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aiidateam / aiida-core

The official repository for the AiiDA code
https://aiida-core.readthedocs.io
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numpy.narray size issue raised from pymatgen #5767

Closed unkcpz closed 1 year ago

unkcpz commented 1 year ago

Is anyone had the same issue encountered, to be honest, I am a bit sick of dependencies handled by pymatgen I think this is not the first time we have problem with it. In AiiDAlab, we pinned the numpy version to workaround this. Now I encounter it again with sssp workflow, not sure tune numpy version is a good idea.

  File "/opt/conda/lib/python3.9/site-packages/pymatgen/core/lattice.py", line 22, in <module>
    from pymatgen.util.coord import pbc_shortest_vectors
  File "/opt/conda/lib/python3.9/site-packages/pymatgen/util/coord.py", line 17, in <module>
    from . import coord_cython as cuc
  File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

numpy version 1.21.4. pymatgen version 2022.1.9 (I think this pinned by aiida-core)

danielhollas commented 1 year ago

@unkcpz perhaps related what I reported here:

https://github.com/aiidalab/aiidalab-docker-stack/issues/320

I think in AiiDAlab this issue is compounded by the fact that aiida-core and its dependencies are installed via conda, but app dependencies are installed via pip, which might lead to these mismatches (but I haven't confirmed this)