[SciPy-dev] CVS scipy.test() segfaulting on me on a Fedora2 box
Fernando Perez
Fernando.Perez at colorado.edu
Tue Dec 21 19:26:21 CST 2004
Hi all,
I just updated to current CVS of f2py/scipy and Numeric 23.6, to try to root
out some problems I was encountering with scipy.test(). Now I'm having a
different problem, scipy is segfaulting on me :)
I've narrowed it down to this:
planck[pylab]> python -c 'import scipy;scipy.lib.lapack.test(verbosity=2)'
!! No test file 'test_flapack.py' found for <module
'scipy.lib.lapack.flapack' from '...es/scipy/lib/lapack/flapack.so'>
!! No test file 'test_clapack.py' found for <module
'scipy.lib.lapack.clapack' from '...es/scipy/lib/lapack/clapack.so'>
Found 78 tests for scipy.lib.lapack
!! No test file 'test_calc_lwork.py' found for <module
'scipy.lib.lapack.calc_lwork' from '...scipy/lib/lapack/calc_lwork.so'>
Found 0 tests for __main__
check_gebal (scipy.lib.lapack.test_lapack.test_flapack_complex) ... ok
check_heev (scipy.lib.lapack.test_lapack.test_flapack_complex)Segmentation fault
If I go manually into test_lapack.py and comment out around line 93:
#class test_flapack_complex(_test_lapack):
# lapack = PrefixWrapper(flapack,'c')
# decimal = 5
The whole suite runs fine:
planck[pylab]> python -c 'import scipy;scipy.test(level=10,verbosity=2)'
[...]
check_basic (scipy.signal.signaltools.test_signaltools.test_wiener) ... ok
----------------------------------------------------------------------
Ran 1166 tests in 83.200s
OK
By digging a bit deeper into the testing code, I was able to track the
segfault to this (a defined here is copied from the test code, the matrix so
defined is correctly hermitian as required by cheev, so this shouldn't be a
problem):
In [1]: a = [[1,2,3],[2,2,3],[3,3,6]]
In [2]: import scipy
In [3]: scipy.lib.lapack.flapack.cheev(a)
Segmentation fault
The coredump is not terribly informative (unfortunately I don't have a debug
build of python around to produce more details with):
#0 0x55cd67c2 in ATL_cdotc_xp0yp0aXbX ()
from /usr/lib/python2.3/site-packages/scipy/lib/lapack/flapack.so
#1 0xfee241b8 in ?? ()
#2 0x09bfb880 in ?? ()
#3 0xfee241f8 in ?? ()
#4 0x55cc4228 in cdotc_ ()
from /usr/lib/python2.3/site-packages/scipy/lib/lapack/flapack.so
#5 0x4083e1dc in ?? ()
#6 0x560f1358 in ?? () from
/usr/lib/python2.3/site-packages/scipy/lib/lapack/flapack.so
#7 0x3ed413ce in ?? ()
#8 0x560f1358 in ?? () from
/usr/lib/python2.3/site-packages/scipy/lib/lapack/flapack.so
#9 0x3ed413ce in ?? ()
#10 0xfee24100 in ?? ()
#11 0x00000000 in ?? ()
Other calls to complex routines also appear to segfault, though I didn't test
too many more. I wonder if anyone knows what may be going on here. This
machine has in the past run successfully all scipy tests, and I did not change
my ATLAS installation.
For reference, here are all my version numbers (I just pulled scipy and f2py
from CVS minutes ago, and grabbed Numpy from Sourceforge):
In [9]: print sys.version
2.3.3 (#1, May 7 2004, 10:31:40)
[GCC 3.3.3 20040412 (Red Hat Linux 3.3.3-7)]
In [10]: Numeric.__version__
Out[10]: '23.6'
In [11]: f2py2e.__version__.version
Out[11]: '2.44.240_1906'
In [12]: scipy.__version__
Out[12]: '0.3.2_300.4521'
I installed scipy with a straight 'setup.py install', without touching any of
the config files (as I've done successfully in the past).
Thanks for any help. I'll gladly provide more info if needed,
f
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