[SciPy-Dev] Segfaults building against numpy / scipy on OSX Lion

Ralf Gommers ralf.gommers@googlemail....
Thu Jul 19 16:14:37 CDT 2012


On Thu, Jul 19, 2012 at 9:58 PM, Matthew Brett <matthew.brett@gmail.com>wrote:

> Hi,
>
> On Thu, Jul 19, 2012 at 8:29 AM, Ralf Gommers
> <ralf.gommers@googlemail.com> wrote:
> >
> >
> > On Wed, Jul 18, 2012 at 9:49 PM, Matthew Brett <matthew.brett@gmail.com>
> > wrote:
> >>
> >> Hi,
> >>
> >> Please forgive the half-baked question, but, I'm trying to build our
> >> package nipy (nipy.org) against stock downloaded
> >>
> >> numpy-1.6.2-py2.7-python.org-macosx10.6.dmg
> >> scipy-0.10.1-py2.7-python.org-macosx10.6.dmg
> >
> >
> > You're only building against numpy, and scipy is a runtime dependency,
> > right?
>
> Right - thanks for the clarification.
>
> >>
> >> I'm using latest XCode 4.3.3
> >>
> >> $ clang --version
> >> Apple clang version 3.1 (tags/Apple/clang-318.0.61) (based on LLVM
> 3.1svn)
> >> Target: x86_64-apple-darwin11.4.0
> >> Thread model: posix
> >>
> >> on Lion:
> >>
> >> $ uname -a
> >> Darwin pis-macbook-air 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr  9
> >> 19:33:05 PDT 2012; root:xnu-1699.26.8~1/RELEASE_I386 i386
> >>
> >> I believe the correct incantation for the build is:
> >>
> >> http://scipy.org/Installing_SciPy/Mac_OS_X
> >>
> >> CC=clang CXX=clang FFLAGS=-ff2c python setup.py build_ext -i
> >
> >
> > It has been reported to work for scipy, that's as much as I know. You can
> > try if building scipy in the same way works for you. If it doesn't, the
> > problem may not be in nipy.
>
> Having linked the http://r.research.att.com/tools/ gfortran-4.2 to
> gfortran, this scipy build:
>
> CC=clang FFLAGS=-ff2c python setup.py build_ext -i
>
> builds and passes all tests.
>
> Building and linking nipy with the same flags, and with this scipy on
> the path, passes all tests.
>
> Take this scipy off the path (reverting to the system scipy as
> downloaded) gives another segfault in the same routine as before, but
> a little later:
>
> Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
> 0   _segmentation.so                    0x00000001035eef14 _get_message_mf
> + 20 (mrf.c:59)
> 1   _segmentation.so                    0x00000001035eebee ve_step + 798
> (mrf.c:172)
> 2   _segmentation.so                    0x00000001035ed4dc
> __pyx_pf_4nipy_10algorithms_12segmentation_13_segmentation__ve_step +
> 4604 (_segmentation.c:1103)
> 3   org.python.python                   0x00000001000c1e7d
> PyEval_EvalFrameEx + 25213
>
>
>> This does build, but during the tests, and only on this platform,
> >> segfaults (report attached).
> >>
> >> Is this build / link expected to work?  Did I get the right flags?
> >
> >
> > Not sure. Some things to check: that you have the 64-bit python from
> > python.org, that MACOSX_DEPLOYMENT_TARGET is set to 10.6 during the
> build.
>
> The MACOSX_DEPLOYMENT_TARGET did not seem to make a difference.
>
> > The by far most reliable way to make everything work together is to use
> the
> > exact same compiler. Which is not available anymore with the most recent
> > XCode. You could look into ways to get gcc-4.2 to install on 10.7. And
> make
> > sure to build your binaries on 10.6 for 64-bit 2.7 and on 10.5 for the
> other
> > Python 2.x flavors if you can.
>
> Hum.  I had previously tried the R gcc-4.2 compiler (thanks Scott for
> the link) and run into:
>
> gcc-4.2: /Users/mb312/dev_trees/nipy/libcstat/wrapper/fffpy.c
> In file included from
>
> /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:4,
>                  from
>
> /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:85,
>                  from
> /Users/mb312/dev_trees/nipy/libcstat/wrapper/fffpy.h:1,
>                  from
> /Users/mb312/dev_trees/nipy/libcstat/wrapper/fffpy.c:1:
> /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error:
> stdarg.h: No such file or directory
>
> Anything obvious that I missed?
>

This is typically caused by not having the required SDKs installed, they're
under "Optional Installs" on your XCode dvd.

Ralf
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