matplotlib-users

[Matplotlib-users] Problems installing MPL on OS X 10.6 Snow Leopard with python2.7

[Uri L. <las...@mi...>]

Hi all,

I am trying to install matplotlib on a MacMini Intel Core 2 Duo with a clean
install of Mac OS X 10.6.  I am using python 2.7 that I built from source
using the homebrew package installer.  I also installed numpy 1.5.1 from
source, using the following environment variables:
export MACOSX_DEPLOYMENT_TARGET=10.6
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"

I also used gfortran 4.2.3 precompiled that I downloaded from
http://r.research.att.com/tools/

NOTE: I previously performed this whole install process on a brand new
MacBook Air, and it worked without a problem.

I ran numpy.test() and got the following output:

In [4]: numpy.test()
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 13 2010, 14:21:05) [GCC 4.2.1 (Apple
Inc. build 5664)]
nose version 0.11.4

[...snip...]

Ran 3006 tests in 18.696s

OK (KNOWNFAIL=4, SKIP=1)
Out[4]: <nose.result.TextTestResult run=3006 errors=0 failures=0>

Also, when I try to import numpy.core.multiarray, I get no errors.

Finally, I cloned the latest GitHub MPL and set make.osx to be the following
(note: changed pyversion, pngfamily, pngversion, deployment target, and the
FFLAGS variable):

# build mpl into a local install dir with
# PREFIX=/Users/jdhunter/dev make -f make.osx fetch deps mpl_install
MPLVERSION=1.0rc1
PYVERSION=2.7
PYTHON=python${PYVERSION}
ZLIBVERSION=1.2.3
PNGFAMILY=12
PNGVERSION=1.2.44
FREETYPEVERSION=2.3.11
MACOSX_DEPLOYMENT_TARGET=10.6
OSX_SDK_VER=10.6
ARCH_FLAGS="-arch i386 -arch x86_64"

## You shouldn't need to configure past this point

PKG_CONFIG_PATH="${PREFIX}/lib/pkgconfig"
CFLAGS="-arch i386 -arch x86_64 -I${PREFIX}/include
-I${PREFIX}/include/freetype2 -isysroot
/Developer/SDKs/MacOSX${OSX_SDK_VER}.sdk"
LDFLAGS="-arch i386 -arch x86_64 -L${PREFIX}/lib
-syslibroot,/Developer/SDKs/MacOSX${OSX_SDK_VER}.sdk"
FFLAGS="-arch i386 -arch x86_64"

The install seems to go fine.  I can import matplotlib.  But when I import
matplotlib.pyplot, I get the following:

In [2]: import matplotlib.pyplot
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)


RuntimeError: module compiled against ABI version 2000000 but this version
of numpy is 1000009
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)

/Users/laserson/<ipython console> in <module>()

/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/pyplot.py
in <module>()
     21 from matplotlib.cbook import dedent, silent_list, is_string_like,
is_numlike
     22 from matplotlib import docstring
---> 23 from matplotlib.figure import Figure, figaspect
     24 from matplotlib.backend_bases import FigureCanvasBase
     25 from matplotlib.image import imread as _imread

/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/figure.py
in <module>()
     14 import numpy as np
     15
---> 16 import artist
     17 from artist import Artist, allow_rasterization
     18 from axes import Axes, SubplotBase, subplot_class_factory

/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/artist.py
in <module>()
      4 import matplotlib.cbook as cbook
      5 from matplotlib import docstring, rcParams
----> 6 from transforms import Bbox, IdentityTransform, TransformedBbox,
TransformedPath
      7 from path import Path
      8

/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/transforms.py
in <module>()
     32 import numpy as np
     33 from numpy import ma
---> 34 from matplotlib._path import affine_transform
     35 from numpy.linalg import inv
     36

ImportError: numpy.core.multiarray failed to import


It is strange because when I import numpy.core.multiarray, I have no
problems.  It also raises a RuntimeError, yelling about an ABI
incompatibility.

Does anyone know how to solve this problem?  I was able to get this to work
on another computer..strange that it fails now.

Thanks!
Uri

...................................................................................
Uri Laserson
Graduate Student, Biomedical Engineering
Harvard-MIT Division of Health Sciences and Technology
M +1 917 742 8019
las...@mi...

Re: [Matplotlib-users] Problems installing MPL on OS X 10.6 Snow Leopard with python2.7

[Benjamin R. <ben...@ou...>]

On Monday, December 13, 2010, Uri Laserson <las...@mi...> wrote:
> Hi all,
> I am trying to install matplotlib on a MacMini Intel Core 2 Duo with a clean install of Mac OS X 10.6.  I am using python 2.7 that I built from source using the homebrew package installer.  I also installed numpy 1.5.1 from source, using the following environment variables:
>
>
> export MACOSX_DEPLOYMENT_TARGET=10.6export CFLAGS="-arch i386 -arch x86_64"
>
> export FFLAGS="-m32 -m64"export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch i386 -arch x86_64 -framework Accelerate"
> I also used gfortran 4.2.3 precompiled that I downloaded from http://r.research.att.com/tools/
>
>
> NOTE: I previously performed this whole install process on a brand new MacBook Air, and it worked without a problem.
> I ran numpy.test() and got the following output:
>
>
> In [4]: numpy.test()Running unit tests for numpyNumPy version 1.5.1NumPy is installed in /usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/numpyPython version 2.7.1 (r271:86832, Dec 13 2010, 14:21:05) [GCC 4.2.1 (Apple Inc. build 5664)]
>
> nose version 0.11.4
> [...snip...]
> Ran 3006 tests in 18.696s
> OK (KNOWNFAIL=4, SKIP=1)Out[4]: <nose.result.TextTestResult run=3006 errors=0 failures=0>
>
>
> Also, when I try to import numpy.core.multiarray, I get no errors.
> Finally, I cloned the latest GitHub MPL and set make.osx to be the following (note: changed pyversion, pngfamily, pngversion, deployment target, and the FFLAGS variable):
>
>
> # build mpl into a local install dir with# PREFIX=/Users/jdhunter/dev make -f make.osx fetch deps mpl_installMPLVERSION=1.0rc1PYVERSION=2.7PYTHON=python${PYVERSION}
>
> ZLIBVERSION=1.2.3PNGFAMILY=12PNGVERSION=1.2.44FREETYPEVERSION=2.3.11MACOSX_DEPLOYMENT_TARGET=10.6OSX_SDK_VER=10.6ARCH_FLAGS="-arch i386 -arch x86_64"
>
>
> ## You shouldn't need to configure past this point
> PKG_CONFIG_PATH="${PREFIX}/lib/pkgconfig"CFLAGS="-arch i386 -arch x86_64 -I${PREFIX}/include -I${PREFIX}/include/freetype2 -isysroot /Developer/SDKs/MacOSX${OSX_SDK_VER}.sdk"
>
> LDFLAGS="-arch i386 -arch x86_64 -L${PREFIX}/lib -syslibroot,/Developer/SDKs/MacOSX${OSX_SDK_VER}.sdk"FFLAGS="-arch i386 -arch x86_64"
> The install seems to go fine.  I can import matplotlib.  But when I import matplotlib.pyplot, I get the following:
>
>
> In [2]: import matplotlib.pyplot---------------------------------------------------------------------------RuntimeError                              Traceback (most recent call last)
>
>
>
> RuntimeError: module compiled against ABI version 2000000 but this version of numpy is 1000009---------------------------------------------------------------------------
>
> ImportError                               Traceback (most recent call last)
> /Users/laserson/<ipython console> in <module>()
> /Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/pyplot.py in <module>()
>
>      21 from matplotlib.cbook import dedent, silent_list, is_string_like, is_numlike     22 from matplotlib import docstring---> 23 from matplotlib.figure import Figure, figaspect
>      24 from matplotlib.backend_bases import FigureCanvasBase
>      25 from matplotlib.image import imread as _imread
> /Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/figure.py in <module>()     14 import numpy as np
>
>      15 ---> 16 import artist     17 from artist import Artist, allow_rasterization     18 from axes import Axes, SubplotBase, subplot_class_factory
> /Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/artist.py in <module>()
>
>       4 import matplotlib.cbook as cbook      5 from matplotlib import docstring, rcParams----> 6 from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath      7 from path import Path
>
>       8
> /Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/transforms.py in <module>()     32 import numpy as np     33 from numpy import ma
>
> ---> 34 from matplotlib._path import affine_transform     35 from numpy.linalg import inv     36
> ImportError: numpy.core.multiarray failed to import
>
>
> It is strange because when I import numpy.core.multiarray, I have no problems.  It also raises a RuntimeError, yelling about an ABI incompatibility.
> Does anyone know how to solve this problem?  I was able to get this to work on another computer..strange that it fails now.
>
>
> Thanks!Uri
> ...................................................................................Uri Laserson
> Graduate Student, Biomedical Engineering
> Harvard-MIT Division of Health Sciences and Technology
> M +1 917 742 8019
> las...@mi...
>
>

Can you try importing pyplot from a regular python prompt?  If that
works, then the issue is with ipython messing up the import process of
mpl.

Ben Root

Re: [Matplotlib-users] Problems installing MPL on OS X 10.6 Snow Leopard with python2.7

[Uri L. <las...@mi...>]

>
>
> Can you try importing pyplot from a regular python prompt?  If that
> works, then the issue is with ipython messing up the import process of
> mpl.
>
>
I get exactly the same problem...


laserson@hobbes:~$ python
Python 2.7.1 (r271:86832, Dec 13 2010, 14:21:05)
[GCC 4.2.1 (Apple Inc. build 5664)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> 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
>>>

Re: [Matplotlib-users] Problems installing MPL on OS X 10.6 Snow Leopard with python2.7

[Benjamin R. <ben...@ou...>]

On Monday, December 13, 2010, Uri Laserson <las...@mi...> wrote:
>
> Can you try importing pyplot from a regular python prompt?  If that
> works, then the issue is with ipython messing up the import process of
> mpl.
>
>  I get exactly the same problem...
>
>
> laserson@hobbes:~$ pythonPython 2.7.1 (r271:86832, Dec 13 2010, 14:21:05) [GCC 4.2.1 (Apple Inc. build 5664)] on darwinType "help", "copyright", "credits" or "license" for more information.
>
>>>> import matplotlib>>> import matplotlib.pyplotRuntimeError: module compiled against ABI version 2000000 but this version of numpy is 1000009Traceback (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_transformImportError: numpy.core.multiarray failed to import>>>
>

Well, on my Linux system, when I get that error, it happens when I do
an update of numpy, but fail to rebuild mpl.  Here is the order how I
build things: numpy, scipy, matplotlib.  I would imagine ipython goes
last.

Ben Root

Re: [Matplotlib-users] Problems installing MPL on OS X 10.6 Snow Leopard with python2.7

[Uri L. <las...@mi...>]

>
>
> Well, on my Linux system, when I get that error, it happens when I do
> an update of numpy, but fail to rebuild mpl.  Here is the order how I
> build things: numpy, scipy, matplotlib.  I would imagine ipython goes
> last.
>
>
That has been my order as well.  How can I track down why the import of
numpy.core.multiarray is  causing the problem?  And why would it cause a
problem only when MPL is being imported, but not if I import it manually?

Originally, I tried to build the GitHub trunk version of numpy, but then
abandoned that.  Since MPL is saying that it was built against the 20000...
ABI rather than the 10000... ABI, is it possible the MPL is finding some
other version of numpy lying around?  However, I'm pretty sure I deleted
everything from the git numpy build.  How could I pinpoint which numpy
libraries are being linked against in the MPL build?

Uri

Re: [Matplotlib-users] Problems installing MPL on OS X 10.6 Snow Leopard with python2.7

[Benjamin R. <ben...@ou...>]

On Mon, Dec 13, 2010 at 5:54 PM, Uri Laserson <las...@mi...> wrote:

>
>> Well, on my Linux system, when I get that error, it happens when I do
>> an update of numpy, but fail to rebuild mpl.  Here is the order how I
>> build things: numpy, scipy, matplotlib.  I would imagine ipython goes
>> last.
>>
>>
> That has been my order as well.  How can I track down why the import of
> numpy.core.multiarray is  causing the problem?  And why would it cause a
> problem only when MPL is being imported, but not if I import it manually?
>
> Originally, I tried to build the GitHub trunk version of numpy, but then
> abandoned that.  Since MPL is saying that it was built against the 20000...
> ABI rather than the 10000... ABI, is it possible the MPL is finding some
> other version of numpy lying around?  However, I'm pretty sure I deleted
> everything from the git numpy build.  How could I pinpoint which numpy
> libraries are being linked against in the MPL build?
>
> Uri
>

Uri,

"is it possible the MPL is finding some other version of numpy lying
around?"

Yes, this is really the only remaining explanation.  To find out which numpy
is being used for the build process, I think if you save the output of the
build process for mpl, I am fairly sure that that information is somewhere
near the beginning of the build log.

Ben Root

Re: [Matplotlib-users] Problems installing MPL on OS X 10.6 Snow Leopard with python2.7

[Uri L. <las...@mi...>]

Strangely, it appears to find the correct numpy.

More strangely, I picked a random order of doing things and suddenly it all
works.  I think what I ended up doing is this:

Following builds using default setting without changing anything except:
MACOSX_DEPLOYMENT_TARGET=10.6

python 2.7
numpy 1.5.1 with the flag --fcompiler=gnu95
mpl from github, setting the flags as I have posted earlier

then set these flags:
export MACOSX_DEPLOYMENT_TARGET=10.6
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"

then build scipy 0.8.0 with --fcompiler=gnu95

Then it all worked.  Honestly, I don't understand why it should work because
of this voodoo, but I am happily making figures now...

Also of note, supposedly scipy 0.8 has problems with python 2.7.  Version
0.9 should solve these problems (currently in beta).

Thanks for the help!

Uri

...................................................................................
Uri Laserson
Graduate Student, Biomedical Engineering
Harvard-MIT Division of Health Sciences and Technology
M +1 917 742 8019
las...@mi...


On Tue, Dec 14, 2010 at 17:03, Benjamin Root <ben...@ou...> wrote:

> On Mon, Dec 13, 2010 at 5:54 PM, Uri Laserson <las...@mi...> wrote:
>
>>
>>> Well, on my Linux system, when I get that error, it happens when I do
>>> an update of numpy, but fail to rebuild mpl.  Here is the order how I
>>> build things: numpy, scipy, matplotlib.  I would imagine ipython goes
>>> last.
>>>
>>>
>> That has been my order as well.  How can I track down why the import of
>> numpy.core.multiarray is  causing the problem?  And why would it cause a
>> problem only when MPL is being imported, but not if I import it manually?
>>
>> Originally, I tried to build the GitHub trunk version of numpy, but then
>> abandoned that.  Since MPL is saying that it was built against the 20000...
>> ABI rather than the 10000... ABI, is it possible the MPL is finding some
>> other version of numpy lying around?  However, I'm pretty sure I deleted
>> everything from the git numpy build.  How could I pinpoint which numpy
>> libraries are being linked against in the MPL build?
>>
>> Uri
>>
>
> Uri,
>
>
> "is it possible the MPL is finding some other version of numpy lying
> around?"
>
> Yes, this is really the only remaining explanation.  To find out which
> numpy is being used for the build process, I think if you save the output of
> the build process for mpl, I am fairly sure that that information is
> somewhere near the beginning of the build log.
>
> Ben Root
>