Hi, On Mon, Jun 16, 2014 at 12:51 PM, <[email protected]> wrote: > 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 >
I see - thanks for the summary. I will recompile. Cheers, Matthew _______________________________________________ NumPy-Discussion mailing list [email protected] http://mail.scipy.org/mailman/listinfo/numpy-discussion
