[SciPy-user] Probs with scipy.test() and seg faults
J Analytis
james.analytis at physics.ox.ac.uk
Fri Jun 6 09:03:06 EDT 2003
Hey,
I've copied the two relevant sections from the scipy.test() output below. The
first is to do with finding clapack, but has corrected the problem by using
flapack.
The errors are related to incomplete BLAS sources. INSTALL.txt says I can cure
the prob by using ATLAS or the official release of BLAS libraries. But I'm
using atlas 3.5.2 so I should be ok.
How do i find out if scipy is finding the ATLAS libraries correctly (assuming
that i've installed atlas properly!)? Is ATLAS incomplete? (liblapack.a is
about 5MB, and I wasn't able to find it using the command
python scipy_core/scipy_distutils/system.py
as suggested in the release notes.)
Also do I need to remove the existing scipy if I need to rebuild/reinstall it?
Thanks,
J
###################
****************************************************************
WARNING: Importing clapack failed with the following exception:
-----------
exceptions.ImportError: cannot import name clapack
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by scipy/system_info.py,
then scipy skips building clapack and uses flapack instead.
****************************************************************
No test suite found for scipy.linalg.linalg_version
creating test suite for: scipy.linalg.matfuncs
!! FAILURE building test for scipy.linalg.matfuncs
<string>:1: ImportError: No module named test_matfuncs (in ?)
###################
======================================================================
ERROR: check_random (test_decomp.test_qr)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.2/site-packages/scipy/linalg/tests/test_decomp.py",
line 295, in check_random
q,r = qr(a)
File "/usr/lib/python2.2/site-packages/scipy/linalg/decomp.py", line 359, in
qr
gemm, = get_blas_funcs(('gemm',),(qr,))
File "/usr/lib/python2.2/site-packages/scipy/linalg/blas.py", line 43, in
get_blas_funcs
if ordering and fblas.has_column_major_storage(arrays[ordering[0][1]]):
File "/usr/lib/python2.2/site-packages/scipy_distutils/misc_util.py", line
44, in __getattr__
raise self._info[0],self._info[1]
ImportError: /usr/lib/python2.2/site-packages/scipy/linalg/fblas.so: undefined
symbol: srotmg_
======================================================================
ERROR: check_random_complex (test_decomp.test_qr)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.2/site-packages/scipy/linalg/tests/test_decomp.py",
line 302, in check_random_complex
q,r = qr(a)
File "/usr/lib/python2.2/site-packages/scipy/linalg/decomp.py", line 359, in
qr
gemm, = get_blas_funcs(('gemm',),(qr,))
File "/usr/lib/python2.2/site-packages/scipy/linalg/blas.py", line 43, in
get_blas_funcs
if ordering and fblas.has_column_major_storage(arrays[ordering[0][1]]):
File "/usr/lib/python2.2/site-packages/scipy_distutils/misc_util.py", line
44, in __getattr__
raise self._info[0],self._info[1]
ImportError: /usr/lib/python2.2/site-packages/scipy/linalg/fblas.so: undefined
symbol: srotmg_
======================================================================
ERROR: check_simple (test_decomp.test_qr)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.2/site-packages/scipy/linalg/tests/test_decomp.py",
line 283, in check_simple
q,r = qr(a)
File "/usr/lib/python2.2/site-packages/scipy/linalg/decomp.py", line 359, in
qr
gemm, = get_blas_funcs(('gemm',),(qr,))
File "/usr/lib/python2.2/site-packages/scipy/linalg/blas.py", line 43, in
get_blas_funcs
if ordering and fblas.has_column_major_storage(arrays[ordering[0][1]]):
File "/usr/lib/python2.2/site-packages/scipy_distutils/misc_util.py", line
44, in __getattr__
raise self._info[0],self._info[1]
ImportError: /usr/lib/python2.2/site-packages/scipy/linalg/fblas.so: undefined
symbol: srotmg_
======================================================================
ERROR: check_simple_complex (test_decomp.test_qr)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.2/site-packages/scipy/linalg/tests/test_decomp.py",
line 288, in check_simple_complex
q,r = qr(a)
File "/usr/lib/python2.2/site-packages/scipy/linalg/decomp.py", line 359, in
qr
gemm, = get_blas_funcs(('gemm',),(qr,))
File "/usr/lib/python2.2/site-packages/scipy/linalg/blas.py", line 43, in
get_blas_funcs
if ordering and fblas.has_column_major_storage(arrays[ordering[0][1]]):
File "/usr/lib/python2.2/site-packages/scipy_distutils/misc_util.py", line
44, in __getattr__
raise self._info[0],self._info[1]
ImportError: /usr/lib/python2.2/site-packages/scipy/linalg/fblas.so: undefined
symbol: srotmg_
======================================================================
FAIL: check_basic (test_morestats.test_shapiro)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.2/site-packages/scipy/stats/tests/test_morestats.py",
line 37, in check_basic
assert_almost_equal(pw,0.52459925413131714,6)
File "/usr/lib/python2.2/site-packages/scipy_test/testing.py", line 349, in
assert_almost_equal
assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
DESIRED: 0.52459925413131714
ACTUAL: 0.5246044397354126
----------------------------------------------------------------------
Ran 640 tests in 8.418s
FAILED (failures=1, errors=4)
<unittest.TextTestRunner instance at 0x841022c>
>>>
On Friday 06 June 2003 13:33, Pearu Peterson wrote:
> On Fri, 6 Jun 2003, James Analytis wrote:
> > Hey,
> > I built scipy from the sources as you suggested. On scipy.test() i got
> > these as the last few lines:
> > ----------------------------------------------------------------------
> > Ran 640 tests in 10.232s
> >
> > FAILED (failures=1, errors=4)
> > <unittest.TextTestRunner instance at 0x827c944>
> >
> > ----------------------------------------------------------------------
> > No seg faults! So apart from that one failure things seems to be ok
> > (right?)
>
> Not too bad. Though I wonder what are these errors? Certain scipy tests
> (e.g. stats ones) are known to fail occasionally and that is ok, but in
> principle there should not be any `errors` in scipy tests.
>
> Pearu
>
>
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