[petsc-dev] Problem pip installing petsc4py on existing PETSc installation

Fri Aug 29 09:46:13 CDT 2025

For older release - looks like its best to download the petsc4py source tarball, modify pyproject.toml [as below] - and then install it (with the suggested 'pip' command).

Newer petsc/petsc4py versions have fixes that work with cython-3.1

Satish

On Fri, 29 Aug 2025, Samar Khatiwala via petsc-dev wrote:

> Hi Satish,
> 
> Thanks for taking the time to help debug this. That you ran into the same issue is reassuring in a way (that I wasn’t doing something silly). Sounds like there’s not much to be done about it but hopefully this only affects a few older versions of petsc4py.
> 
> It is bizarre that pip is not accepting that 3.0.12 satisfies the requirement. I thought I found a clever way to override what is in pyproject.toml by specifying “cython==3.0.12” in a constraints.txt file with the -c option. But pip ignored that too and proceeded to download cython 3.1.3.
> 
> As for re-downloading packages (cython, numpy) even when they’re already installed is I think by pip’s design because these are build-time requirements (and not runtime requirements).
> 
> Thanks,
> 
> Samar
> 
> > On Aug 29, 2025, at 1:51 AM, Satish Balay <balay.anl at fastmail.org> wrote:
> > 
> > On Thu, 28 Aug 2025, Satish Balay wrote:
> > 
> >> 
> >> Likely:
> >> 
> >> pip install -v cython=3.0.12 petsc4py==3.21.1
> > 
> > https://urldefense.us/v3/__https://petsc.org/release/petsc4py/install.html__;!!G_uCfscf7eWS!ccM-EknCNavnpHXV7-_uoEddj8ar6876_brlmFbYTOL8M-IaAH5Y_NIbolpNF7JlYXLunOXzURWtoLI0czE1HjrvaZuc3x0XTwfBaw$ 
> > 
> > suggests:
> > 
> > $ python -m pip install src/binding/petsc4py
> > 
> > However:
> >>>>> 
> > balay at pj02:~/petsc$ which cython
> > ~/.local/bin/cython
> > balay at pj02:~/petsc$ cython --version
> > Cython version 3.0.12
> > balay at pj02:~/petsc$ 
> > balay at pj02:~/petsc$ PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-linux-c-debug python -m pip install --verbose src/binding/petsc4py
> > Using pip 23.3.2 from /usr/lib/python3.12/site-packages/pip (python 3.12)
> > Defaulting to user installation because normal site-packages is not writeable
> > Processing ./src/binding/petsc4py
> >  Running command pip subprocess to install build dependencies
> >  Collecting cython>=3
> >    Downloading cython-3.1.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (4.7 kB)
> >  Collecting numpy
> >    Downloading numpy-2.3.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
> >       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.1/62.1 kB 2.1 MB/s eta 0:00:00
> >  Collecting setuptools
> >    Downloading setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
> >  Downloading cython-3.1.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (3.3 MB)
> >     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 8.3 MB/s eta 0:00:00
> >  Downloading numpy-2.3.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.6 MB)
> >     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.6/16.6 MB 8.0 MB/s eta 0:00:00
> >  Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB)
> >     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 8.9 MB/s eta 0:00:00
> >  Installing collected packages: setuptools, numpy, cython
> >  Successfully installed cython-3.1.3 numpy-2.3.2 setuptools-80.9.0
> > ....
> > <<<<
> > 
> > I'm not sure why `3.0.12` is not satisfying the `cython>=3` requirement - and `cython-3.1.3` is installed for this requirement
> > 
> > Ok - try to force 3.0.12:
> >>>> 
> > balay at pj02:~/petsc$ git diff
> > diff --git a/src/binding/petsc4py/pyproject.toml b/src/binding/petsc4py/pyproject.toml
> > index 6987c0389ed..35b08945f2a 100644
> > --- a/src/binding/petsc4py/pyproject.toml
> > +++ b/src/binding/petsc4py/pyproject.toml
> > @@ -1,6 +1,6 @@
> > [build-system]
> > requires = [
> > -  "cython >= 3",
> > +  "cython == 3.0.12",
> >   "numpy",
> >   "setuptools",
> > ]
> > balay at pj02:~/petsc$ PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-linux-c-debug python -m pip install --verbose src/binding/petsc4py
> > Using pip 23.3.2 from /usr/lib/python3.12/site-packages/pip (python 3.12)
> > Defaulting to user installation because normal site-packages is not writeable
> > Processing ./src/binding/petsc4py
> >  Running command pip subprocess to install build dependencies
> >  Collecting cython==3.0.12
> >    Downloading Cython-3.0.12-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.3 kB)
> >  Collecting numpy
> >    Downloading numpy-2.3.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
> >       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.1/62.1 kB 1.9 MB/s eta 0:00:00
> >  Collecting setuptools
> >    Downloading setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
> >  Downloading Cython-3.0.12-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.5 MB)
> >     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 41.4 MB/s eta 0:00:00
> >  Downloading numpy-2.3.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.6 MB)
> >     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.6/16.6 MB 4.9 MB/s eta 0:00:00
> >  Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB)
> >     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 5.2 MB/s eta 0:00:00
> >  Installing collected packages: setuptools, numpy, cython
> >  Successfully installed cython-3.0.12 numpy-2.3.2 setuptools-80.9.0
> > ...
> > ...
> >  Building wheel for petsc4py (pyproject.toml) ... done
> >  Created wheel for petsc4py: filename=petsc4py-3.21.6-cp312-cp312-linux_x86_64.whl size=11282654 sha256=462b32dc3706d841a0fca5c7e9ba7b6127b0633cd943eef3784dc8f956375c1b
> >  Stored in directory: /tmp/pip-ephem-wheel-cache-du9_e3hc/wheels/ab/ca/ed/9a2ee0271ce3654f467915ae1f28d46ace120416127b0c8cf1
> > Successfully built petsc4py
> > Installing collected packages: petsc4py
> > Successfully installed petsc4py-3.21.6
> > balay at pj02:~/petsc$ pip list --user
> > Package  Version
> > -------- -------
> > Cython   3.0.12
> > petsc4py 3.21.6
> > balay at pj02:~/petsc$ git branch
> > * release-3.21
> > balay at pj02:~/petsc$ 
> >>>>> 
> > 
> > Ok - now 3.0.12 is getting used (the local install is skipped again - and a new pkg is downloaded/installed as part of the build?) , and the build is now successful
> > 
> > Satish
> 