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

[Ralf Gommers]

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 14de485c053cc275682bc7de0316fc
> ca72b341f8
> https://github.com/scipy/scipy/tree/14de485c053cc275682bc7de0316fc
> ca72b341f8
>
> 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
>

This is with an already built SciPy right, without rebuilding? That would
explain the uninformative traceback.

Cheers,
Ralf



>
> 2nd traceback:
>
> ImportError while importing test module '/Users/markmikofski/Projects/
> scipy/build/testenv/lib/python3.6/site-packages/scipy/
> integrate/tests/test_banded_ode_solvers.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> scipy/integrate/__init__.py:93: in <module>
>     from ._bvp import solve_bvp
> scipy/integrate/_bvp.py:10: in <module>
>     from scipy.sparse.linalg import splu
> scipy/sparse/linalg/__init__.py:114: in <module>
>     from .isolve import *
> scipy/sparse/linalg/isolve/__init__.py:8: in <module>
>     from .lgmres import lgmres
> scipy/sparse/linalg/isolve/lgmres.py:13: in <module>
>     from ._gcrotmk import _fgmres
> scipy/sparse/linalg/isolve/_gcrotmk.py:10: in <module>
>     from scipy.linalg import (get_blas_funcs, qr, solve, svd, qr_insert,
> lstsq)
> E   ImportError: cannot import name 'qr_insert'
>
> I apologize for not trying to research and trouble shoot this more myself,
> but I've a tight window while my kids are at gymnastics to go running, and
> you all know the drill, just thought I'd ask to see if anyone had ever run
> across this issue before.
>
> Thanks for your help! Sorry for the intrusion!
>
> All the best,
> Mark
>
> --
> Mark Mikofski, PhD (2005)
> *Fiat Lux*
>
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>
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