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Import issue on Mac M1

See original GitHub issue

Describe the bug import cdlib.algorithms Apple M1 chip

(dynamo-dev) Ks-MacBook-Pro:dynamo-tutorials random$ python
Python 3.9.7 (default, Sep 16 2021, 08:50:36) 
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cdlib
>>> import cdlib.algorithms
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/random/opt/anaconda3/envs/dynamo-dev/lib/python3.9/site-packages/cdlib/algorithms/__init__.py", line 2, in <module>
    from .crisp_partition import *
  File "/Users/random/opt/anaconda3/envs/dynamo-dev/lib/python3.9/site-packages/cdlib/algorithms/crisp_partition.py", line 2, in <module>
    import infomap as imp
  File "/Users/random/opt/anaconda3/envs/dynamo-dev/lib/python3.9/site-packages/infomap.py", line 35, in <module>
    import _infomap
ImportError: dlopen(/Users/random/opt/anaconda3/envs/dynamo-dev/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so, 0x0002): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
  Referenced from: /Users/random/opt/anaconda3/envs/dynamo-dev/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so
  Reason: tried: '/usr/local/opt/libomp/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)

(cdlib-test) Ks-MacBook-Pro:16725-medical-imaging random$ python
Python 3.8.12 | packaged by conda-forge | (default, Jan 30 2022, 23:36:06) 
[Clang 11.1.0 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cdlib
>>> import cdlib.algorithms
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/random/opt/anaconda3/envs/cdlib-test/lib/python3.8/site-packages/cdlib/algorithms/__init__.py", line 2, in <module>
    from .crisp_partition import *
  File "/Users/random/opt/anaconda3/envs/cdlib-test/lib/python3.8/site-packages/cdlib/algorithms/crisp_partition.py", line 2, in <module>
    import infomap as imp
  File "/Users/random/opt/anaconda3/envs/cdlib-test/lib/python3.8/site-packages/infomap.py", line 35, in <module>
    import _infomap
ImportError: dlopen(/Users/random/opt/anaconda3/envs/cdlib-test/lib/python3.8/site-packages/_infomap.cpython-38-darwin.so, 0x0002): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
  Referenced from: /Users/random/opt/anaconda3/envs/cdlib-test/lib/python3.8/site-packages/_infomap.cpython-38-darwin.so
  Reason: tried: '/usr/local/opt/libomp/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)

To Reproduce installed via pip

Name: cdlib
Version: 0.2.5
Summary: Community Discovery Library
Home-page: https://github.com/GiulioRossetti/cdlib
Author: Giulio Rossetti
Author-email: giulio.rossetti@gmail.com
License: BSD-Clause-2
Location: /Users/random/opt/anaconda3/envs/cdlib-test/lib/python3.8/site-packages
Requires: angel-cd, bimlpa, chinese-whispers, cython, demon, dynetx, eva-lcd, future, infomap, karateclub, leidenalg, markov-clustering, matplotlib, networkx, nf1, numpy, pandas, pooch, pulp, pyclustering, python-igraph, python-Levenshtein, python-louvain, scikit-learn, scipy, seaborn, thresholdclustering, tqdm, wurlitzer

Operating System
- macOS Monterey
Python version
tried in conda env 3.7, 3.8, 3.9

Expected behavior Import successfully (cdlib worked and tested in 2021)

I treid brew install libomp but it does not work. The laptop is relatively new (released last year) and there are almost no messy system level customizations on this laptop.

Thanks for providing the community with the package! It is convenient, powerful and with good documentation.

Issue Analytics

State:
Created 2 years ago
Comments:6 (2 by maintainers)

Top GitHub Comments

2reactions

Yquetzalcommented, Mar 17, 2022

@dummyindex Following your problem, we modified the library structure so that you are not blocked by external packages that cannot install on your architecture. So now cdlib should work, you just cannot use infomap. I reported the problem to infomap managers, if you need it you can go to their GitHub and see that current workaround they propose, hopefully there is a simpler solution soon. Feel free to report any additional issue.

0reactions

GiulioRossetticommented, Mar 1, 2022

@Yquetzal I think that having a “light” version of CDlib should be easy to achieve (we already have something similar with the pip package). If you can spot all the “troubling” dependencies I’ll take care of revising the packaging pipeline and updating the installation instructions.