[Numpy-discussion] Switch to using ATLAS for OSX binary wheels
Matthew Brett
matthew.brett at gmail.com
Thu Jun 19 06:39:57 EDT 2014
Hi,
On Mon, Jun 16, 2014 at 1:00 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> Hi,
>
> On Mon, Jun 16, 2014 at 12:51 PM, <josef.pktd at gmail.com> wrote:
>> On Mon, Jun 16, 2014 at 7:10 AM, Matthew Brett <matthew.brett at gmail.com> wrote:
>>> Hi,
>>>
>>> On Sun, Jun 15, 2014 at 10:51 PM, Ralf Gommers <ralf.gommers at gmail.com> wrote:
>>>>
>>>>
>>>>
>>>> On Sat, Jun 14, 2014 at 11:56 AM, Matthew Brett <matthew.brett at gmail.com>
>>>> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On Friday, June 13, 2014, Ralf Gommers <ralf.gommers at gmail.com> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Jun 13, 2014 at 2:07 PM, Matthew Brett <matthew.brett at 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,
Cheers,
Matthew
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