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markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂
http://pyemma.org
GNU Lesser General Public License v3.0
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PyEMMA on MAC M1 - installation not working #1572

Closed toth12 closed 1 year ago

toth12 commented 2 years ago

Dear All,

I am trying to install pyemma on a MAC M1 laptop with Python 3.10.6. I have tried various installation procedures and nothing seems to be working. Below are the outputs of different procedures. I also tried to follow this (https://github.com/markovmodel/PyEMMA/issues/1524 see lucl13 commented on 16 Jul) but no success, could you please advice me how to proceed? Thanks, Gabor

  1. Conda installation

(base) user@arm64-apple-darwin20 pyemma % conda activate au_env (au_env) user@arm64-apple-darwin20 pyemma % conda config --add channels conda-forge

Warning: 'conda-forge' already in 'channels' list, moving to the top (au_env) user@arm64-apple-darwin20 pyemma % conda install pyemma

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

  1. Pip installation

(au_env) user@arm64-apple-darwin20 pyemma % pip install pyemma

Collecting pyemma Using cached pyEMMA-2.5.11.tar.gz (1.6 MB) Installing build dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [162 lines of output] Collecting setuptools Using cached setuptools-65.3.0-py3-none-any.whl (1.2 MB) Collecting wheel Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) Collecting numpy>=1.10 Using cached numpy-1.23.2-cp310-cp310-macosx_11_0_arm64.whl (13.3 MB) Collecting Cython>=0.22 Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB) Collecting scipy Using cached scipy-1.9.0-cp310-cp310-macosx_12_0_arm64.whl (29.9 MB) Collecting mdtraj Using cached mdtraj-1.9.7.tar.gz (2.1 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting deeptime Using cached deeptime-0.4.2-cp310-cp310-macosx_12_0_arm64.whl Collecting pyparsing Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB) Collecting astunparse Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB) Collecting scikit-learn Using cached scikit_learn-1.1.2-cp310-cp310-macosx_12_0_arm64.whl (7.7 MB) Collecting threadpoolctl Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting six<2.0,>=1.6.1 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting joblib>=1.0.0 Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB) Building wheels for collected packages: mdtraj Building wheel for mdtraj (pyproject.toml): started Building wheel for mdtraj (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error

    × Building wheel for mdtraj (pyproject.toml) did not run successfully.
    │ exit code: 1
    ╰─> [116 lines of output]
        C compiler:
        Attempting to autodetect OpenMP support... Did not detect OpenMP support
        Attempting to autodetect SSE3   support... Did not detect SSE3 support
        Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
        Attempting to autodetect NEON   support... Did not detect NEON support

        running bdist_wheel
        running build
        running build_py
        creating build
        creating build/lib.macosx-11.0-arm64-cpython-310
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/version.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/io.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/trajectory.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/element.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/topology.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/selection.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/residue_names.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/gro.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/xyzfile.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/lammpstrj.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/hoomdxml.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/prmtop.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/openmmxml.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/lh5.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/registry.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/mol2.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/psf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/hdf5.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/gsd.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/amberrst.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/netcdf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/arc.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/mdcrd.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/delay_import.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/zipped.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/contextmanagers.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/unitcell.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/six.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/singleton.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/rotation.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/validation.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/docstrings.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/docscrape.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/testing.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/mdinspect.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/mdconvert.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/internal.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/dssp.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/sasa.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/rg.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/alignment.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/angle.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/order.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/dihedral.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/distance.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/rdf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/shape.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/hbond.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/contact.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/netcdfreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/xtcreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/dcdreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/basereporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/hdf5reporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/scalar_couplings.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/shift_wrappers.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/pdbfile.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/doctests.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/prefix.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_definitions.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/constants.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/mymatrix.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_math.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/baseunit.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_operators.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/quantity.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/basedimension.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        copying mdtraj/formats/pdb/data/residues.xml -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        running build_ext
        building 'mdtraj.formats.xtc' extension
        creating build/temp.macosx-11.0-arm64-cpython-310
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc/src
        arm64-apple-darwin20.0.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -arch arm64 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/private/var/folders/f2/skrbd8xn0mdf1wfmzx2l26pc0000gn/T/pip-build-env-ysxekzv1/overlay/lib/python3.10/site-packages/numpy/core/include -I/opt/homebrew/Caskroom/miniconda/base/envs/au_env/include/python3.10 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
        error: command 'arm64-apple-darwin20.0.0-clang' failed: No such file or directory
        [end of output]

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

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

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. (au_env) user@arm64-apple-darwin20 pyemma %

  1. Installation from source

(au_env) user@arm64-apple-darwin20 pyemma % pip install --upgrade setuptools pip install --upgrade cython pip install --upgrade numpy pip install --upgrade scipy pip install --upgrade matplotlib Requirement already satisfied: setuptools in /opt/homebrew/Caskroom/miniconda/base/envs/au_env/lib/python3.10/site-packages (65.3.0) Collecting cython Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB) Installing collected packages: cython Successfully installed cython-0.29.32 Collecting numpy Using cached numpy-1.23.2-cp310-cp310-macosx_11_0_arm64.whl (13.3 MB) Installing collected packages: numpy Successfully installed numpy-1.23.2 Collecting scipy Using cached scipy-1.9.0-cp310-cp310-macosx_12_0_arm64.whl (29.9 MB) Requirement already satisfied: numpy<1.25.0,>=1.18.5 in /opt/homebrew/Caskroom/miniconda/base/envs/au_env/lib/python3.10/site-packages (from scipy) (1.23.2) Installing collected packages: scipy Successfully installed scipy-1.9.0 Collecting matplotlib Using cached matplotlib-3.5.3-cp310-cp310-macosx_11_0_arm64.whl (7.2 MB) Collecting packaging>=20.0 Using cached packaging-21.3-py3-none-any.whl (40 kB) Collecting cycler>=0.10 Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB) Collecting pillow>=6.2.0 Using cached Pillow-9.2.0-cp310-cp310-macosx_11_0_arm64.whl (2.8 MB) Requirement already satisfied: numpy>=1.17 in /opt/homebrew/Caskroom/miniconda/base/envs/au_env/lib/python3.10/site-packages (from matplotlib) (1.23.2) Collecting kiwisolver>=1.0.1 Using cached kiwisolver-1.4.4-cp310-cp310-macosx_11_0_arm64.whl (63 kB) Collecting pyparsing>=2.2.1 Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB) Collecting fonttools>=4.22.0 Using cached fonttools-4.37.1-py3-none-any.whl (957 kB) Collecting python-dateutil>=2.7 Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting six>=1.5 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Installing collected packages: six, pyparsing, pillow, kiwisolver, fonttools, cycler, python-dateutil, packaging, matplotlib Successfully installed cycler-0.11.0 fonttools-4.37.1 kiwisolver-1.4.4 matplotlib-3.5.3 packaging-21.3 pillow-9.2.0 pyparsing-3.0.9 python-dateutil-2.8.2 six-1.16.0 (au_env) user@arm64-apple-darwin20 pyemma % pip install pyemma

Collecting pyemma Using cached pyEMMA-2.5.11.tar.gz (1.6 MB) Installing build dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [162 lines of output] Collecting setuptools Using cached setuptools-65.3.0-py3-none-any.whl (1.2 MB) Collecting wheel Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) Collecting numpy>=1.10 Using cached numpy-1.23.2-cp310-cp310-macosx_11_0_arm64.whl (13.3 MB) Collecting Cython>=0.22 Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB) Collecting scipy Using cached scipy-1.9.0-cp310-cp310-macosx_12_0_arm64.whl (29.9 MB) Collecting mdtraj Using cached mdtraj-1.9.7.tar.gz (2.1 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting deeptime Using cached deeptime-0.4.2-cp310-cp310-macosx_12_0_arm64.whl Collecting pyparsing Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB) Collecting astunparse Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB) Collecting scikit-learn Using cached scikit_learn-1.1.2-cp310-cp310-macosx_12_0_arm64.whl (7.7 MB) Collecting threadpoolctl Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting six<2.0,>=1.6.1 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting joblib>=1.0.0 Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB) Building wheels for collected packages: mdtraj Building wheel for mdtraj (pyproject.toml): started Building wheel for mdtraj (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error

    × Building wheel for mdtraj (pyproject.toml) did not run successfully.
    │ exit code: 1
    ╰─> [116 lines of output]
        C compiler:
        Attempting to autodetect OpenMP support... Did not detect OpenMP support
        Attempting to autodetect SSE3   support... Did not detect SSE3 support
        Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
        Attempting to autodetect NEON   support... Did not detect NEON support

        running bdist_wheel
        running build
        running build_py
        creating build
        creating build/lib.macosx-11.0-arm64-cpython-310
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/version.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/io.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/trajectory.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/element.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/topology.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/selection.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/residue_names.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/gro.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/xyzfile.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/lammpstrj.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/hoomdxml.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/prmtop.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/openmmxml.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/lh5.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/registry.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/mol2.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/psf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/hdf5.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/gsd.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/amberrst.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/netcdf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/arc.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/mdcrd.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/delay_import.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/zipped.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/contextmanagers.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/unitcell.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/six.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/singleton.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/rotation.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/validation.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/docstrings.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/docscrape.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/testing.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/mdinspect.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/mdconvert.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/internal.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/dssp.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/sasa.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/rg.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/alignment.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/angle.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/order.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/dihedral.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/distance.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/rdf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/shape.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/hbond.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/contact.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/netcdfreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/xtcreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/dcdreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/basereporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/hdf5reporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/scalar_couplings.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/shift_wrappers.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/pdbfile.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/doctests.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/prefix.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_definitions.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/constants.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/mymatrix.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_math.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/baseunit.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_operators.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/quantity.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/basedimension.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        copying mdtraj/formats/pdb/data/residues.xml -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        running build_ext
        building 'mdtraj.formats.xtc' extension
        creating build/temp.macosx-11.0-arm64-cpython-310
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc/src
        arm64-apple-darwin20.0.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -arch arm64 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/private/var/folders/f2/skrbd8xn0mdf1wfmzx2l26pc0000gn/T/pip-build-env-1v3eidbm/overlay/lib/python3.10/site-packages/numpy/core/include -I/opt/homebrew/Caskroom/miniconda/base/envs/au_env/include/python3.10 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
        error: command 'arm64-apple-darwin20.0.0-clang' failed: No such file or directory
        [end of output]

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

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

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

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

  1. Installing pyemma 2.5.9 with pip

(au_env) gabortoth@arm64-apple-darwin20 pyemma % pip install pyemma

Collecting pyemma Using cached pyEMMA-2.5.11.tar.gz (1.6 MB) Installing build dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [162 lines of output] Collecting setuptools Using cached setuptools-65.3.0-py3-none-any.whl (1.2 MB) Collecting wheel Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) Collecting numpy>=1.10 Using cached numpy-1.23.2-cp310-cp310-macosx_11_0_arm64.whl (13.3 MB) Collecting Cython>=0.22 Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB) Collecting scipy Using cached scipy-1.9.0-cp310-cp310-macosx_12_0_arm64.whl (29.9 MB) Collecting mdtraj Using cached mdtraj-1.9.7.tar.gz (2.1 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting deeptime Using cached deeptime-0.4.2-cp310-cp310-macosx_12_0_arm64.whl Collecting pyparsing Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB) Collecting astunparse Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB) Collecting scikit-learn Using cached scikit_learn-1.1.2-cp310-cp310-macosx_12_0_arm64.whl (7.7 MB) Collecting threadpoolctl Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting six<2.0,>=1.6.1 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting joblib>=1.0.0 Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB) Building wheels for collected packages: mdtraj Building wheel for mdtraj (pyproject.toml): started Building wheel for mdtraj (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error

    × Building wheel for mdtraj (pyproject.toml) did not run successfully.
    │ exit code: 1
    ╰─> [116 lines of output]
        C compiler:
        Attempting to autodetect OpenMP support... Did not detect OpenMP support
        Attempting to autodetect SSE3   support... Did not detect SSE3 support
        Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
        Attempting to autodetect NEON   support... Did not detect NEON support

        running bdist_wheel
        running build
        running build_py
        creating build
        creating build/lib.macosx-11.0-arm64-cpython-310
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/version.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/io.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/trajectory.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/element.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/topology.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/selection.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/residue_names.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/gro.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/xyzfile.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/lammpstrj.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/hoomdxml.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/prmtop.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/openmmxml.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/lh5.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/registry.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/mol2.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/psf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/hdf5.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/gsd.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/amberrst.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/netcdf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/arc.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/mdcrd.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/delay_import.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/zipped.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/contextmanagers.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/unitcell.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/six.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/singleton.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/rotation.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/validation.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/docstrings.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/docscrape.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/testing.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/mdinspect.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/mdconvert.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/internal.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/dssp.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/sasa.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/rg.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/alignment.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/angle.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/order.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/dihedral.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/distance.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/rdf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/shape.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/hbond.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/contact.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/netcdfreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/xtcreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/dcdreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/basereporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/hdf5reporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/scalar_couplings.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/shift_wrappers.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/pdbfile.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/doctests.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/prefix.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_definitions.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/constants.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/mymatrix.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_math.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/baseunit.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_operators.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/quantity.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/basedimension.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        copying mdtraj/formats/pdb/data/residues.xml -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        running build_ext
        building 'mdtraj.formats.xtc' extension
        creating build/temp.macosx-11.0-arm64-cpython-310
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc/src
        arm64-apple-darwin20.0.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -arch arm64 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/private/var/folders/f2/skrbd8xn0mdf1wfmzx2l26pc0000gn/T/pip-build-env-1v3eidbm/overlay/lib/python3.10/site-packages/numpy/core/include -I/opt/homebrew/Caskroom/miniconda/base/envs/au_env/include/python3.10 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
        error: command 'arm64-apple-darwin20.0.0-clang' failed: No such file or directory
        [end of output]

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

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

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. (au_env) gabortoth@arm64-apple-darwin20 pyemma % pip install pyEMMA==2.5.9

Collecting pyEMMA==2.5.9 Using cached pyEMMA-2.5.9.tar.gz (1.6 MB) Installing build dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [162 lines of output] Collecting setuptools Using cached setuptools-65.3.0-py3-none-any.whl (1.2 MB) Collecting wheel Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) Collecting numpy>=1.10 Using cached numpy-1.23.2-cp310-cp310-macosx_11_0_arm64.whl (13.3 MB) Collecting Cython>=0.22 Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB) Collecting scipy Using cached scipy-1.9.0-cp310-cp310-macosx_12_0_arm64.whl (29.9 MB) Collecting mdtraj Using cached mdtraj-1.9.7.tar.gz (2.1 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting deeptime Using cached deeptime-0.4.2-cp310-cp310-macosx_12_0_arm64.whl Collecting pyparsing Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB) Collecting astunparse Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB) Collecting scikit-learn Using cached scikit_learn-1.1.2-cp310-cp310-macosx_12_0_arm64.whl (7.7 MB) Collecting threadpoolctl Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting six<2.0,>=1.6.1 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting joblib>=1.0.0 Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB) Building wheels for collected packages: mdtraj Building wheel for mdtraj (pyproject.toml): started Building wheel for mdtraj (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error

    × Building wheel for mdtraj (pyproject.toml) did not run successfully.
    │ exit code: 1
    ╰─> [116 lines of output]
        C compiler:
        Attempting to autodetect OpenMP support... Did not detect OpenMP support
        Attempting to autodetect SSE3   support... Did not detect SSE3 support
        Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
        Attempting to autodetect NEON   support... Did not detect NEON support

        running bdist_wheel
        running build
        running build_py
        creating build
        creating build/lib.macosx-11.0-arm64-cpython-310
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/version.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/io.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        copying mdtraj/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/trajectory.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/element.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/topology.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/selection.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        copying mdtraj/core/residue_names.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/core
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/gro.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/xyzfile.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/lammpstrj.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/hoomdxml.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/prmtop.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/openmmxml.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/lh5.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/registry.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/mol2.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/psf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/hdf5.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/gsd.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/amberrst.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/netcdf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/arc.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        copying mdtraj/formats/mdcrd.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/delay_import.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/zipped.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/contextmanagers.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/unitcell.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/six.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/singleton.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/rotation.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        copying mdtraj/utils/validation.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/docstrings.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/docscrape.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        copying mdtraj/testing/testing.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/testing
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/mdinspect.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        copying mdtraj/scripts/mdconvert.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/scripts
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/internal.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/dssp.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/sasa.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/rg.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/alignment.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/angle.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/order.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/dihedral.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/distance.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/rdf.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/shape.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/hbond.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        copying mdtraj/geometry/contact.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/geometry
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/netcdfreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/xtcreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/dcdreporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/basereporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        copying mdtraj/reporters/hdf5reporter.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/reporters
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/scalar_couplings.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        copying mdtraj/nmr/shift_wrappers.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/nmr
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/pdbfile.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/doctests.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/prefix.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_definitions.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/constants.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/mymatrix.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_math.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/baseunit.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/unit_operators.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/quantity.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        copying mdtraj/utils/unit/basedimension.py -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/utils/unit
        creating build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        copying mdtraj/formats/pdb/data/residues.xml -> build/lib.macosx-11.0-arm64-cpython-310/mdtraj/formats/pdb/data
        running build_ext
        building 'mdtraj.formats.xtc' extension
        creating build/temp.macosx-11.0-arm64-cpython-310
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc
        creating build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc/src
        arm64-apple-darwin20.0.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -arch arm64 -fPIC -O2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -arch arm64 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniconda/base/envs/au_env/include -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/private/var/folders/f2/skrbd8xn0mdf1wfmzx2l26pc0000gn/T/pip-build-env-3hwwjvx9/overlay/lib/python3.10/site-packages/numpy/core/include -I/opt/homebrew/Caskroom/miniconda/base/envs/au_env/include/python3.10 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.macosx-11.0-arm64-cpython-310/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
        error: command 'arm64-apple-darwin20.0.0-clang' failed: No such file or directory
        [end of output]

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

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

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

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

clonker commented 2 years ago

Hi, this is a problem of mdtraj not being available on M1 yet. You can circumvent this by manual installation of first mdtraj and then pyemma. So:

  1. clone mdtraj and pyemma into separate directories (git clone https://github.com/mdtraj/mdtraj and git clone https://github.com/markovmodel/pyemma)
  2. install installation and run dependencies pip install deeptime cython pybind11 pyyaml decorator h5py matplotlib pathos psutil tqdm
  3. install mdtraj: enter mdtraj directory and install: pip install .
  4. install pyemma: enter pyemma directory and install with python setup.py install. Until there is an M1-compatible mdtraj version out there, this is the best we can do, unfortunately
toth12 commented 2 years ago

@clonker Thanks, I will test it and report back so that you can close the issue; I note that when I was trying before there was also a problem related to deeptime on the M1, thanks again

clonker commented 1 year ago

Cheers!