[SciPy-User] Scipy test failure

Bruce Southey bsouthey@gmail....
Wed Apr 7 08:58:28 CDT 2010


On 04/07/2010 08:08 AM, John Reid wrote:
> Hi,
>
> My scipy tests fail although I seem to have built numpy correctly using
> a similar configuration. I'm on OpenSuse with gcc 4.2.3 and I'm using
> the svn versions of numpy and scipy (2.0.0dev8324 and 0.8.0dev6310). I'm
> using UMFpack and GotoBlas. My python was compiled with a pre-release
> version of gcc 4.1.2
>
> python2.5 -c "import numpy; numpy.test()"
>
> gives me 4 known failures.
>
>
> python2.5 -c "import scipy; scipy.test()"
>
> gives me a lot of errors (see below) and then a segmentation fault. I've
> checked to see if I'm using different fortran compilers. As far as I can
> tell I'm just using gfortran.
>
> What can I do to track down the problem?
>
> Thanks in advance,
> John.
>
>
>
> Here's the scipy test output:
> /usr/local/lib/python2.5/site-packages/scipy/linsolve/__init__.py:4:
> DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve
>     warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve',
> DeprecationWarning)
> /usr/local/lib/python2.5/site-packages/scipy/splinalg/__init__.py:3:
> DeprecationWarning: scipy.splinalg has moved to scipy.sparse.linalg
>     warn('scipy.splinalg has moved to scipy.sparse.linalg',
> DeprecationWarning)
> ............................................................................................................................................................................................................................................................................../usr/local/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:512:
> 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/local/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:453:
> 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/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:190:
> FutureWarning: Using oned_as default value ('column') This will change
> to 'row' in future versions
>     oned_as=oned_as)
> ........................./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:435:
> FutureWarning: Using oned_as default value ('column') This will change
> to 'row' in future versions
>     mfw = MatFile5Writer(StringIO())
> ....../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:450:
> FutureWarning: Using oned_as default value ('column') This will change
> to 'row' in future versions
>     wtr = MatFile5Writer(sio)
> ../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:99:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     return MatFile5Reader(byte_stream, **kwargs)
> .............................../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:633:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(stream)
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:637:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(stream, squeeze_me=True)
> ../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:641:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(stream, byte_order=boc.native_code)
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:645:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(stream, byte_order=boc.swapped_code)
> ../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:652:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(stream)
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:654:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(stream, chars_as_strings=False)
> ../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:664:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(file(estring_fname))
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:674:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(stream)
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:679:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(stream)
> ../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio4.py:338:
> DeprecationWarning: Matlab 4 files only support<=2 dimensions; future
> versions of scipy will raise an error when trying to write>2D arrays to
> matlab 4 format files
>     DeprecationWarning,
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:699:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(file(func_eg))
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:703:
> FutureWarning: Using oned_as default value ('column') This will change
> to 'row' in future versions
>     wtr = MatFile5Writer(stream)
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:709:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(file(double_eg), mat_dtype=False)
> ./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:712:
> FutureWarning: Using struct_as_record default value (False) This will
> change to True in future versions
>     rdr = MatFile5Reader(file(double_eg), mat_dtype=True)
> ..............................................................................................................................Warning:
> 1000000 bytes requested, 20 bytes read.
> ./usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:139:
> DeprecationWarning: `write_array` is deprecated!
>
> This function is replaced by numpy.savetxt which allows the same
> functionality
> through a different syntax.
>
>     warnings.warn(depdoc, DeprecationWarning)
> /usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:139:
> DeprecationWarning: `read_array` is deprecated!
>
> The functionality of read_array is in numpy.loadtxt which allows the same
> functionality using different syntax.
>
>     warnings.warn(depdoc, DeprecationWarning)
> ...........................................Exception
> exceptions.AttributeError: "'netcdf_file' object has no attribute
> 'mode'" in<bound method netcdf_file.close of
> <scipy.io.netcdf.netcdf_file object at 0xb33ae4cc>>  ignored
> ............/usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:139:
> DeprecationWarning: `npfile` is deprecated!
>
> You can achieve the same effect as using npfile using numpy.save and
> numpy.load.
>
> You can use memory-mapped arrays and data-types to map out a
> file format for direct manipulation in NumPy.
>
>     warnings.warn(depdoc, DeprecationWarning)
> ...../usr/local/lib/python2.5/warnings.py:41: ComplexWarning: Casting
> complex values to real discards the imaginary part
>     lineno = caller.f_lineno
> ..../usr/local/lib/python2.5/site-packages/scipy/io/wavfile.py:20:
> WavFileWarning: Unfamiliar format bytes
>     warnings.warn("Unfamiliar format bytes", WavFileWarning)
> /usr/local/lib/python2.5/site-packages/scipy/io/wavfile.py:92:
> WavFileWarning: chunk not understood
>     warnings.warn("chunk not understood", WavFileWarning)
> ................................Running unit tests for scipy
> NumPy version 2.0.0.dev8324
> NumPy is installed in /usr/local/lib/python2.5/site-packages/numpy
> SciPy version 0.8.0.dev6310
> SciPy is installed in /usr/local/lib/python2.5/site-packages/scipy
> Python version 2.5.2 (r252:60911, May  9 2008, 15:14:37) [GCC 4.1.2
> 20070115 (prerelease) (SUSE Linux)]
> nose version 0.11.3
> [ 91  61  11  79 119] [ 91  61  11  79 119]
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>    [ 63 110]
>    [ 20  75]
>    [ 50  37]] [[ 38 124]
>    [ 26   7]
>    [ 63 110]
>    [ 20  75]
>    [ 50  37]]
> [[
> ......................E.....FF................................................................................................................................SSSSSS......SSSSSS...FFFSSSS........................................................EE.......F.......Warning:
> invalid value encountered in divide
> .....Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> ............................................/usr/local/lib/python2.5/site-packages/scipy/linalg/decomp.py:1180:
> DeprecationWarning: qr econ argument will be removed after scipy 0.7.
> The economy transform will then be available through the mode='economic'
> argument.
>     "the mode='economic' argument.", DeprecationWarning)
> ........................
>
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>    
First run tests in verbose mode that will at least identify the test. I 
would guess that it is the eigenvalue tests especially given the usage 
of GotoBlas.


$ python2.5 -c "import scipy; scipy.test(verbose=10)"

 From one of Robert's instructions:

$ gdb python2.5
...
(gdb) run
Starting program ...
... # Possibly another (gdb) prompt:
(gdb) continue  #<- Type this.
Python 2.6.2 ...


>>> >>>  import numpy  #<- Type this and do whatever else is necessary to reproduce the crash.
>>>        
... (gdb) bt # <- Type this. .... # <- Copy-paste these results here.

Bruce


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