pip install petsc fails on macOS High Sierra

[Marco Magliulo]

I do not know if the reported issue is related to this one. I am currently unable to pip install petsc. I am working in a virtual environment and use Python 3.5.2 I do not understand the error message either. Here is the full output of $ pip install :

Collecting petsc
  Using cached https://files.pythonhosted.org/packages/5a/6c/494af329ab9bde8fff6aa8667e379c6cb942cbc13d4b1a2e4e27e562e5b3/petsc-3.9.2.tar.gz
Installing collected packages: petsc
  Running setup.py install for petsc ... error
    Complete output from command /Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/bin/python3 -u -c "import setuptools, tokenize;__file__='/private/var/folders/dh/33jm7d0j1ss8vy_3786wjlg9p0cf6h/T/pip-install-vek1_hto/petsc/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/dh/33jm7d0j1ss8vy_3786wjlg9p0cf6h/T/pip-record-mpkszpgr/install-record.txt --single-version-externally-managed --compile:
    running install
    PETSc: configure
    configure options:
        --prefix=/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/lib/python3.5/site-packages/petsc
        PETSC_ARCH=arch-python-macosx-10.6-x86_64
        --with-shared-libraries=1
        --with-debugging=0
        --with-c2html=0
        --with-cc=/usr/local/bin/mpicc
        --with-cxx=/usr/local/bin/mpicxx
        --with-fc=/usr/local/bin/mpif90
    Configure does not support Python 3 yet, attempting to run as
      python2 './configure' '--prefix=/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/lib/python3.5/site-packages/petsc' 'PETSC_ARCH=arch-python-macosx-10.6-x86_64' '--with-shared-libraries=1' '--with-debugging=0' '--with-c2html=0' '--with-cc=/usr/local/bin/mpicc' '--with-cxx=/usr/local/bin/mpicxx' '--with-fc=/usr/local/bin/mpif90'
    Traceback (most recent call last):
      File "./configure", line 12, in <module>
        os.execlp('python2', 'python2', *sys.argv)
      File "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/Resources/Python.app/Contents/MacOS/../../../../lib/python3.5/os.py", line 598, in execlp
        execvp(file, args)
      File "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/Resources/Python.app/Contents/MacOS/../../../../lib/python3.5/os.py", line 615, in execvp
        _execvpe(file, args)
      File "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/Resources/Python.app/Contents/MacOS/../../../../lib/python3.5/os.py", line 660, in _execvpe
        raise last_exc.with_traceback(tb)
      File "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/Resources/Python.app/Contents/MacOS/../../../../lib/python3.5/os.py", line 650, in _execvpe
        exec_func(fullname, *argrest)
    FileNotFoundError: [Errno 2] No such file or directory
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/dh/33jm7d0j1ss8vy_3786wjlg9p0cf6h/T/pip-install-vek1_hto/petsc/setup.py", line 296, in <module>
        **metadata)
      File "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/lib/python3.5/site-packages/setuptools/__init__.py", line 129, in setup
        return distutils.core.setup(**attrs)
      File "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/lib/python3.5/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/lib/python3.5/distutils/dist.py", line 955, in run_commands
        self.run_command(cmd)
      File "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/lib/python3.5/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/private/var/folders/dh/33jm7d0j1ss8vy_3786wjlg9p0cf6h/T/pip-install-vek1_hto/petsc/setup.py", line 212, in run
        config(prefix, self.dry_run)
      File "/private/var/folders/dh/33jm7d0j1ss8vy_3786wjlg9p0cf6h/T/pip-install-vek1_hto/petsc/setup.py", line 148, in config
        if status != 0: raise RuntimeError(status)
    RuntimeError: 256

    ----------------------------------------
Command "/Users/marco.magliulo/Library/Enthought/Canopy/edm/envs/User/bin/python3 -u -c "import setuptools, tokenize;__file__='/private/var/folders/dh/33jm7d0j1ss8vy_3786wjlg9p0cf6h/T/pip-install-vek1_hto/petsc/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/dh/33jm7d0j1ss8vy_3786wjlg9p0cf6h/T/pip-record-mpkszpgr/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/dh/33jm7d0j1ss8vy_3786wjlg9p0cf6h/T/pip-install-vek1_hto/petsc/

Note: when I do pip install petsc with Python 3.6.5, everything goes fine

[Lisandro Dalcin]

PETSc needs a Python 2 interpreter to run its own configure script. Given that you are using Python 3, you need to somehow expose a python2 command in your $PATH. Still not sure why things works with 3.6.5, but maybe somehow in that environment you have Python 2 available as well?

In any case, pip install petsc is expected to fail from time to time. PETSc is not a Python package, and it has been quite difficult over the years to keep it pip-installable. My recommendation is always to build PETSc by hand with the usual configure --prefix=<previx> && make && make install, then export PETSC_DIR=<prefix>, and finally pip install petsc4py.

Or maybe start using Anaconda Python and the conda-forge packages, we already provide petsc,slepc and the *4py packages (though we do not support complex numbers yet).

So, in short, try to add to your PATH some directory that have a python2 command available, and try again.

[Lisandro Dalcin]

@MarcoMagliulo Any news? Can I close this issue?