[petsc-dev] Problem pip installing petsc4py on existing PETSc installation
Samar Khatiwala
samar.khatiwala at earth.ox.ac.uk
Fri Aug 29 22:40:20 CDT 2025
Hi Satish,
That worked!
I had already tried no-build-isolation after installing numpy and cython== 3.0.12 but pip immediately crashed and I couldn’t figure out the problem. I see now that I was missing wheel.
Thank you!
Best,
Samar
> On Aug 30, 2025, at 12:24 AM, Satish Balay <balay.anl at fastmail.org> wrote:
>
>
> Ah - looks like the option to use is: --no-build-isolation (if the build requirements are already installed)
>
> Satish
>
> ----------
> balay at pj02:~/petsc$ python -m pip install --user wheel numpy setuptools cython==3.0.12
> Collecting wheel
> Downloading wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
> Requirement already satisfied: numpy in /usr/lib64/python3.12/site-packages (1.26.4)
> Requirement already satisfied: setuptools in /usr/lib/python3.12/site-packages (69.0.3)
> 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)
> Downloading Cython-3.0.12-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.5 MB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 6.3 MB/s eta 0:00:00
> Downloading wheel-0.45.1-py3-none-any.whl (72 kB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 72.5/72.5 kB 4.1 MB/s eta 0:00:00
> Installing collected packages: wheel, cython
> Successfully installed cython-3.0.12 wheel-0.45.1
> balay at pj02:~/petsc$ PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-linux-c-debug python -m pip install --verbose --no-build-isolation 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 Preparing metadata (pyproject.toml)
> <snip>
> Preparing metadata (pyproject.toml) ... done
> Requirement already satisfied: numpy<2 in /usr/lib64/python3.12/site-packages (from petsc4py==3.21.6) (1.26.4)
> Building wheels for collected packages: petsc4py
> Running command Building wheel for petsc4py (pyproject.toml)
> running bdist_wheel
> running build
> running build_src
> using Cython 3.0.12
> cythonizing 'petsc4py/PETSc.pyx' -> 'petsc4py/PETSc.c'
> <snip>
> Building wheel for petsc4py (pyproject.toml) ... done
> Created wheel for petsc4py: filename=petsc4py-3.21.6-cp312-cp312-linux_x86_64.whl size=11288013 sha256=72be29eb718c43875e423ba22dbbcd0fd33a078c042a89373ae67a6bf886abd0
> Stored in directory: /tmp/pip-ephem-wheel-cache-yhfxq7hs/wheels/ab/ca/ed/9a2ee0271ce3654f467915ae1f28d46ace120416127b0c8cf1
> Successfully built petsc4py
> Installing collected packages: petsc4py
> Successfully installed petsc4py-3.21.6
> balay at pj02:~/petsc$ python -m pip list --user
> Package Version
> -------- -------
> Cython 3.0.12
> petsc4py 3.21.6
> wheel 0.45.1
> balay at pj02:~/petsc$
>
>
> On Fri, 29 Aug 2025, Satish Balay wrote:
>
>> 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
>>>
>>
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