[SciPy-Dev] Many errors/failures running scipy.test() using latest numpy and scipy

Thu Jun 30 09:03:31 EDT 2011

On 06/30/2011 01:20 PM, Vincent Schut wrote:
> On 06/21/2011 06:15 PM, Pauli Virtanen wrote:
>> Tue, 21 Jun 2011 10:51:18 -0500, Benjamin Root wrote:
>> [clip]
>>> The first error has to do with the netcdf file (I thought that was fixed
>>> by now?). Then, some of the errors are related to the gmres module (I
>>> see that is already known).  Then, there are many errors for
>>> "test_arpack.test_real_nonsymmetric_modes",
>>> "test_arpack.test_complex_nonsymmetric_modes", and
>>> "test_arpack.test_hermitian_modes". Lastly, there is a single failure
>>> for "test_morestats.TestAnderson".
>>>
>>> I hope this is useful.
>>
>> All of the ARPACK failures are GMRES-related.
>>
>> These appear to be very strongly platform-dependent for some reason.
>> I don't see them, and it is somewhat difficult to believe that the
>> calculation could be this unstable because of rounding error.
>>
>> Can you check if your GMRES works at all, i.e., try a simple 6 x 6
>> complex-valued matrix? The current test cases don't actually cover
>> it properly, and at least Gfortran 4.5.2 does miscompile the GMRES
>> routines in some cases. Not sure about 4.6.0 that you use, but
>> compiler issues remain a possibility (esp. since it is a .0 release).
>>
>> Maybe using a different gfortran version makes these go away?
>>
>> F90=gfortran-4.4 python setup.py build
>>
>> 	Pauli
>
> Hi,
>
> I have these same failures and errors in scipy.test():
> (KNOWNFAIL=12, SKIP=24, errors=49, failures=33)
> Most of these are arpack related.
> I tried with:
> F90=g95 python setup.py build
> instead of the default gfortran, but it makes no difference. I also
> tried with different blas/lapack, also no difference.
>
> downgrading gfortran is not a real option, alas. It's too much fuss to
> downgrade the entire gcc suite on my system (or could I just install a
> different gfortran sitting besides the default one?)
>
> gcc/gfortran is 4.6.1, cpu is AMD Phenom(tm) II X6 1055T
>
> anything I could do to diagnose this further? I'd like to have a working
> scipy again...
>
> Vincent.

OK, to follow up on myself:
found out how to install gfortran-4.4 alongside 4.6.1.
Built scipy with F90=gfortran-4.4, and this resolves most of the errors!

I still have 3 errors an d2 failures left, I'll paste them here for 
reference:

ERROR: test_netcdf.test_read_example_data
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python2.7/site-packages/nose/case.py", line 187, in 
runTest
     self.test(*self.arg)
   File 
"/usr/lib/python2.7/site-packages/scipy/io/tests/test_netcdf.py", line 
124, in test_read_example_data
     f = netcdf_file(fname, 'r')
   File "/usr/lib/python2.7/site-packages/scipy/io/netcdf.py", line 205, 
in __init__
     self._read()
   File "/usr/lib/python2.7/site-packages/scipy/io/netcdf.py", line 492, 
in _read
     self._read_var_array()
   File "/usr/lib/python2.7/site-packages/scipy/io/netcdf.py", line 536, 
in _read_var_array
     typecode, size, dtype_, begin_, vsize) = self._read_var()
   File "/usr/lib/python2.7/site-packages/scipy/io/netcdf.py", line 624, 
in _read_var
     attributes = self._read_att_array()
   File "/usr/lib/python2.7/site-packages/scipy/io/netcdf.py", line 522, 
in _read_att_array
     attributes[name] = self._read_values()
   File "/usr/lib/python2.7/site-packages/scipy/io/netcdf.py", line 649, 
in _read_values
     values = fromstring(values, dtype='>%s%d' % (typecode, size))
TypeError: data type ">d8" not understood

======================================================================
ERROR: gaussian gradient magnitude filter 1
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python2.7/site-packages/nose/case.py", line 187, in 
runTest
     self.test(*self.arg)
   File 
"/usr/lib/python2.7/site-packages/scipy/ndimage/tests/test_ndimage.py", 
line 670, in test_gaussian_gradient_magnitude01
     1.0)
   File "/usr/lib/python2.7/site-packages/scipy/ndimage/filters.py", 
line 479, in gaussian_gradient_magnitude
     cval, extra_arguments = (sigma,))
   File "/usr/lib/python2.7/site-packages/scipy/ndimage/filters.py", 
line 450, in generic_gradient_magnitude
     numpy.sqrt(output, output)
TypeError: ufunc 'sqrt' output (typecode 'd') could not be coerced to 
provided output parameter (typecode 'i') according to the casting rule 
'same_kind'

======================================================================
ERROR: gaussian gradient magnitude filter 2
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python2.7/site-packages/nose/case.py", line 187, in 
runTest
     self.test(*self.arg)
   File 
"/usr/lib/python2.7/site-packages/scipy/ndimage/tests/test_ndimage.py", 
line 685, in test_gaussian_gradient_magnitude02
     output)
   File "/usr/lib/python2.7/site-packages/scipy/ndimage/filters.py", 
line 479, in gaussian_gradient_magnitude
     cval, extra_arguments = (sigma,))
   File "/usr/lib/python2.7/site-packages/scipy/ndimage/filters.py", 
line 450, in generic_gradient_magnitude
     numpy.sqrt(output, output)
TypeError: ufunc 'sqrt' output (typecode 'd') could not be coerced to 
provided output parameter (typecode 'i') according to the casting rule 
'same_kind'

======================================================================
FAIL: test_iterative.test_convergence(<function qmr at 0x38ac8c0>, 
<nonsymposdef>)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python2.7/site-packages/nose/case.py", line 187, in 
runTest
     self.test(*self.arg)
   File 
"/usr/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/tests/test_iterative.py", 
line 152, in check_convergence
     assert_equal(info,0)
   File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 
313, in assert_equal
     raise AssertionError(msg)
AssertionError:
Items are not equal:
  ACTUAL: 100
  DESIRED: 0

======================================================================
FAIL: test_expon (test_morestats.TestAnderson)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/usr/lib/python2.7/site-packages/scipy/stats/tests/test_morestats.py", 
line 72, in test_expon
     assert_array_less(crit[:-1], A)
   File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 
868, in assert_array_less
     header='Arrays are not less-ordered')
   File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 
612, in assert_array_compare
     chk_same_position(x_id, y_id, hasval='inf')
   File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 
587, in chk_same_position
     raise AssertionError(msg)
AssertionError:
Arrays are not less-ordered

x and y inf location mismatch:
  x: array([ 0.911,  1.065,  1.325,  1.587])
  y: array(inf)

----------------------------------------------------------------------
Ran 5570 tests in 61.753s

FAILED (KNOWNFAIL=12, SKIP=24, errors=3, failures=2)