Remove -march=native from MOODS/python /setup.py?

[zia1138]

Dear @jhkorhonen,

Thanks for maintaining MOODS-python for so long! I was curious if you could remove the -march=native flag from setup.py:

MOODS/python/setup.py

Line 11 in 568b8fc

common_compile_args = ['-march=native', '-O3', '-fPIC', '--std=c++11']

It impacts both pypy installs for M1 mac and for AMD CPUs. On AMD CPUs, it can lead to illegal instruction errors. Happy to submit a PR as well.

Thanks again!

[gokceneraslan]

Thanks for reporting Zia, we're having the same issue. Here is the exception from our CI/CD instance:

collecting ... Fatal Python error: Illegal instruction
Current thread 0x00007f7d5fea7740 (most recent call first):
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 1166 in create_module
  File "<frozen importlib._bootstrap>", line 556 in module_from_spec
  File "<frozen importlib._bootstrap>", line 657 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 991 in _find_and_load
  File "<frozen importlib._bootstrap>", line 1014 in _gcd_import
  File "/usr/local/lib/python3.8/importlib/__init__.py", line 127 in import_module
  File "/builds/code/.tox/default/lib/python3.8/site-packages/MOODS/parsers.py", line 14 in swig_import_helper
  File "/builds/code/.tox/default/lib/python3.8/site-packages/MOODS/parsers.py", line 17 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 843 in exec_module
  File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 991 in _find_and_load
  File "/builds/code/.tox/default/lib/python3.8/site-packages/package/model/interpret.py", line 4 in <module>

[gokceneraslan]

Interestingly this only happens in the Python 3.8 CI/CD tests where the python:3.8-bullseye docker image is used.

[gokceneraslan]

Since the PyPI moods-python is a source package, I think the issue we are having is a bioconda problem where this issue actually seems to be fixed (bioconda/bioconda-recipes@76c748b also see bioconda/bioconda-recipes#9970). I think I will switch to the PyPI moods-python source package (and recompile it) in our pipeline (i.e. pip install moods-python instead of conda install moods-python) to make sure it's compiled for the right architecture.

[gokceneraslan]

Any news?