RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject

[ZQiwen]

Hi! I am installing LASIF following the instructions on http://lasif.net/prerequisites.html
Everything went well until testing LASIF by executing py.test in the toplevel LASIF directory.

I got the following errors:

============================================================= test session starts =============================================================
platform linux -- Python 3.7.6, pytest-5.4.3, py-1.8.1, pluggy-0.13.1
rootdir: /home/zhuqw/LASIF, inifile: pytest.ini
collected 191 items / 2 errors / 189 selected                                                                                          

=================================================================== ERRORS ====================================================================
____________________________________________ ERROR collecting lasif/tests/test_adjoint_sources.py _____________________________________________
lasif/tests/test_adjoint_sources.py:17: in <module>
    from scipy.io import loadmat
../.conda/envs/lasif/lib/python3.7/site-packages/scipy/io/__init__.py:97: in <module>
    from .matlab import loadmat, savemat, whosmat, byteordercodes
../.conda/envs/lasif/lib/python3.7/site-packages/scipy/io/matlab/__init__.py:11: in <module>
    from .mio import loadmat, savemat, whosmat
../.conda/envs/lasif/lib/python3.7/site-packages/scipy/io/matlab/mio.py:9: in <module>
    from .mio4 import MatFile4Reader, MatFile4Writer
../.conda/envs/lasif/lib/python3.7/site-packages/scipy/io/matlab/mio4.py:14: in <module>
    from .mio_utils import squeeze_element, chars_to_strings
mio_utils.pyx:1: in init scipy.io.matlab.mio_utils
    ???
E   RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
____________________________________________ ERROR collecting lasif/tests/test_adjoint_sources.py _____________________________________________
lasif/tests/test_adjoint_sources.py:17: in <module>
    from scipy.io import loadmat
../.conda/envs/lasif/lib/python3.7/site-packages/scipy/io/__init__.py:97: in <module>
    from .matlab import loadmat, savemat, whosmat, byteordercodes
../.conda/envs/lasif/lib/python3.7/site-packages/scipy/io/matlab/__init__.py:11: in <module>
    from .mio import loadmat, savemat, whosmat
../.conda/envs/lasif/lib/python3.7/site-packages/scipy/io/matlab/mio.py:9: in <module>
    from .mio4 import MatFile4Reader, MatFile4Writer
../.conda/envs/lasif/lib/python3.7/site-packages/scipy/io/matlab/mio4.py:14: in <module>
    from .mio_utils import squeeze_element, chars_to_strings
mio_utils.pyx:1: in init scipy.io.matlab.mio_utils
    ???
E   RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
=========================================================== short test summary info ===========================================================
ERROR lasif/tests/test_adjoint_sources.py - RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from...
ERROR lasif/tests/test_adjoint_sources.py - RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================== 2 errors in 5.78s ==============================================================

The package version I am using:
Python 3.7.6
numpy 1.18.5
scipy 1.4.1

How can I install LASIF correctly in Python 3.7.6 ?

[krischer]

I think the errors you see are due to an incorrect numpy installation. Trying to reinstall these might rectify that particular error.

That being said LASIF does not support Python 3 and currently only works with Python 2.7. I'd be happy to accept a PR that ports it to Python 3 but currently I have no plans to do it myself.

There is a fork of LASIF that works with Python 3 (https://github.com/dirkphilip/LASIF_2.0) that is actively being worked on. Scope and features are a bit different and that's why they are separate repositories. I don't know what you want to do to I cannot give any further advice.

Cheers!

[ZQiwen]

Hi Krischer, thx for responding.

I added ignore::RuntimeWarning to the pytest.ini file in the main directory of LASIF so the errors about 'numpy.ufunc size' are ignored, just as what LASIF_2.0 did. But then came more errors and fails:

...
...
==========82 failed, 73 passed, 4 skipped, 38 errors in 87.36s (0:01:27)==========

It seems to me that most errors and fails are due to differences between different versions of packages (e.g. cPickle in Python 2 is replaced by pickle in Python 3 and import_string should be imported from werkzeug.utils instead of werkzeug for Werkzeug 1.0.1). Dealing with all these errors and fails could really take some time.

The good thing is that the LASIF_2.0 you had mentioned was installed smoothly on my cmomputer without any errors or warnings.

I am now working on a full-waveform tomography of the crust and upper mantle beneath Taiwan area in a relatively small scale. It seems to me that LASIF offers a propriate workflow framework for such a project.

Is there a document describing the differences between LASIF and LASIF_2.0 from the aspect of practicle applications? Any comments on these two repositories would be appreciated. 😀