[SciPy-User] scipy trunk build / segfault problem

Ralf Gommers ralf.gommers@googlemail....
Tue Oct 27 05:52:51 CDT 2009


Hi,

At the moment I seem to be unable to build SciPy. A few weeks ago on the
same machine it worked fine. I collected as much info as I could below.


OS: OS X 10.6, Snow Leopard

gcc: $ gcc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5646)

$ gfortran --version
GNU Fortran (GCC) 4.2.3
(from http://r.research.att.com/tools/)

$ python --version
Python 2.6.1
(default OS X Python)


Before each build I remove old files with:
$ rm -rf build/
$  sudo rm /Library/Python/2.6/site-packages/numpy.egg-link
(and same for SciPy)


Then I build NumPy (r7593) in-place with:
$ LDFLAGS="-lgfortran -arch x86_64" FFLAGS="-arch x86_64"
$ NPY_SEPARATE_COMPILATION=1 python setupscons.py scons -i
$ python setupegg.py develop
(from http://projects.scipy.org/numpy/wiki/BuildWithNumScons , also rebuilt
once used default setup.py, made no difference)


Now the in-place build of SciPy (r6053) with:
$ LDFLAGS="-lgfortran -arch x86_64" FFLAGS="-arch x86_64"
$ NPY_SEPARATE_COMPILATION=1 python setupscons.py scons -i
fails with message: http://pastebin.com/m62fe52de


Building with:
$ LDFLAGS="-lgfortran -arch x86_64" FFLAGS="-arch x86_64"
$ python setup.py build_ext -i
$ sudo python setupegg.py develop
seems to work (build output: http://pastebin.com/d31a920fc) but then
segfaults with the message "Python quit unexpectedly while using the
multiarray.so plug-in":
>>> import scipy
>>> import scipy.linalg
Segmentation fault


Tried getting a traceback with gdb, but I think that I need to rebuild
Python itself for that to be useful?:

(gdb) run scipyimport.py
Starting program: /usr/bin/python scipyimport.py
Reading symbols for shared libraries .++..... done

Program received signal SIGTRAP, Trace/breakpoint trap.
0x00007fff5fc01028 in __dyld__dyld_start ()
(gdb) bt
#0  0x00007fff5fc01028 in __dyld__dyld_start ()
#1  0x0000000100000000 in ?? ()
(gdb)
#0  0x00007fff5fc01028 in __dyld__dyld_start ()
#1  0x0000000100000000 in ?? ()


Any pointers would be highly appreciated!

Thanks,
Ralf
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