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

Tue Jun 5 14:46:31 EDT 2018

That's what I did. After brew installing openblas on my local machine, I
saved https://github.com/scipy/scipy/blob/master/site.cfg.example as
site.cfg, uncommented the [openblas] section, lines 129-133 as of 444a95b0,
and changed them to the specific path that homebrew told me were the
library and include directories (/usr/local/opt/openblas/lib and
/usr/local/opt/openblas/include
in my specific case) .

On Tue, Jun 5, 2018 at 11:30 AM, Ralf Gommers <ralf.gommers at gmail.com>
wrote:

>
>
> 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/14de485c053cc275682bc7de
>> 0316fcca72b341f8
>> >>
>> >> 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/python
>> 3.6/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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>> SciPy-Dev at python.org
>> https://mail.python.org/mailman/listinfo/scipy-dev
>>
>
>
> _______________________________________________
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>
>

-- 
Mark Mikofski, PhD (2005)
*Fiat Lux*
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