[SciPy-dev] FC3 successes and OS X issues with current revisions

Tom Loredo loredo at astro.cornell.edu
Mon Jan 9 14:58:38 CST 2006


Just installed the current SVN revisions (numpy 1862, scipy 1544) 
on FC3 and OS X (10.3.9), with FFTW2 on both platforms.

On both platforms, numpy.test(1,1) runs without errors---yippee!

On both platforms, "import scipy" complains about overwriting fft
and ifft.

>>> import scipy
scipy.Overwriting fft=<function fft at 0x1147530> from scipy.fftpack.basic (was <function fft at 0x1041fb0> from numpy.dft.fftpack)
Overwriting ifft=<function ifft at 0x1147570> from scipy.fftpack.basic (was <function inverse_fft at 0x1047030> from numpy.dft.fftpack)

On FC3, scipy.test() showed one failure with stats, in test_gamma.  The
failure message indicated it was attempting a small pvalue
calculation.  I thought it could be a statistical fluke (do enough
significance tests and you expect one to fail); a repeated scipy.test()
has no failures.  Yippee!  Perhaps this slight complexity with
stats tests should be mentioned somewhere in the install docs.
I've seen it once before.

On OS X, scipy.test() gives the "empty cblas, clapack" warnings Chris
mentioned earlier (in comparison, numarray verifies it is using
"external linear algebra support).  It gives 10 failures, copied
below.  The fft failures are notable because of the import complaint.
A simple "by hand" test shows that numpy.fft and numpy.ifft appear to
work fine, but scipy.fft and scipy.ifft have problems (the real part of
ifft(fft(x)) does not equal x; largest differences are order unity).
scipy passed this "by hand" test yesterday on OS X; it also passes
it today on FC3.

I also installed numarray on both platforms from CVS.  On FC3, the
numarray tests stall at "fft" .  Ctl-C gets no response; I had to stop
the job and kill it via "kill".  The tests all ran an passed
last week.  I don't know if there is any interaction with numpy/scipy
in this regard.  In contrast, the tests all *pass* on OS X, even
the fft test.  It's weird that on FC 3, scipy passes but numarray
fails fft tests, while on OS X the reverse is true.  FWIW I
reinstalled FFTW2 yesterday on OS X (*before* I installed
yesterday's scipy svn, which *passed* my "by hand" fft test).

I also installed mpl-0.86 from PyPI on FC3.  Apart from the
fft overwrite complaints, it appears to work fine on a
selection of example files.  Even the specgram example
works, producing a plot looking like it always has.
The boxplot demo fails, but I haven't looked into the problem;
I doubt it is a scipy issue.  The OS X install is still
running (it's an old, slow G3!).


-Tom

~~~~~~~~~~~~~~~~~
OS X scipy.test() output (selected)

..FSkipping check_djbfft (failed to import FFT)
...F..F..FF.FSkipping check_djbfft (failed to import FFT)
...Skipping check_djbfft (failed to import FFT: No module named FFT)

<snip>

======================================================================
FAIL: check_definition (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 86, in check_definition
    assert_array_almost_equal(diff(sin(x),2),direct_diff(sin(x),2))
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 87.5%):
        Array 1: [ -6.3519652e-15  -3.8268343e-01  -7.0710678e-01  -9.2387953e-01
  -1.0000000e+00  -9.2387953e-01  -7.0710678e-01  -3.82...
        Array 2: [ -7.3854931e-15   6.5259351e-15  -2.4942634e-15  -7.5636114e-17
   1.4745663e-15  -1.9133685e-15   2.2804788e-16   8.70...


======================================================================
FAIL: check_random_even (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_hilbert)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 332, in check_random_even
    assert_array_almost_equal(direct_hilbert(direct_ihilbert(f)),f)
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  6.9388939e-18+0.j   0.0000000e+00-0.j   4.9065389e-18-0.j
   0.0000000e+00-0.j   0.0000000e+00-0.j   0.0000000e+00-0....
        Array 2: [-0.3331645 -0.0799056  0.0523087  0.1059192  0.0973615  0.3480509
  0.0293455  0.1978315 -0.2975818  0.1814041  0.47725...


======================================================================
FAIL: check_definition (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_shift)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 390, in check_definition
    assert_array_almost_equal(shift(sin(x),a),direct_shift(sin(x),a))
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 88.8888888889%):
        Array 1: [ 0.0998334  0.4341242  0.7160532  0.9116156  0.9972237  0.9625519
  0.8117822  0.5630995  0.2464987 -0.0998334 -0.43412...
        Array 2: [ 0.0998334  0.0938127  0.0764768  0.0499167  0.0173359 -0.0173359
 -0.0499167 -0.0764768 -0.0938127 -0.0998334 -0.09381...


======================================================================
FAIL: check_random_even (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_tilbert)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 240, in check_random_even
    assert_array_almost_equal(direct_tilbert(direct_itilbert(f,h),h),f)
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [ 0.+0.j  0.-0.j  0.-0.j  0.-0.j  0.-0.j  0.-0.j  0.-0.j  0.-0.j  0.-0.j
  0.-0.j  0.-0.j  0.-0.j  0.-0.j  0.-0.j  0.-0....
        Array 2: [-0.0340787  0.1267954  0.1694414 -0.2523478 -0.5171198  0.0171597
  0.428051  -0.4324979  0.3333228 -0.0747354 -0.18897...


======================================================================
FAIL: check_definition (scipy.fftpack.basic.test_basic.test_fft)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 98, in check_definition
    assert_array_almost_equal(y,y1)
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [ 20.+0.j   0.+0.j  -4.+4.j   0.+0.j  -4.+0.j   0.-0.j  -4.-4.j   0.-0.j]
        Array 2: [ 20.       +3.j         -0.7071068+0.7071068j  -7.       +4.j
  -0.7071068-0.7071068j  -4.       -3.j          0.707106...


======================================================================
FAIL: check_definition (scipy.fftpack.basic.test_basic.test_fftn)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 425, in check_definition
    assert_array_almost_equal(y,direct_dftn(x))
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 22.2222222222%):
        Array 1: [[ 45. +0.j         -4.5+2.5980762j  -4.5-2.5980762j]
 [-13.5+7.7942286j   0. +0.j          0. +0.j       ]
 [-13.5-7.79...
        Array 2: [[ 45. +0.j         -4.5+2.5980762j  -4.5-2.5980762j]
 [-13.5+0.j         -0. +0.j         -0. -0.j       ]
 [-13.5+0.j ...


======================================================================
FAIL: check_definition (scipy.fftpack.basic.test_basic.test_ifft)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 183, in check_definition
    assert_array_almost_equal(y,y1)
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [ 2.5+0.j   0. -0.j  -0.5-0.5j  0. -0.j  -0.5+0.j   0. +0.j  -0.5+0.5j
  0. +0.j ]
        Array 2: [ 2.5      +0.375j      0.0883883+0.0883883j -0.125    -0.5j
  0.0883883-0.0883883j -0.5      -0.375j     -0.0883883-0.0...


======================================================================
FAIL: check_random_real (scipy.fftpack.basic.test_basic.test_ifft)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 217, in check_random_real
    assert_array_almost_equal (ifft(fft(x)),x)
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 98.0392156863%):
        Array 1: [ 0.9217905 +0.0000000e+00j  0.3038689 +8.7076316e-18j
  0.7451523 +1.0449158e-16j  0.3900691 -1.6948749e-17j
  0.501015...
        Array 2: [ 0.9217905  0.3507541  0.5222262  0.2261792  0.886283   0.0956462
  0.3059122  0.2456351  0.9575797  0.4694345  0.32742...


======================================================================
FAIL: check_definition (scipy.fftpack.basic.test_basic.test_ifftn)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 594, in check_definition
    assert_array_almost_equal(y,direct_idftn(x))
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 22.2222222222%):
        Array 1: [[ 5. +0.j        -0.5-0.2886751j -0.5+0.2886751j]
 [-1.5-0.8660254j  0. +0.j         0. +0.j       ]
 [-1.5+0.8660254j ...
        Array 2: [[ 5. +0.j        -0.5-0.2886751j -0.5+0.2886751j]
 [-1.5+0.j        -0. -0.j        -0. +0.j       ]
 [-1.5+0.j        ...


======================================================================
FAIL: check_definition (scipy.fftpack.basic.test_basic.test_irfft)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 341, in check_definition
    assert_array_almost_equal(y,ifft(x1))
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/numpy/testing/utils.py", line 183, in assert_array_almost_equal
    assert cond,\
AssertionError: 
Arrays are not almost equal (mismatch 50.0%):
        Array 1: [ 2.625     -1.6856602 -0.375     -1.1856602  0.625      0.4356602 -0.375
  0.9356602]
        Array 2: [ 2.625+0.j -0.375-0.j -0.375-0.j -0.375-0.j  0.625+0.j -0.375+0.j
 -0.375+0.j -0.375+0.j]


----------------------------------------------------------------------
Ran 1208 tests in 28.166s

FAILED (failures=10)




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