Still SciPy installation problems on SUSE linux
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. 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.
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@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
Nils Wagner wrote:
Sebastian Busch wrote:
... 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). ... Please deinstall the rpm's provided by SUSE ! They are incomplete.
Thanks. I did so and installed the precompiled ATLAS 3.6.0 library, then completed it with LAPACK. I also installed IPython & f2py. Now, things work fine. Before, I tried to work the ATLAS developer version, perhaps this was not a good idea. It still gives " Overwriting info=<function info at 0x41c716bc> from scipy.misc (was <function info at 0x40885534> from numpy.lib.utils) " but, according to David, this is not a problem. Thanks again, Sebastian.
participants (2)
-
Nils Wagner -
Sebastian Busch