[SciPy-Dev] SciPy 0.9.0.dev6651 test failures (segfault)

Bruce Southey bsouthey@gmail....
Fri Aug 27 13:14:32 CDT 2010


  On 08/27/2010 10:58 AM, Gökhan Sever wrote:
> Hello,
>
> Again on Fedora 13 Virtualbox setup:
> Linux a 2.6.33.6-147.2.4.fc13.i686 #1 SMP Fri Jul 23 17:27:40 UTC 2010 
> i686 i686 i386 GNU/Linux
>
>
> Python 2.6.4 (r264:75706, Jun  4 2010, 18:20:16)
> [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scipy
> >>> scipy.test('full')
> Running unit tests for scipy
> NumPy version 2.0.0.dev8671
> NumPy is installed in /usr/lib/python2.6/site-packages/numpy
> SciPy version 0.9.0.dev6651
> SciPy is installed in /usr/lib/python2.6/site-packages/scipy
> Python version 2.6.4 (r264:75706, Jun  4 2010, 18:20:16) [GCC 4.4.4 
> 20100503 (Red Hat 4.4.4-2)]
> nose version 0.11.3
> ................................................................................................................................................................................................................................................................................/usr/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:670: 
> 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)
> ....../usr/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:601: 
> UserWarning:
> The required storage space exceeds the available storage space: nxest
> or nyest too small, or s too small.
> The weighted least-squares spline corresponds to the current set of
> knots.
>   warnings.warn(message)
> .............................................K..K............................................................Warning: 
> divide by zero encountered in log
> Warning: invalid value encountered in multiply
> Warning: divide by zero encountered in log
> Warning: invalid value encountered in multiply
> Warning: divide by zero encountered in log
> Warning: invalid value encountered in multiply
> .Warning: divide by zero encountered in log
> Warning: invalid value encountered in multiply
> Warning: divide by zero encountered in log
> Warning: invalid value encountered in multiply
> .Warning: divide by zero encountered in log
> Warning: invalid value encountered in multiply
> Warning: divide by zero encountered in log
> Warning: invalid value encountered in multiply
> .........Warning: divide by zero encountered in log
> Warning: invalid value encountered in multiply
> Warning: divide by zero encountered in log
> Warning: invalid value encountered in multiply
> ...................................................................................................................................................................................................................................................................................................................................................../usr/lib/python2.6/site-packages/scipy/io/recaster.py:328: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   test_arr = arr.astype(T)
> ../usr/lib/python2.6/site-packages/scipy/io/recaster.py:375: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   return arr.astype(idt)
> ../usr/lib/python2.6/site-packages/scipy/io/wavfile.py:30: 
> WavFileWarning: Unfamiliar format bytes
>   warnings.warn("Unfamiliar format bytes", WavFileWarning)
> /usr/lib/python2.6/site-packages/scipy/io/wavfile.py:120: 
> WavFileWarning: chunk not understood
>   warnings.warn("chunk not understood", WavFileWarning)
> .......................................................................................F............................................/usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:86: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.blas_func(x,y,n=3,incy=5)
> ....../usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:196: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.blas_func(x,y,n=3,incy=5)
> .................../usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:279: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.blas_func(x,y,n=3,incy=5)
> ..................................................................SSSSSS......SSSSSS......SSSS.....................................................FF........F..Warning: 
> invalid value encountered in divide
> .....Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> .......................................................................................................................................................................................................K............................................./usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:89: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.blas_func(x,y,n=3,incy=5)
> ....../usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:199: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.blas_func(x,y,n=3,incy=5)
> .................../usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:282: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.blas_func(x,y,n=3,incy=5)
> ....................................................................../usr/lib/python2.6/site-packages/scipy/linalg/matfuncs.py:94: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   return dot(dot(vr,diag(exp(s))),vri).astype(t)
> .................................................................................................................................................................................................................................................../usr/lib/python2.6/site-packages/scipy/ndimage/tests/test_ndimage.py:56: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   a = a.astype(numpy.float64)
> /usr/lib/python2.6/site-packages/scipy/ndimage/tests/test_ndimage.py:58: 
> ComplexWarning: Casting complex values to real discards the imaginary part
>   b = b.astype(numpy.float64)
> ......................................................................................................Warning: 
> invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> .....................................................................Warning: 
> invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> ........................Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> ..............................................9 7
> ....F...............Warning: invalid value encountered in divide
> ................./usr/lib/python2.6/site-packages/scipy/signal/filter_design.py:247: 
> BadCoefficients: Badly conditioned filter coefficients (numerator): 
> the results may be meaningless
>   "results may be meaningless", BadCoefficients)
> ..............................................................................................................................................................................................................................................................................................SSSSSSSSSSS..........Segmentation 
> fault (core dumped)
>
>
> -- 
> Gökhan
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev@scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
Hi,
It would be useful to know which test is involved regardless of the 
issue. Can you please run the tests with the verbose option such as: 
'scipy.test(verbose=10)'?

This may have something to do with your numpy problem so please fix that 
up once you have identified the test (failure in linalg would confirm 
that).

As a reference, my Fedora 13 x64 bit system uses gfortran - 'gcc version 
4.4.4 20100630 (Red Hat 4.4.4-10) (GCC)'.

Did you completely wipe the previous numpy installation especially the 
installed numpy files in $PATH2PYTHON/site-packages/ and remove any 
prior build directories?
If so, then you need to create suitable site.cfg file to ensure the 
correct compiler is being used because something has changed in either 
your distro or numpy install.

Bruce




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