything merged, including Cython 3 support.

[lindsayad]

sounds great!

[EirikJaccheri]

Hi,
Has the problem been fixed? Because i get a similar error on my Ubuntu 22.04.5 LTS computer, both when i pip install and when i tried to build from source. One thing i find curious is that it is reverting to an older version of numpy, even if i have numpy 2.1.2 installed.

Collecting numpy<2
Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)

Full error:
`python3 -m pip install src/binding/petsc4py
Defaulting to user installation because normal site-packages is not writeable
Processing ./src/binding/petsc4py
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Collecting numpy<2
Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
Collecting petsc<3.23,>=3.22
Using cached petsc-3.22.0-py3-none-linux_x86_64.whl
Building wheels for collected packages: petsc4py
Building wheel for petsc4py (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for petsc4py (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [11 lines of output]
running bdist_wheel
running build
running build_src
********************************************************************************

    You need Cython >= 3.0.0 (you have version 0.29.28)
  
      $ /usr/bin/python3 -m pip install --upgrade cython
  
  ********************************************************************************
  error: unsatisfied build requirement 'Cython >= 3.0.0'
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for petsc4py
Failed to build petsc4py
ERROR: Could not build wheels for petsc4py, which is required to install pyproject.toml-based projects`

[connorjward]

This is surprising. We now have full support for numpy 2 and cython 3. Are you using up-to-date install scripts?

[EirikJaccheri]

Hi,
Thanks for the quick response:-)

I followed this installation guide for installing petsc4py from source: https://petsc.org/release/petsc4py/install.html

I used the following command

$ python -m pip install src/binding/petsc4py

In the release branch of petsc in gitlab

git clone -b release https://gitlab.com/petsc/petsc.git petsc

Should this have the correct install scripts?

Eirik

[connorjward]

I would have thought so. However this is far from a standard way of installing PETSc for Firedrake:

• We install a number of external packages during PETSc configure like a direct solver and mesh partitioner.
• We install a fork of PETSc instead of the release version (we carry around one small patch, which we would love to get rid of).
• When installing petsc4py manually the command I usually run is: python -m pip install --no-deps src/binding/petsc4py. You need to pass --no-deps because otherwise it will try to install a pip version of PETSc which we don't want. You might also need to set PETSC_DIR and PETSC_ARCH environment variables.

May I ask why you aren't using the Firedrake install script?

[EirikJaccheri]

I only need petsc4py and not Firedrake.

I realize that this might not be the right forum to ask, but it was the only place i found someone having a similar issue...

I tried installing with --no-deops and got the same issue.

[connorjward]

Yes this would be better asked directly to PETSc: https://gitlab.com/petsc/petsc/-/issues.

As a last suggestion beforehand though have you simply tried upgrading Cython:

$ python -m pip install -U cython