<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jun 5, 2018 at 11:14 AM, Matthew Brett <span dir="ltr"><<a href="mailto:matthew.brett@gmail.com" target="_blank">matthew.brett@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<div><div class="h5"><br>
On Sat, Jun 2, 2018 at 6:05 PM, Ralf Gommers <<a href="mailto:ralf.gommers@gmail.com">ralf.gommers@gmail.com</a>> wrote:<br>
><br>
><br>
> On Sat, Jun 2, 2018 at 9:57 AM, Mark Alexander Mikofski<br>
> <<a href="mailto:mikofski@berkeley.edu">mikofski@berkeley.edu</a>> wrote:<br>
>><br>
>> Hi All,<br>
>><br>
>> I am having issues using<br>
>><br>
>> python runtest.py<br>
>><br>
>> from scipy master branch since commit<br>
>> 14de485c053cc275682bc7de0316fc<wbr>ca72b341f8<br>
>><br>
>> <a href="https://github.com/scipy/scipy/tree/14de485c053cc275682bc7de0316fcca72b341f8" rel="noreferrer" target="_blank">https://github.com/scipy/<wbr>scipy/tree/<wbr>14de485c053cc275682bc7de0316fc<wbr>ca72b341f8</a><br>
>><br>
>> there are two tracebacks, I think this may have something to do with<br>
>> changes to LAPACK and dropping Apple Accelerate support, but not sure, and<br>
>> don't know how to fix it. Should I brew install openblas? (I'm going to try<br>
>> that)<br>
><br>
><br>
> Yes that is the recommendation (if you're not using Anaconda).<br>
><br>
><br>
>><br>
>> Use anaconda and create a conda env? (maybe this next?)<br>
><br>
><br>
> If you're already using Anaconda, and the numpy from the defaults channel,<br>
> SciPy should automatically link against MKL.<br>
><br>
><br>
>><br>
>> Currently I'm using python 3.6 from homebrew in a virtualenv with wheels<br>
>> from PyPI, after I create the virtualenv using the homebrew python-3<br>
>> interpreter, I do pip install requirements.txt (see attached).<br>
>><br>
>> 1st traceback:<br>
>><br>
>> ImportError while importing test module<br>
>> '/Users/markmikofski/Projects/<wbr>scipy/build/testenv/lib/<wbr>python3.6/site-packages/scipy/<wbr>cluster/tests/test_hierarchy.<wbr>py'.<br>
>> Hint: make sure your test modules/packages have valid Python names.<br>
>> Traceback:<br>
>> scipy/cluster/__init__.py:27: in <module><br>
>> from . import vq, hierarchy<br>
>> scipy/cluster/vq.py:75: in <module><br>
>> from scipy.spatial.distance import cdist<br>
>> scipy/spatial/__init__.py:97: in <module><br>
>> from ._spherical_voronoi import SphericalVoronoi<br>
>> scipy/spatial/_spherical_<wbr>voronoi.py:19: in <module><br>
>> from scipy.spatial.distance import pdist<br>
>> scipy/spatial/distance.py:123: in <module><br>
>> from ..linalg import norm<br>
>> scipy/linalg/__init__.py:207: in <module><br>
>> from ._decomp_update import *<br>
>> _decomp_update.pyx:1: in init scipy.linalg._decomp_update<br>
>> ???<br>
>> E ImportError:<br>
>> dlopen(/Users/markmikofski/<wbr>Projects/scipy/build/testenv/<wbr>lib/python3.6/site-packages/<wbr>scipy/linalg/<a href="http://cython_lapack.cpython-36m-darwin.so" rel="noreferrer" target="_blank">cython_lapack.<wbr>cpython-36m-darwin.so</a>,<br>
>> 2): Symbol not found: _cbbcsd_<br>
>> E Referenced from:<br>
>> /Users/markmikofski/Projects/<wbr>scipy/build/testenv/lib/<wbr>python3.6/site-packages/scipy/<wbr>linalg/<a href="http://cython_lapack.cpython-36m-darwin.so" rel="noreferrer" target="_blank">cython_lapack.cpython-<wbr>36m-darwin.so</a><br>
>> E Expected in: flat namespace<br>
>> E in<br>
>> /Users/markmikofski/Projects/<wbr>scipy/build/testenv/lib/<wbr>python3.6/site-packages/scipy/<wbr>linalg/<a href="http://cython_lapack.cpython-36m-darwin.so" rel="noreferrer" target="_blank">cython_lapack.cpython-<wbr>36m-darwin.so</a><br>
<br>
</div></div>I am getting the same error, for OpenBLAS v0.3.0, on the Travis-CI<br>
macOS machines, using our usual wheel-building procedure (+OpenBLAS):<br>
<br>
* Python 3.4: <a href="https://travis-ci.org/matthew-brett/scipy-wheels/jobs/388298604" rel="noreferrer" target="_blank">https://travis-ci.org/matthew-<wbr>brett/scipy-wheels/jobs/<wbr>388298604</a><br>
* Python 3.5: <a href="https://travis-ci.org/matthew-brett/scipy-wheels/jobs/388298605" rel="noreferrer" target="_blank">https://travis-ci.org/matthew-<wbr>brett/scipy-wheels/jobs/<wbr>388298605</a></blockquote><div><br></div><div>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):<br><br><pre>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</pre><br></div><div>Ralf<br> <br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
It might also happen on Python 2.7, but that is segfaulting too often<br>
to get a full traceback:<br>
<br>
<a href="https://travis-ci.org/matthew-brett/scipy-wheels/jobs/388298603" rel="noreferrer" target="_blank">https://travis-ci.org/matthew-<wbr>brett/scipy-wheels/jobs/<wbr>388298603</a><br>
<br>
Cheers,<br>
<br>
Matthew<br>
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