Closed toth12 closed 1 year 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:
git clone https://github.com/mdtraj/mdtraj
and git clone https://github.com/markovmodel/pyemma
)pip install deeptime cython pybind11 pyyaml decorator h5py matplotlib pathos psutil tqdm
pip install .
python setup.py install
.
Until there is an M1-compatible mdtraj version out there, this is the best we can do, unfortunately@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
Cheers!
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
(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
and use the search bar at the top of the page.
(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
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 %
(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
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
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
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
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.