[SciPy-dev] CVS scipy.test() segfaulting on me on a Fedora2 box

[Charles Harris]

Hi Fernando,

Am I missing something? I don't get scipy.lib when I install from cvs, so I am wondering if something has changed and I need to checkout scipy again?

Anyway, scipy.linalg.lapack.flapack.cheev(a) runs fine here on Fedora Core 3, but I am using the blas libraries that came with the distro. Is Atlas to be preferred to blas?

As to optimization, I usually find -O2 runs faster than -O3 and that -mtune can make a big difference.


-----Original Message-----
From: scipy-dev-bounces at scipy.net on behalf of Fernando Perez
Sent: Tue 12/21/2004 6:26 PM
To: scipy
Subject: [SciPy-dev] CVS scipy.test() segfaulting on me on a Fedora2 box
 
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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