On Thu, Jun 19, 2014 at 11:39 AM, Matthew Brett <matthew.br...@gmail.com> wrote: > Hi, > > On Mon, Jun 16, 2014 at 1:00 PM, Matthew Brett <matthew.br...@gmail.com> > wrote: >> Hi, >> >> On Mon, Jun 16, 2014 at 12:51 PM, <josef.p...@gmail.com> wrote: >>> On Mon, Jun 16, 2014 at 7:10 AM, Matthew Brett <matthew.br...@gmail.com> >>> wrote: >>>> Hi, >>>> >>>> On Sun, Jun 15, 2014 at 10:51 PM, Ralf Gommers <ralf.gomm...@gmail.com> >>>> wrote: >>>>> >>>>> >>>>> >>>>> On Sat, Jun 14, 2014 at 11:56 AM, Matthew Brett <matthew.br...@gmail.com> >>>>> wrote: >>>>>> >>>>>> >>>>>> >>>>>> On Friday, June 13, 2014, Ralf Gommers <ralf.gomm...@gmail.com> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Fri, Jun 13, 2014 at 2:07 PM, Matthew Brett <matthew.br...@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? >>>>> >>>>> >>>>> 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 >>> >> >> I see - thanks for the summary. I will recompile. > > Last call - binaries recompiled, tested, more comments here: > > https://github.com/numpy/numpy/issues/4007 > > I'm planning to upload these binaries to pypi later on today,
Done - please test and let me know of any problems, Cheers, Matthew _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion