ValueError: numpy.dtype size changed, may indicate binary incompatibility

Alice Chen

When running the example notebook "tutorial.ipynb" from the Example Scripts, from the very first line, this is the error that appears:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[4], line 1
----> 1 import illustris_python as il
      2 import numpy as np

File ~/illustris_python/__init__.py:3
      1 __all__ = ["groupcat", "snapshot", "util", "sublink", "lhalotree"]
----> 3 from . import *

File ~/illustris_python/groupcat.py:8
      6 from os.path import isfile
      7 import numpy as np
----> 8 import h5py
     11 def gcPath(basePath, snapNum, chunkNum=0):
     12     """ Return absolute path to a group catalog HDF5 file (modify as needed). """

File /opt/conda/lib/python3.11/site-packages/h5py/__init__.py:25
     19 # --- Library setup -----------------------------------------------------------
     20 
     21 # When importing from the root of the unpacked tarball or git checkout,
     22 # Python sees the "h5py" source directory and tries to load it, which fails.
     23 # We tried working around this by using "package_dir" but that breaks Cython.
     24 try:
---> 25     from . import _errors
     26 except ImportError:
     27     import os.path as _op

File h5py/_errors.pyx:1, in init h5py._errors()

ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

The package illustrious_python doesn't load properly and the rest of the script cannot be run. Is there a way to fix this?
Thank you in advance.

Dylan Nelson
  • 7 Oct

I guess that you have significantly changed the python environment, i.e. installing new versions of key packages.

I can reset your Lab to default, erasing everything that is there, which will fix the problem. Let me know if you would like me to do this.

Alice Chen
  • 7 Oct

Hi Dr. Nelson, yes please reset my Lab to default if possible. Thank you so much

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