[SciPy-user] scipy 0.7.0.dev4373 + atlas FAILED (failures=2, errors=12)

Robert Kern robert.kern@gmail....
Fri May 16 17:15:54 CDT 2008


On Fri, May 16, 2008 at 4:58 PM, Xavier Gnata <xavier.gnata@gmail.com> wrote:

> Here it is. Ok it is long but I cannot cut it without removing an
> interesting part :

Well, the parts interesting to me are the ones starting here:

> ======================================================================
> ERROR: Failure: ImportError
> (/usr/lib/python2.5/site-packages/scipy/linalg/clapack.so: undefined
> symbol: clapack_sgesv)
> ----------------------------------------------------------------------

This looks like an ATLAS build problem. Specifically, it looks like
you didn't make a full LAPACK for ATLAS. I'm not current on the build
process for recent ATLASes. I *think* that if you pass the correct
--with-netlib-lapack to ./configure, it will correctly merge a full
LAPACK. But it might not. Instructions for doing this manually are
here:

  http://svn.scipy.org/svn/scipy/trunk/INSTALL.txt

This does not involve recompiling ATLAS.

But you can probably save yourself a lot of trouble by just installing
the atlas3-base (and possibly atlas3-sse or atlas3-sse2 if you have
those capabilities) and their corresponding -dev packages. It's an old
version, but provides a reasonable speedup for the effort expended.

> ======================================================================
> FAIL: test_texture2 (test_segment.TestSegment)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File
> "/usr/lib/python2.5/site-packages/scipy/ndimage/tests/test_segment.py",
> line 152, in test_texture2
>    assert_array_almost_equal(tem0, truth_tem0, decimal=6)
>  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
> 255, in assert_array_almost_equal
>    header='Arrays are not almost equal')
>  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
> 240, in assert_array_compare
>    assert cond, msg
> AssertionError:
> Arrays are not almost equal
>
> (mismatch 66.6666666667%)
>  x: array([  0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
>         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
>         1.91816598e-01,   1.02515288e-01,   9.30087343e-02,...
>  y: array([ 0.        ,  0.        ,  0.        ,  0.        ,  0.        ,
>        0.        ,  0.13306101,  0.08511007,  0.05084148,  0.07550675,
>        0.4334695 ,  0.03715914,  0.00289055,  0.02755581,  0.48142046,
>        0.03137803,  0.00671277,  0.51568902,  0.01795249,  0.49102375,
> 1.        ], dtype=float32)

This might be an actual bug in the (heavily in-development) image
segmentation code.

> ======================================================================
> FAIL: test_pbdv (test_basic.TestCephes)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File
> "/usr/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
> line 368, in test_pbdv
>    assert_equal(cephes.pbdv(1,0),(0.0,0.0))
>  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
> 139, in assert_equal
>    assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg),
> verbose)
>  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
> 145, in assert_equal
>    assert desired == actual, msg
> AssertionError:
> Items are not equal:
> item=1
>
>  ACTUAL: 1.0
>  DESIRED: 0.0

Not sure about this one. Probably a real bug.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
 -- Umberto Eco


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