<div dir="ltr">That's what I did. After brew installing openblas on my local machine, I saved <a href="https://github.com/scipy/scipy/blob/master/site.cfg.example">https://github.com/scipy/scipy/blob/master/site.cfg.example</a> 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
<span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">/usr/local/opt/openblas/include in my specific case</span>) .</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jun 5, 2018 at 11:30 AM, Ralf Gommers <span dir="ltr"><<a href="mailto:ralf.gommers@gmail.com" target="_blank">ralf.gommers@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">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="m_71959176643531049h5"><br>
On Sat, Jun 2, 2018 at 6:05 PM, Ralf Gommers <<a href="mailto:ralf.gommers@gmail.com" target="_blank">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" target="_blank">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/scipy<wbr>/tree/14de485c053cc275682bc7de<wbr>0316fcca72b341f8</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/python<wbr>3.6/site-packages/scipy/cluste<wbr>r/tests/test_hierarchy.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_voron<wbr>oi.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/Pro<wbr>jects/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>
>> 2): Symbol not found: _cbbcsd_<br>
>> E Referenced from:<br>
>> /Users/markmikofski/Projects/s<wbr>cipy/build/testenv/lib/python3<wbr>.6/site-packages/scipy/linalg/<a href="http://cython_lapack.cpython-36m-darwin.so" rel="noreferrer" target="_blank"><wbr>cython_lapack.cpython-36m-<wbr>darwin.so</a><br>
>> E Expected in: flat namespace<br>
>> E in<br>
>> /Users/markmikofski/Projects/s<wbr>cipy/build/testenv/lib/python3<wbr>.6/site-packages/scipy/linalg/<a href="http://cython_lapack.cpython-36m-darwin.so" rel="noreferrer" target="_blank"><wbr>cython_lapack.cpython-36m-<wbr>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/388298<wbr>604</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/388298<wbr>605</a></blockquote><div><br></div></div></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-<wbr>brett/scipy-wheels/venv/bin/..<wbr>/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-<wbr>brett/scipy-wheels/venv/bin/..<wbr>/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/Users/travis/build/matthew-<wbr>brett/scipy-wheels/venv/bin/..<wbr>/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
FOUND:
libraries = ['blas']
library_dirs = ['/usr/lib']
define_macros = [('NO_ATLAS_INFO', 1)]
language = f77</pre><span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888"><div>Ralf<br> <br></div></font></span><span class=""><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/388298<wbr>603</a><br>
<br>
Cheers,<br>
<br>
Matthew<br>
<div class="m_71959176643531049HOEnZb"><div class="m_71959176643531049h5">______________________________<wbr>_________________<br>
SciPy-Dev mailing list<br>
<a href="mailto:SciPy-Dev@python.org" target="_blank">SciPy-Dev@python.org</a><br>
<a href="https://mail.python.org/mailman/listinfo/scipy-dev" rel="noreferrer" target="_blank">https://mail.python.org/mailma<wbr>n/listinfo/scipy-dev</a><br>
</div></div></blockquote></span></div><br></div></div>
<br>______________________________<wbr>_________________<br>
SciPy-Dev mailing list<br>
<a href="mailto:SciPy-Dev@python.org">SciPy-Dev@python.org</a><br>
<a href="https://mail.python.org/mailman/listinfo/scipy-dev" rel="noreferrer" target="_blank">https://mail.python.org/<wbr>mailman/listinfo/scipy-dev</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div><span style="font-size:12.8px">Mark Mikofski, PhD (2005)</span><br></div><div><span style="font-size:12.8px"><i>Fiat Lux</i></span><br></div></div></div></div>
</div>