[SciPy-user] Still SciPy installation problems on SUSE linux

Nils Wagner nwagner at iam.uni-stuttgart.de
Tue Aug 15 10:20:23 CDT 2006


Sebastian Busch wrote:
> Dear list,
>
> I posted about this already some days ago -- thank you David and Eric
> for your advice.
>
> I tried to install SciPy the way Eric proposed. I didn't install pyfits,
> IPython, and F2Py. After fighting a long time with LAPACK and atlas, I
> decided to try lapack & blas provided by SUSE (which doesn't seem to
> change much, as far as I can see).
>
> Before installing again, I simply deleted the corresponding directories,
> e.g. /usr/lib/python2.4/site-packages/numpy/
>
> numpy.test works fine (matplotlib is also working), however scipy.test
> gives an error about integers in arrays -- I attached the output. It
> comes from
>
> import scipy
> scipy.test()
>
>
> I hope you have again some ideas,
> thanks,
> Sebastian.
>
>   
Please deinstall the rpm's provided by SUSE ! They are incomplete.
It's very easy to compile both BLAS and LAPACK.
See http://www.scipy.org/Installing_SciPy/BuildingGeneral

Compiling ATLAS takes a while but it accelerates your computations
afterwards.
Note that it is important to build a complete library.
http://pong.tamu.edu/tiki/tiki-view_blog_post.php?blogId=6&postId=97

Once you have installed these libraries you can install
numpy/scipy/matplotlib.

Nils

> ------------------------------------------------------------------------
>
> Overwriting info=<function info at 0x40728924> from scipy.misc (was <function info at 0x40702064> from numpy.lib.utils)
> import signal -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import lib.lapack -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import cluster -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import linsolve.umfpack -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> Overwriting fft=<function fft at 0x40c79e9c> from scipy.fftpack.basic (was <module 'numpy.fft' from '/usr/lib/python2.4/site-packages/numpy/fft/__init__.pyc'> from /usr/lib/python2.4/site-packages/numpy/fft/__init__.pyc)
> import linsolve -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import integrate -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import optimize -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import special -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import lib.blas -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import linalg -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import maxentropy -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
> import stats -> failed: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
>   Found 4 tests for scipy.io.array_import
>   Found 397 tests for scipy.ndimage
> Warning: FAILURE importing tests for <module 'scipy.sparse.sparse' from '...ckages/scipy/sparse/sparse.pyc'>
> /usr/lib/python2.4/site-packages/scipy/linsolve/_superlu.py:1: ImportError: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename (in ?)
>   Found 20 tests for scipy.fftpack.pseudo_diffs
> Warning: FAILURE importing tests for <module 'scipy.optimize.optimize' from '...es/scipy/optimize/optimize.pyc'>
> /usr/lib/python2.4/site-packages/scipy/optimize/lbfgsb.py:30: ImportError: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename (in ?)
>   Found 5 tests for scipy.interpolate.fitpack
>   Found 1 tests for scipy.interpolate
>   Found 12 tests for scipy.io.mmio
>   Found 18 tests for scipy.fftpack.basic
> Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/umfpack.pyc'>
> /usr/lib/python2.4/site-packages/scipy/linsolve/_superlu.py:1: ImportError: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename (in ?)
> Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '.../linsolve/umfpack/__init__.pyc'>
> /usr/lib/python2.4/site-packages/scipy/linsolve/_superlu.py:1: ImportError: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename (in ?)
> Warning: FAILURE importing tests for <module 'scipy.optimize.zeros' from '...kages/scipy/optimize/zeros.pyc'>
> /usr/lib/python2.4/site-packages/scipy/optimize/lbfgsb.py:30: ImportError: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename (in ?)
>   Found 16 tests for scipy.io.mio
> Warning: FAILURE importing tests for <module 'scipy.special.basic' from '...ckages/scipy/special/basic.pyc'>
> /usr/lib/python2.4/site-packages/scipy/linalg/lapack.py:17: ImportError: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename (in ?)
> Warning: FAILURE importing tests for <module 'scipy.sparse' from '...ages/scipy/sparse/__init__.pyc'>
> /usr/lib/python2.4/site-packages/scipy/linsolve/_superlu.py:1: ImportError: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename (in ?)
>   Found 4 tests for scipy.fftpack.helper
>   Found 0 tests for __main__
> Warning: 1000000 bytes requested, 20 bytes read.
> ...E................................................................................................................................................................................................................................................................................................................................................................................................................................./usr/lib/python2.4/site-packages/scipy/interpolate/fitpack2.py:410: UserWarning: 
> The coefficients of the spline returned have been computed as the
> minimal norm least-squares solution of a (numerically) rank deficient
> system (deficiency=7). If deficiency is large, the results may be
> inaccurate. Deficiency may strongly depend on the value of eps.
>   warnings.warn(message)
> ........................................................
> ======================================================================
> ERROR: check_integer (scipy.io.tests.test_array_import.test_read_array)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python2.4/site-packages/scipy/io/tests/test_array_import.py", line 55, in check_integer
>     from scipy import stats
>   File "/usr/lib/python2.4/site-packages/scipy/stats/__init__.py", line 7, in ?
>     from stats import *
>   File "/usr/lib/python2.4/site-packages/scipy/stats/stats.py", line 191, in ?
>     import scipy.special as special
>   File "/usr/lib/python2.4/site-packages/scipy/special/__init__.py", line 10, in ?
>     import orthogonal
>   File "/usr/lib/python2.4/site-packages/scipy/special/orthogonal.py", line 66, in ?
>     from scipy.linalg import eig
>   File "/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py", line 8, in ?
>     from basic import *
>   File "/usr/lib/python2.4/site-packages/scipy/linalg/basic.py", line 17, in ?
>     from lapack import get_lapack_funcs
>   File "/usr/lib/python2.4/site-packages/scipy/linalg/lapack.py", line 17, in ?
>     from scipy.linalg import flapack
> ImportError: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename
>
> ----------------------------------------------------------------------
> Ran 477 tests in 8.052s
>
> FAILED (errors=1)
>
> Don't worry about a warning regarding the number of bytes read.
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   


 



More information about the SciPy-user mailing list