[SciPy-user] back with a problem in scipy installation...

Eric Emsellem emsellem@obs.univ-lyon1...
Wed Feb 7 09:20:29 CST 2007


Hi again (sorry for the second post: the first one was scrubbed),


I now went through a full install of atlas, lapack, blas, numpy, scipy
again.
I still have some failure in scipy (none in numpy except for the umfpack
which I haven't installed) you can find below.
I also include the explicit site.cfg that I had to twiggle in order for
scipy to find atlas (no Environment variable or other way did the work
for some reason): it looks weird if I compare it to "advised" site.cfg
but this is the only option that recognised atlas properly.

any help is welcome as always.
thanks again
Eric
=======================
below is a summary of:

1/ the failure in scipy
2/ my site.cfg used for building numpy and scipy

***************************************************************************************************
******** Output of scipy.test() = (starting with some failure due to the
lack of umfpack and then..):
....................
Warning: FAILURE importing tests for <module
'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/umfpack.pyc'>
/usr/local/lib/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17:
AttributeError: 'module' object has no attribute 'umfpack' (in ?)
................................
Found 4 tests for scipy.io.recaster
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack'
from '.../linsolve/umfpack/__init__.pyc'>
/usr/local/lib/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17:
AttributeError: 'module' object has no attribute 'umfpack' (in ?)
...................
..zswap:n=4
..zswap:n=3
..................Residual: 1.05006950608e-07
.........................................................................................
======================================================================
FAIL: check_syevr (scipy.lib.tests.test_lapack.test_flapack_float)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/usr/local/lib/python2.4/site-packages/scipy/lib/lapack/tests/esv_tests.py",
line 41, in check_syevr
    assert_array_almost_equal(w,exact_w)
  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
line 230, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
line 215, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 33.3333333333%)
 x: array([-0.66992444,  0.48769444,  9.18222618], dtype=float32)
 y: array([-0.66992434,  0.48769389,  9.18223045])

======================================================================
FAIL: check_syevr_irange (scipy.lib.tests.test_lapack.test_flapack_float)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/usr/local/lib/python2.4/site-packages/scipy/lib/lapack/tests/esv_tests.py",
line 66, in check_syevr_irange
    assert_array_almost_equal(w,exact_w[rslice])
  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
line 230, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
line 215, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 33.3333333333%)
 x: array([-0.66992444,  0.48769444,  9.18222618], dtype=float32)
 y: array([-0.66992434,  0.48769389,  9.18223045])

----------------------------------------------------------------------
Ran 1619 tests in 5.764s

FAILED (failures=2)

***************************************************************************************************
******** My site.cfg used for both numpy and scipy
******** it finds atlas, but that's all. If I uncomment the lines on
lapack_opt and blas_opt, it finds the

[DEFAULT]
library_dirs = /usr/local/lib/atlas
include_dirs = /usr/local/lib/atlas
[atlas]
library_dirs = /usr/local/lib/atlas
atlas_libs = lapack, f77blas, cblas, atlas
# [blas_opt]
# library_dirs = /usr/local/lib/atlas
# blas_libs = fblas, f77blas, cblas
# [lapack_opt]
# library_dirs = /usr/local/lib/atlas
# lapack_libs = lapack
[blas]
library_dirs = /usr/local/lib/atlas
libraries = f77blas, cblas, atlas
#
[lapack]
library_dirs = /usr/local/lib/atlas
libraries = lapack, f77blas, cblas, atlas
[fftw]
libraries = fftw3

-- 
====================================================================
Eric Emsellem                             emsellem@obs.univ-lyon1.fr
                           Centre de Recherche Astrophysique de Lyon
9 av. Charles-Andre                        tel: +33 (0)4 78 86 83 84
69561 Saint-Genis Laval Cedex              fax: +33 (0)4 78 86 83 86
France                    http://www-obs.univ-lyon1.fr/eric.emsellem
====================================================================


More information about the SciPy-user mailing list