Lots of warnings, errors and a segmentation fault in scipy.test()

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Lots of warnings, errors and a segmentation fault in scipy.test()

Gerrit Holl-4
Hi,

I recently installed scipy from source ("bleeding edge"). When running
the test, I get a lot of warnings and errors, and finally fail with a
segmentation fault:

Paste from http://bpaste.net/show/11710/ repeated below. I didn't get
any relevant warnings during compilation. Should I be worried? What
can I run in addition to track this down?

$ python -c "import scipy; scipy.test()"
Running unit tests for scipy
NumPy version 2.0.0.dev-12d0200
NumPy is installed in
/storage4/home/gerrit/.local/lib/python2.6/site-packages/numpy
SciPy version 0.9.0.dev6975
SciPy is installed in
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy
Python version 2.6.6 (r266:84292, Sep 15 2010, 16:22:56) [GCC 4.4.5]
nose version 0.11.1
...................................................................................................................................................../storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/cluster/vq.py:582:
UserWarning: One of the clusters is empty. Re-run kmean with a
different initialization.
  warnings.warn("One of the clusters is empty. "
............................/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py:420:
ComplexWarning: Casting complex values to real discards the imaginary
part
  y1 = fftn(x.astype(np.float32))
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py:421:
ComplexWarning: Casting complex values to real discards the imaginary
part
  y2 = fftn(x.astype(np.float64)).astype(np.complex64)
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py:429:
ComplexWarning: Casting complex values to real discards the imaginary
part
  y1 = fftn(x.astype(np.float32))
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py:430:
ComplexWarning: Casting complex values to real discards the imaginary
part
  y2 = fftn(x.astype(np.float64)).astype(np.complex64)
......................K.............................................................................../storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:673:
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)
....../storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:604:
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
.........................................................../storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/io/matlab/mio.py:232:
FutureWarning: Using oned_as default value ('column') This will change
to 'row' in future versions
  oned_as=oned_as)
............................................................................................................................................................................................................................................................................./storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/io/wavfile.py:31:
WavFileWarning: Unfamiliar format bytes
  warnings.warn("Unfamiliar format bytes", WavFileWarning)
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/io/wavfile.py:121:
WavFileWarning: chunk not understood
  warnings.warn("chunk not understood", WavFileWarning)
.................................................................................ESSSSSS......SSSSSS......SSSS.......................................................Segmentation
fault

regards,
Gerrit.

--
Gerrit Holl
PhD student at Department of Space Science, LuleƄ University of
Technology, Kiruna, Sweden
http://www.sat.ltu.se/members/gerrit/
_______________________________________________
SciPy-User mailing list
[hidden email]
http://mail.scipy.org/mailman/listinfo/scipy-user
Reply | Threaded
Open this post in threaded view
|

Re: Lots of warnings, errors and a segmentation fault in scipy.test()

Pauli Virtanen-3
Mon, 29 Nov 2010 11:11:20 +0100, Gerrit Holl wrote:
[clip]
> Paste from http://bpaste.net/show/11710/ repeated below. I didn't get
> any relevant warnings during compilation. Should I be worried? What can
> I run in addition to track this down?
>
> $ python -c "import scipy; scipy.test()"

Please run "scipy.test(verbose=2)" so we can see where the crash occurs.

--
Pauli Virtanen

_______________________________________________
SciPy-User mailing list
[hidden email]
http://mail.scipy.org/mailman/listinfo/scipy-user
Reply | Threaded
Open this post in threaded view
|

Re: Lots of warnings, errors and a segmentation fault in scipy.test()

Gerrit Holl-2
Hi,

On 29 November 2010 12:39, Pauli Virtanen <[hidden email]> wrote:
> Mon, 29 Nov 2010 11:11:20 +0100, Gerrit Holl wrote:
> [clip]
>> Paste from http://bpaste.net/show/11710/ repeated below. I didn't get
>> any relevant warnings during compilation. Should I be worried? What can
>> I run in addition to track this down?
>>
>> $ python -c "import scipy; scipy.test()"
>
> Please run "scipy.test(verbose=2)" so we can see where the crash occurs.

It occurs in test_complex_dotc, test_blas.TestFBLAS1Simple:

test_complex_dotc (test_blas.TestFBLAS1Simple) ... Segmentation fault

Full log at: http://www.sat.ltu.se/~gerrit/crashlog

Something incompatible between scipy and BLAS?

Gerrit.

--
Exploring space at http://gerrit-explores.blogspot.com/
Personal homepage at http://www.topjaklont.org/
Asperger Syndroom: http://www.topjaklont.org/nl/asperger.html
_______________________________________________
SciPy-User mailing list
[hidden email]
http://mail.scipy.org/mailman/listinfo/scipy-user
Reply | Threaded
Open this post in threaded view
|

Re: Lots of warnings, errors and a segmentation fault in scipy.test()

Pauli Virtanen-3
Mon, 29 Nov 2010 14:57:53 +0100, Gerrit Holl wrote:
[clip]
> test_complex_dotc (test_blas.TestFBLAS1Simple) ... Segmentation fault
>
> Full log at: http://www.sat.ltu.se/~gerrit/crashlog
>
> Something incompatible between scipy and BLAS?

Possibilities:

- Your BLAS installation is broken or its C/ZDOTC routines are buggy.

- You have compiled the BLAS library and Scipy with different Fortran
  compilers whose ABI is not compatible (I'm not sure how strictly
  Fortran standards specify intercompatibility).

In both cases, you would get a similar crash with a pure-Fortran program
invoking ZDOTC or CDOTC.

--
Pauli Virtanen

_______________________________________________
SciPy-User mailing list
[hidden email]
http://mail.scipy.org/mailman/listinfo/scipy-user