Mac Book Pro M1 Big Sur version 11.2.1 INSTALLING MDAnalysis

[Loo Kang]

Hello All

My current Python version in this new M1 MBP is 2.7.16, I have difficulty in installing MDAnalysis, as I cannot install pip. Can someone instruct me please?

[Suliman Sharif]

Are you using the sys python for mac installed in /user/bin/python??

You can do a brew install of the python3 which will be installed to /use/local/bin and alias your python path env.

Every mac comes with python 2 still....even with the M1 chips..... that sucks. 

On Mon, Mar 1, 2021, 3:01 PM Loo Kang <lodki...@gmail.com> wrote:

Hello All

My current Python version in this new M1 MBP is 2.7.16, I have difficulty in installing MDAnalysis, as I cannot install pip. Can someone instruct me please?

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[Loo Kang]

thanks, I already brew to python3 and am able to pip3. 

However, when I $ pip install --upgrade MDAnalysis, I got the following error

Collecting MDAnalysis

  Using cached https://files.pythonhosted.org/packages/9e/19/1d32ded1891605facf6faf6e0de4ff6bd33db3f7983d84cfc10074363990/MDAnalysis-1.0.1.tar.gz

    ERROR: Command errored out with exit status 1:

     command: /Library/Developer/CommandLineTools/usr/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/vg/wytp3d0d2w3c3rlp1fp3f33r0000gn/T/pip-install-kvsmru_x/MDAnalysis/setup.py'"'"'; __file__='"'"'/private/var/folders/vg/wytp3d0d2w3c3rlp1fp3f33r0000gn/T/pip-install-kvsmru_x/MDAnalysis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info

         cwd: /private/var/folders/vg/wytp3d0d2w3c3rlp1fp3f33r0000gn/T/pip-install-kvsmru_x/MDAnalysis/

    Complete output (2981 lines):

    /bin/sh: svnversion: command not found

    Attempting to autodetect OpenMP support... Did not detect OpenMP support.

    No openmp compatible compiler found default to serial build.

    Will not attempt to use Cython.

    non-existing path in 'numpy/distutils': 'site.cfg'

    Could not locate executable gfortran

    Could not locate executable f95

    Could not locate executable f90

    Could not locate executable f77

    Could not locate executable xlf90

    Could not locate executable xlf

    Could not locate executable ifort

    Could not locate executable ifc

    Could not locate executable g77

    Could not locate executable g95

    Could not locate executable pgfortran

    don't know how to compile Fortran code on platform 'posix'

    _configtest.c:1:5: warning: incompatible redeclaration of library function 'exp' [-Wincompatible-library-redeclaration]

    int exp (void);

I did not paste the rest of the error messages because they are too long. 

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[irfan....@googlemail.com]

Unfortunately at this time MDAnalysis does not support either Big Sur (see: https://github.com/MDAnalysis/mdanalysis/issues/3101) nor the Apple M1 chip.

In both cases it's due to us not having access to the infrastructure of us to develop & test on that platform. It is likely that we will bring out Big Sur support once github actions releases Big Sur (it's currently in a closed beta), but this will only be to our current develop code.

As for M1, this is probably going to take longer unless we can get access to that infrastructure :(

Probably the best thing to do would be to look into installing it via Rosetta, maybe one of the other users might have some experience with that, but I can't guarantee it'll work.

- Irfan