On Mon, Jun 16, 2014 at 7:10 AM, Matthew Brett <[email protected]> wrote: > Hi, > > On Sun, Jun 15, 2014 at 10:51 PM, Ralf Gommers <[email protected]> wrote: >> >> >> >> 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. > > Yes, sorry - that does look like the normal homebrew install path, I > didn't realize it had the exotic framework parts to it. > > I just ran these commands on my machine: > > SPI=https://nipy.bic.berkeley.edu/scipy_installers > BREW_BIN=/usr/local/Cellar/python/2.7.6/bin > curl -O > $SPI/numpy-1.8.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl > curl -O > $SPI/scipy-0.14.0-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl > $BREW_BIN/pip install > numpy-1.8.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl > $BREW_BIN/pip install > scipy-0.14.0-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl > $BREW_BIN/python -c "import scipy; scipy.test()" > > and the scipy tests passed. > > I built the scipy wheel against numpy 1.8.1 - but - aren't the numpies > binary compatible? What difference would I expect to see if I'd built > scipy against numpy 1.5.1 or 1.7 ?
I summarized here what David explained a while ago about the difference between forward and backwards binary compatibility http://stackoverflow.com/questions/17709641/valueerror-numpy-dtype-has-the-wrong-size-try-recompiling/18369312#18369312 Josef > > Cheers, > > Matthew > _______________________________________________ > NumPy-Discussion mailing list > [email protected] > http://mail.scipy.org/mailman/listinfo/numpy-discussion _______________________________________________ NumPy-Discussion mailing list [email protected] http://mail.scipy.org/mailman/listinfo/numpy-discussion
