[SciPy-User] Problems installing scipy on OS X 10.6 (Snow Leopard): libarpack

Ralf Gommers ralf.gommers@googlemail....
Tue Dec 14 09:20:27 CST 2010


On Tue, Dec 14, 2010 at 11:00 PM, Uri Laserson <laserson@mit.edu> wrote:

> Thanks for the help.  I will probably retry with scipy 0.9.0.  Strangely
> enough, I did something on my computer and it worked.  I think that what
> ended up happening was building numpy 1.5.1 with all the normal defaults on
> the computer.  Building MPL on top of that was then fine.  And finally, I
> used the special compile flags only for scipy 0.8.0.  Both numpy as scipy
> pass numpy.test() and scipy.test()
>
> When I perform numpy.test('full') as you suggest, I get some
> fortran-related errors, like:
> ERROR: test_return_real.TestF90ReturnReal.test_all
> ERROR: test_return_integer.TestF77ReturnInteger.test_all
> etc. (12 in total)
>
> Are these significant?
>

If it all works for you probably not, but there was an issue with those
errors a few months ago. They are related to 32/64-bit architecture errors
as well. If you have any problem with that again, please send me your full
build and test logs.

Cheers,
Ralf



> Uri
>
>
> ...................................................................................
> Uri Laserson
> Graduate Student, Biomedical Engineering
> Harvard-MIT Division of Health Sciences and Technology
> M +1 917 742 8019
> laserson@mit.edu
>
>
>
> On Tue, Dec 14, 2010 at 06:08, Ralf Gommers <ralf.gommers@googlemail.com>wrote:
>
>>
>>
>> On Tue, Dec 14, 2010 at 12:38 AM, Uri Laserson <laserson@mit.edu> wrote:
>>
>>> Hi Ralf,
>>>
>>> Sor for my delayed response, I missed this message in my inbox.
>>>
>>
>> No problem at all.
>>
>>
>>> I have since moved forward with this problem, but I now have a runtime
>>> problem.
>>>
>>> I am using python2.7 I built myself through the homebrew package manager.
>>>
>>> Output from my compilers is as follows:
>>> laserson@hobbes:~$ gcc -v
>>> Using built-in specs.
>>> Target: i686-apple-darwin10
>>> Configured with: /var/tmp/gcc/gcc-5664~89/src/configure
>>> --disable-checking --enable-werror --prefix=/usr --mandir=/share/man
>>> --enable-languages=c,objc,c++,obj-c++
>>> --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib
>>> --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10-
>>> --host=x86_64-apple-darwin10 --target=i686-apple-darwin10
>>> --with-gxx-include-dir=/include/c++/4.2.1
>>> Thread model: posix
>>> gcc version 4.2.1 (Apple Inc. build 5664)
>>>
>>> laserson@hobbes:~$ g++ -v
>>> Using built-in specs.
>>> Target: i686-apple-darwin10
>>> Configured with: /var/tmp/gcc/gcc-5664~89/src/configure
>>> --disable-checking --enable-werror --prefix=/usr --mandir=/share/man
>>> --enable-languages=c,objc,c++,obj-c++
>>> --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib
>>> --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10-
>>> --host=x86_64-apple-darwin10 --target=i686-apple-darwin10
>>> --with-gxx-include-dir=/include/c++/4.2.1
>>> Thread model: posix
>>> gcc version 4.2.1 (Apple Inc. build 5664)
>>>
>>> laserson@hobbes:~$ gfortran -v
>>> Using built-in specs.
>>> Target: i686-apple-darwin8
>>> Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/local
>>> --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/
>>> --build=i686-apple-darwin8 --host=i686-apple-darwin8
>>> --target=i686-apple-darwin8 --enable-languages=fortran
>>> Thread model: posix
>>> gcc version 4.2.3
>>>
>>> I installed numpy and scipy loosely based on the directions here:
>>> http://mail.scipy.org/pipermail/numpy-discussion/2010-August/052227.html
>>>
>>> I see that unfortunately that mail did not receive any response, I don't
>> remember seeing it. The info in it is not entirely correct.
>>
>>
>>> More specifically, after installing gfortran, I downloaded the following
>>> versions of numpy and scipy:
>>> numpy 1.5.1
>>> scipy 0.8.0
>>>
>>
>> scipy 0.8.0 has one issue with python 2.7. You should either use the 0.8.x
>> svn branch or 0.9.0b1 from svn or Sourceforge.
>>
>>>
>>> I then set the following environment variables:
>>> export MACOSX_DEPLOYMENT_TARGET=10.6
>>>
>> This is OK.
>>
>>
>>> export CFLAGS="-arch i386 -arch x86_64"
>>> export FFLAGS="-m32 -m64"
>>> export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch i386 -arch
>>> x86_64 -framework Accelerate"
>>>
>>
>> This is incorrect. When you build with distutils, CFLAGS/FFLAGS will
>> overwrite all flags, not append them. You should just leave this out,
>> default flags work fine with numpy 1.5.1 + scipy as specified above.
>>
>>
>>>
>>> Then I built and installed numpy as follows (note: sudo is not needed, as
>>> I took ownership of /usr/local):
>>> python setup.py build --fcompiler=gnu95
>>> python setup.py install
>>>
>>> The results of numpy.test() are:
>>> >>> numpy.test()
>>>
>>
>> Looks OK. As a sanity check, run numpy.test('full'). There are some extra
>> distutils tests that get run like that.
>>
>>
>>> Running unit tests for numpy
>>> NumPy version 1.5.1
>>> NumPy is installed in
>>> /usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/numpy
>>> Python version 2.7.1 (r271:86832, Dec  7 2010, 12:37:47) [GCC 4.2.1
>>> (Apple Inc. build 5664)]
>>> nose version 0.11.4
>>> ....
>>> Ran 3006 tests in 18.312s
>>>
>>> OK (KNOWNFAIL=4, SKIP=1)
>>> <nose.result.TextTestResult run=3006 errors=0 failures=0>
>>>
>>> Then I installed scipy as follows:
>>> python setup.py build --fcompiler=gnu95
>>> python setup.py install
>>>
>>> and ran the tests, giving output:
>>> >>> scipy.test()
>>> Running unit tests for scipy
>>> NumPy version 1.5.1
>>> NumPy is installed in
>>> /usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/numpy
>>> SciPy version 0.8.0
>>> SciPy is installed in
>>> /usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/scipy
>>> Python version 2.7.1 (r271:86832, Dec  7 2010, 12:37:47) [GCC 4.2.1
>>> (Apple Inc. build 5664)]
>>> nose version 0.11.4
>>> RuntimeError: module compiled against ABI version 2000000 but this
>>> version of numpy is 1000009
>>> ....
>>> Ran 4405 tests in 87.505s
>>>
>>> OK (KNOWNFAIL=19, SKIP=28)
>>> <nose.result.TextTestResult run=4405 errors=0 failures=0>
>>>
>>> Note the RuntimeError listed above:
>>> RuntimeError: module compiled against ABI version 2000000 but this
>>> version of numpy is 1000009
>>>
>>
>> That looks like you have some other numpy install hanging around.
>>
>>
>>>
>>> I can still import scipy fine.  However, I then have a problem after
>>> building matplotlib (GitHub).  I can build it fine:
>>>
>>> ============================================================================
>>> BUILDING MATPLOTLIB
>>>             matplotlib: 1.0.0
>>>                 python: 2.7.1 (r271:86832, Dec  7 2010, 12:37:47)  [GCC
>>>                         4.2.1 (Apple Inc. build 5664)]
>>>               platform: darwin
>>>
>>> REQUIRED DEPENDENCIES
>>>                  numpy: 1.5.1
>>>              freetype2: 12.0.6
>>>
>>> OPTIONAL BACKEND DEPENDENCIES
>>>                 libpng: 1.2.44
>>>                Tkinter: Tkinter: 81008, Tk: 8.5, Tcl: 8.5
>>>                   Gtk+: no
>>>                         * Building for Gtk+ requires pygtk; you must be
>>> able
>>>                         * to "import gtk" in your build/install
>>> environment
>>>        Mac OS X native: yes
>>>                     Qt: no
>>>                    Qt4: no
>>>                  Cairo: no
>>>
>>> However, when I import matplotlib.pyplot, I get:
>>> >>> import matplotlib.pyplot
>>> RuntimeError: module compiled against ABI version 2000000 but this
>>> version of numpy is 1000009
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File
>>> "/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/pyplot.py",
>>> line 23, in <module>
>>>     from matplotlib.figure import Figure, figaspect
>>>   File
>>> "/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/figure.py",
>>> line 16, in <module>
>>>     import artist
>>>   File
>>> "/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/artist.py",
>>> line 6, in <module>
>>>     from transforms import Bbox, IdentityTransform, TransformedBbox,
>>> TransformedPath
>>>   File
>>> "/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/transforms.py",
>>> line 34, in <module>
>>>     from matplotlib._path import affine_transform
>>> ImportError: numpy.core.multiarray failed to import
>>>
>>>
>>> However, when I separately try to import numpy.core.multiarray, I have no
>>> problem.
>>>
>>> Same problem as with scipy I guess.
>>
>> Cheers,
>> Ralf
>>
>>
>> Any ideas?
>>>
>>> Thanks!
>>> Uri
>>>
>>>
>>>
>>>
>>> On Wed, Dec 8, 2010 at 06:18, Ralf Gommers <ralf.gommers@googlemail.com>wrote:
>>>
>>>>
>>>>
>>>> On Wed, Dec 8, 2010 at 4:06 AM, Uri Laserson <laserson@mit.edu> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I am on a MacMini with Intel processor.  I just installed OS X 10.6 and
>>>>> the latest Xcode that I could download, which included gcc 4.2.  I am using
>>>>> python 2.7 built from source using homebrew.  I installed the gfortran 4.2.3
>>>>> binaries from http://r.research.att.com/tools/.
>>>>>
>>>>> I am trying to install numpy and scipy.  numpy installs fine with or
>>>>> without switching to g++-4.0.  I have successfully installed it using pip
>>>>> and also directly from source from the git repository.
>>>>>
>>>>> Scipy is giving me errors on install (the same errors whether I use pip
>>>>> or try the svn repository).  I installed it successfully yesterday on a new
>>>>> Macbook Air using pip, after changing the symlinks to point to g++-4.0.
>>>>>  However, today on my MacMini, I am getting errors after following the same
>>>>> protocol.
>>>>>
>>>>> The errors I am getting are here:
>>>>> https://gist.github.com/732293
>>>>>
>>>>
>>>> The error indicates that 32 and 64 bit binaries are being mixed. Can you
>>>> tell us the following:
>>>> - what build command you used
>>>> - what Python you are using (from python.org, from Apple,
>>>> self-compiled?)
>>>> - the output of "gcc -v", "g++ -v" and "gfortran -v"
>>>>
>>>> Ralf
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>
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>>
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