[SciPy-Dev] runtest issue mac os with master 14de485c053cc275682bc7de0316fcca72b341f8

[Matthew Brett]

Hi,

On Sat, Jun 2, 2018 at 6:05 PM, Ralf Gommers <ralf.gommers at gmail.com> wrote:
>
>
> On Sat, Jun 2, 2018 at 9:57 AM, Mark Alexander Mikofski
> <mikofski at berkeley.edu> wrote:
>>
>> Hi All,
>>
>> I am having issues using
>>
>>     python runtest.py
>>
>> from scipy master branch since commit
>> 14de485c053cc275682bc7de0316fcca72b341f8
>>
>> https://github.com/scipy/scipy/tree/14de485c053cc275682bc7de0316fcca72b341f8
>>
>> there are two tracebacks, I think this may have something to do with
>> changes to LAPACK and dropping Apple Accelerate support, but not sure, and
>> don't know how to fix it. Should I brew install openblas? (I'm going to try
>> that)
>
>
> Yes that is the recommendation (if you're not using Anaconda).
>
>
>>
>> Use anaconda and create a conda env? (maybe this next?)
>
>
> If you're already using Anaconda, and the numpy from the defaults channel,
> SciPy should automatically link against MKL.
>
>
>>
>> Currently I'm using python 3.6 from homebrew in a virtualenv with wheels
>> from PyPI, after I create the virtualenv using the homebrew python-3
>> interpreter, I do pip install requirements.txt (see attached).
>>
>> 1st traceback:
>>
>> ImportError while importing test module
>> '/Users/markmikofski/Projects/scipy/build/testenv/lib/python3.6/site-packages/scipy/cluster/tests/test_hierarchy.py'.
>> Hint: make sure your test modules/packages have valid Python names.
>> Traceback:
>> scipy/cluster/__init__.py:27: in <module>
>>     from . import vq, hierarchy
>> scipy/cluster/vq.py:75: in <module>
>>     from scipy.spatial.distance import cdist
>> scipy/spatial/__init__.py:97: in <module>
>>     from ._spherical_voronoi import SphericalVoronoi
>> scipy/spatial/_spherical_voronoi.py:19: in <module>
>>     from scipy.spatial.distance import pdist
>> scipy/spatial/distance.py:123: in <module>
>>     from ..linalg import norm
>> scipy/linalg/__init__.py:207: in <module>
>>     from ._decomp_update import *
>> _decomp_update.pyx:1: in init scipy.linalg._decomp_update
>>     ???
>> E   ImportError:
>> dlopen(/Users/markmikofski/Projects/scipy/build/testenv/lib/python3.6/site-packages/scipy/linalg/cython_lapack.cpython-36m-darwin.so,
>> 2): Symbol not found: _cbbcsd_
>> E     Referenced from:
>> /Users/markmikofski/Projects/scipy/build/testenv/lib/python3.6/site-packages/scipy/linalg/cython_lapack.cpython-36m-darwin.so
>> E     Expected in: flat namespace
>> E    in
>> /Users/markmikofski/Projects/scipy/build/testenv/lib/python3.6/site-packages/scipy/linalg/cython_lapack.cpython-36m-darwin.so

I am getting the same error, for OpenBLAS v0.3.0, on the Travis-CI
macOS machines, using our usual wheel-building procedure (+OpenBLAS):

* Python 3.4: https://travis-ci.org/matthew-brett/scipy-wheels/jobs/388298604
* Python 3.5: https://travis-ci.org/matthew-brett/scipy-wheels/jobs/388298605

It might also happen on Python 2.7, but that is segfaulting too often
to get a full traceback:

https://travis-ci.org/matthew-brett/scipy-wheels/jobs/388298603

Cheers,

Matthew