Error updating Dedalus via pip

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eric.w....@gmail.com

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Nov 18, 2025, 11:49:04 AMNov 18
to Dedalus Users
Hello,

I've installed Dedalus on an Apple Silicon Mac using the full stack conda installation, and I am attempting to update using pip.

After activating the miniconda environment, and running

    CC=mpicc pip3 install --upgrade --force-reinstall --no-deps --no-cache --no-build-isolation http://github.com/dedalusproject/dedalus/zipball/master/

I obtain the following error (copied below). Any idea on how to fix it?

Cheers,
Eric

  Downloading http://github.com/dedalusproject/dedalus/zipball/master/

     - 24.5 MB 23.3 MB/s 0:00:01

  Preparing metadata (pyproject.toml) ... error

  error: subprocess-exited-with-error

  

  × Preparing metadata (pyproject.toml) did not run successfully.

  │ exit code: 1

  ╰─> [20 lines of output]

      Traceback (most recent call last):

        File "/Users/erichester/miniforge3/envs/d3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>

          main()

          ~~~~^^

        File "/Users/erichester/miniforge3/envs/d3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main

          json_out['return_val'] = hook(**hook_input['kwargs'])

                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^

        File "/Users/erichester/miniforge3/envs/d3/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel

          return hook(metadata_directory, config_settings)

        File "/Users/erichester/miniforge3/envs/d3/lib/python3.13/site-packages/setuptools/build_meta.py", line 377, in prepare_metadata_for_build_wheel

          self.run_setup()

          ~~~~~~~~~~~~~~^^

        File "/Users/erichester/miniforge3/envs/d3/lib/python3.13/site-packages/setuptools/build_meta.py", line 522, in run_setup

          super().run_setup(setup_script=setup_script)

          ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^

        File "/Users/erichester/miniforge3/envs/d3/lib/python3.13/site-packages/setuptools/build_meta.py", line 320, in run_setup

          exec(code, locals())

          ~~~~^^^^^^^^^^^^^^^^

        File "<string>", line 19, in <module>

      ModuleNotFoundError: No module named 'Cython'

      [end of output]

  

  note: This error originates from a subprocess, and is likely not a problem with pip.

error: metadata-generation-failed


× Encountered error while generating package metadata.

╰─> See above for output.


note: This is an issue with the package mentioned above, not pip.

hint: See above for details.

Daniel Lecoanet

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Nov 19, 2025, 10:42:36 AMNov 19
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It seems to say it cannot find Cython. If you run pip list does it show cython as installed?

Daniel

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Eric Hester

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Nov 19, 2025, 11:09:59 AMNov 19
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Ah! Silly me. Thanks Daniel. Installing Cython fixed that issue.

Now a trickier one — mpicc complains that it can’t find the desired compiler x86_64-apple-darwin13.4.0-clang in PATH:

Is there a default location to point to following the conda install approach for Apple Silicon?

Cheers,
Eric

Error message:

     \ 24.5 MB 21.6 MB/s 0:00:01

  Preparing metadata (pyproject.toml) ... done

Building wheels for collected packages: dedalus

  Building wheel for dedalus (pyproject.toml) ... error

  error: subprocess-exited-with-error

  

  × Building wheel for dedalus (pyproject.toml) did not run successfully.

  │ exit code: 1

  ╰─> [124 lines of output]

      

      Configuration:

        INCLUDE_MPI = True

        INCLUDE_FFTW = True

        FFTW_STATIC = False

        CYTHON_PROFILE = False

      

      Looking for mpi include path:

        Found matching library in /Users/erichester/miniforge3/envs/d3/lib

      Looking for mpi library path:

        Found matching library in /Users/erichester/miniforge3/envs/d3/lib

      Looking for fftw include path:

        Found matching library in /Users/erichester/miniforge3/envs/d3/lib

      Looking for fftw library path:

        Found matching library in /Users/erichester/miniforge3/envs/d3/lib

      

      running bdist_wheel

      running build

      running build_py

      creating build/lib.macosx-10.13-x86_64-cpython-313/dedalus


… Skipping stuff …


      copying dedalus/libraries/dedalus_sphere/sphere.py -> build/lib.macosx-10.13-x86_64-cpython-313/dedalus/libraries/dedalus_sphere

      copying dedalus/libraries/dedalus_sphere/annulus.py -> build/lib.macosx-10.13-x86_64-cpython-313/dedalus/libraries/dedalus_sphere

      creating build/lib.macosx-10.13-x86_64-cpython-313/dedalus/libraries/fftw

      copying dedalus/libraries/fftw/__init__.py -> build/lib.macosx-10.13-x86_64-cpython-313/dedalus/libraries/fftw

      copying dedalus/dedalus.cfg -> build/lib.macosx-10.13-x86_64-cpython-313/dedalus

      copying dedalus/examples.tar.gz -> build/lib.macosx-10.13-x86_64-cpython-313/dedalus

      running build_ext

      building 'dedalus.core.transposes' extension

      creating build/temp.macosx-10.13-x86_64-cpython-313/dedalus/core

      mpicc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/erichester/miniforge3/envs/d3/include -fPIC -O2 -isystem /Users/erichester/miniforge3/envs/d3/include -I/Users/erichester/miniforge3/envs/d3/lib/python3.13/site-packages/numpy/_core/include -I/Users/erichester/miniforge3/envs/d3/lib/python3.13/site-packages/mpi4py/include -I/Users/erichester/miniforge3/envs/d3/include -Idedalus/libraries/fftw/ -I/Users/erichester/miniforge3/envs/d3/include -I/Users/erichester/miniforge3/envs/d3/include/python3.13 -c dedalus/core/transposes.c -o build/temp.macosx-10.13-x86_64-cpython-313/dedalus/core/transposes.o -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Wno-unused-function -fopenmp

      --------------------------------------------------------------------------

      The Open MPI wrapper compiler was unable to find the specified compiler

      x86_64-apple-darwin13.4.0-clang in your PATH.

      

      Note that this compiler was either specified at configure time or in

      one of several possible environment variables.

      --------------------------------------------------------------------------

      error: command '/Users/erichester/miniforge3/envs/d3/bin/mpicc' failed with exit code 1

      [end of output]

  

  note: This error originates from a subprocess, and is likely not a problem with pip.

  ERROR: Failed building wheel for dedalus

Failed to build dedalus

ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (dedalus)


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Keaton Burns

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Nov 19, 2025, 11:45:26 AMNov 19
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mpicc from conda is looking for the conda-supplied c-compilers. Try installing “c-compiler” with conda too.


Eric Hester

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Nov 19, 2025, 12:28:07 PMNov 19
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Problem fixed! 

(For reference, I specifically ran "conda install conda-forge::c-compiler” in my dedalus conda environment.)

Cheers,
Eric

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