On Friday, June 13, 2014, Ralf Gommers <ralf.gommers@gmail.com> wrote:

On Fri, Jun 13, 2014 at 2:07 PM, Matthew Brett <matthew.brett@gmail.com> wrote:

Hi,

Summary : I'm planning to upload OSX wheels for numpy and scipy using
the ATLAS blas / lapack library instead of the default OSX Accelerate
framework.

We've run into some trouble with a segfault in recent OSX Accelerate:

https://github.com/numpy/numpy/issues/4007

and Accelerate also doesn't play well with multiprocessing.

https://github.com/numpy/numpy/issues/4776

Because there's nothing I love more than half-day compilation runs on
my laptop, I've built ATLAS binaries with gcc 4.8, and linked numpy
and scipy to them to make OSX wheels.  These pass all tests in i386
and x86_64 mode, including numpy, scipy, matplotlib, pandas:

https://travis-ci.org/matthew-brett/scipy-stack-osx-testing/builds/27442987

The build process needs some automating, but it's recorded here:

https://github.com/matthew-brett/numpy-atlas-binaries

It's possible to get travis-ci to build these guys from a bare machine
and then upload them somewhere, but I haven't tried to do that.

Meanwhile Sturla kindly worked up a patch to numpy to work round the
Accelerate segfault [1].  I haven't tested that, but given I'd already
built the wheels, I prefer the ATLAS builds because they work with
multiprocessing.

I propose uploading these wheels as the default for numpy and scipy.
Does anyone have any objection or comments before I go ahead and do
that?

From your README and wscript I don't see what numpy version you're using to compile scipy against. I got the impression that you used 1.8.1, but it should be numpy 1.5.1 for the 2.7 build, and 1.7.1 for 3.x.

I've tried the scipy 0.14.0 python2.7 wheel, but I get import errors (see below). Your wheels should work with all common Python installs (mine is homebrew) right?

Ralf

    $ python2.7 -c "import scipy; scipy.test()"
    Running unit tests for scipy
    NumPy version 1.9.0.dev-056ab73
    NumPy is installed in /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
    SciPy version 0.14.0
    SciPy is installed in /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy
    Python version 2.7.5 (default, Jun 18 2013, 21:21:44) [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)]
    nose version 1.3.0
    E...............EEEEEE............EEEEEEEEEE
    ======================================================================
    ERROR: Failure: ImportError (dlopen(/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/cluster/_hierarchy_wrap.so, 2): Symbol not found: _PyModule_Create2
      Referenced from: /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/cluster/_hierarchy_wrap.so
      Expected in: flat namespace
     in /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/cluster/_hierarchy_wrap.so)
    ----------------------------------------------------------------------
    Traceback (most recent call last):
      File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/loader.py", line 413, in loadTestsFromName
        addr.filename, addr.module)
      File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
        return self.importFromDir(dir_path, fqname)
      File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
        mod = load_module(part_fqname, fh, filename, desc)
      File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/cluster/__init__.py", line 27, in <module>
        from . import vq, hierarchy
      File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 175, in <module>
        from . import _hierarchy_wrap
    ImportError: dlopen(/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/cluster/_hierarchy_wrap.so, 2): Symbol not found: _PyModule_Create2
      Referenced from: /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/cluster/_hierarchy_wrap.so
      Expected in: flat namespace
     in /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/cluster/_hierarchy_wrap.so

...

<42 more errors>

That is strange homebrew is one of tests in the grid and the installation path looks strange.

Can you try downloading the wheel from the url and installing from the local file?

Cheers,

Matthew 

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