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

[Ralf Gommers]

On Tue, Jun 5, 2018 at 11:14 AM, Matthew Brett <matthew.brett at gmail.com>
wrote:

> 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/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
>
> 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


You're cloning OpenBLAS 0.3.0 but it's not detected (you'll either need a
site.cfg or install it to one of the regular locations):

openblas_info:

  libraries  not found in
['/Users/travis/build/matthew-brett/scipy-wheels/venv/bin/../lib',
'/usr/local/lib', '/usr/lib']

  NOT AVAILABLE



atlas_blas_threads_info:

Setting PTATLAS=ATLAS

  libraries ptf77blas,ptcblas,atlas not found in
['/Users/travis/build/matthew-brett/scipy-wheels/venv/bin/../lib',
'/usr/local/lib', '/usr/lib']

  NOT AVAILABLE



atlas_blas_info:

  libraries f77blas,cblas,atlas not found in
['/Users/travis/build/matthew-brett/scipy-wheels/venv/bin/../lib',
'/usr/local/lib', '/usr/lib']

  NOT AVAILABLE



  FOUND:

    libraries = ['blas']

    library_dirs = ['/usr/lib']

    define_macros = [('NO_ATLAS_INFO', 1)]

    language = f77


Ralf


>
>
> 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
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