[SciPy-user] scipy install errors

Alastair Basden a.g.basden@durham.ac...
Tue Feb 19 05:49:50 CST 2008


Hi,

Thanks for the various responses.

Have tried installing numpy/scipy with the svn versions as suggested, 
using 
python setup.py config_fc --fcompiler=gnu95 build

This has worked for numpy, but not for scipy:


Found executable /usr/bin/gfortran
customize Gnu95FCompiler using build_clib
building 'arpack' library
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form 
-fno-second-underscore -fPIC -O3 -funroll-loops -march=opteron -mmmx 
-m3dnow -msse2 -msse
Fortran f90 compiler: /usr/bin/gfortran -Wall -fno-second-underscore -fPIC 
-O3 -funroll-loops -march=opteron -mmmx -m3dnow -msse2 -msse
Fortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form 
-fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 
-funroll-loops -march=opteron -mmmx -m3dnow -msse2 -msse
compile options: '-Iscipy/splinalg/eigen/arpack/ARPACK/SRC -c'
gfortran:f77: scipy/splinalg/eigen/arpack/ARPACK/SRC/dnaupe.f
scipy/splinalg/eigen/arpack/ARPACK/SRC/dnaupe.f:0: internal compiler 
error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://www.suse.de/feedback> for instructions.
scipy/splinalg/eigen/arpack/ARPACK/SRC/dnaupe.f:0: internal compiler 
error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://www.suse.de/feedback> for instructions.
error: Command "/usr/bin/gfortran -Wall -ffixed-form 
-fno-second-underscore -fPIC -O3 -funroll-loops -march=opteron -mmmx 
-m3dnow -msse2 -msse -Iscipy/splinalg/eigen/arpack/ARPACK/SRC -c -c 
scipy/splinalg/eigen/arpack/ARPACK/SRC/dnaupe.f -o 
build/temp.linux-x86_64-2.5/scipy/splinalg/eigen/arpack/ARPACK/SRC/dnaupe.o" 
failed with exit status 1



If I try the scipy installation with just setup.py build, it seems to 
work, but then in python:
>>import scipy.special
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File 
"/data/hamilton/dph1agb/lib/python2.5/site-packages/scipy/special/__init__.py", 
line 8, in <module>
    from basic import *
  File 
"/data/hamilton/dph1agb/lib/python2.5/site-packages/scipy/special/basic.py", 
line 8, in <module>
    from _cephes import *
ImportError: 
/data/hamilton/dph1agb/lib/python2.5/site-packages/scipy/special/_cephes.so: 
undefined symbol: _gfortran_filename

So (not surprisingly) it seems to need the gfortran specified...


Note - using the svn numpy and the scipy0.6, the scipy.special.kv function 
is still behaving incorrectly, so it is a problem with scipy, not numpy (I 
had wondered whether it was the ufunc interface or something).

Thanks...

Platform is Suse 10.0 on AMD 64 processors.  lapack/atlas has been 
compiled by me.




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