On Fri, Jun 13, 2014 at 2:07 PM, Matthew Brett <[email protected]> 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> ... > Cheers, > > Matthew > > [1] http://mail.scipy.org/pipermail/numpy-discussion/2014-June/070333.html > _______________________________________________ > NumPy-Discussion mailing list > [email protected] > http://mail.scipy.org/mailman/listinfo/numpy-discussion >
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