On Sat, Jun 14, 2014 at 11:56 AM, Matthew Brett <[email protected]> wrote:
> > > On Friday, June 13, 2014, Ralf Gommers <[email protected]> wrote: > >> >> >> >> 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> >> > > 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? > That's what I did (easier than remembering the magic pip incantation). The install path looks fine to me, maybe homebrew changed it recently? I can try to update my install, will take a few days though. Ralf > > Cheers, > > Matthew > > _______________________________________________ > NumPy-Discussion mailing list > [email protected] > http://mail.scipy.org/mailman/listinfo/numpy-discussion > >
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