[Numpy-discussion] scipy 0.7.1rc2 released

Matthieu Brucher matthieu.brucher@gmail....
Mon Jun 8 09:32:09 CDT 2009


David,

I've checked out the trunk, and the segmentation fault isn't there
anymore (the trunk is labeled 0.8.0 though)

Here is the log from the remaining errors with the MKL:

======================================================================
ERROR: Failure: ImportError
(/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/linalg/atlas_version.so:
undefined symbol: ATL_buildinfo)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/linalg/tests/test_atlas_version.py",
line 8, in <module>
    import scipy.linalg.atlas_version
ImportError: /data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/linalg/atlas_version.so:
undefined symbol: ATL_buildinfo

======================================================================
ERROR: test_io.test_imread
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/nose/case.py",
line 182, in runTest
    self.test(*self.arg)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/ndimage/tests/test_io.py",
line 8, in test_imread
    img = ndi.imread(lp)
AttributeError: 'module' object has no attribute 'imread'

======================================================================
ERROR: test_outer_v (test_lgmres.TestLGMRES)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/tests/test_lgmres.py",
line 52, in test_outer_v
    x0, count_0 = do_solve(outer_k=6, outer_v=outer_v)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/tests/test_lgmres.py",
line 29, in do_solve
    x0, flag = lgmres(A, b, x0=zeros(A.shape[0]), inner_m=6, tol=1e-14, **kw)
TypeError: 'module' object is not callable

======================================================================
ERROR: test_preconditioner (test_lgmres.TestLGMRES)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/tests/test_lgmres.py",
line 41, in test_preconditioner
    x0, count_0 = do_solve()
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/tests/test_lgmres.py",
line 29, in do_solve
    x0, flag = lgmres(A, b, x0=zeros(A.shape[0]), inner_m=6, tol=1e-14, **kw)
TypeError: 'module' object is not callable

======================================================================
ERROR: test_iv_cephes_vs_amos (test_basic.TestBessel)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 1691, in test_iv_cephes_vs_amos
    self.check_cephes_vs_amos(iv, iv, rtol=1e-12, atol=1e-305)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 1672, in check_cephes_vs_amos
    assert_tol_equal(c1, c2, err_msg=(v, z), rtol=rtol, atol=atol)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 38, in assert_tol_equal
    verbose=verbose, header=header)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 377, in assert_array_compare
    val = comparison(x[~xnanid], y[~ynanid])
IndexError: 0-d arrays can't be indexed

======================================================================
FAIL: test_lorentz (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py",
line 292, in test_lorentz
    3.7798193600109009e+00]),
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 537, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 395, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
 x: array([  1.00000000e+03,   1.00000000e-01,   3.80000000e+00])
 y: array([  1.43067808e+03,   1.33905090e-01,   3.77981936e+00])

======================================================================
FAIL: test_multi (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py",
line 188, in test_multi
    0.5101147161764654,  0.5173902330489161]),
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 537, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 395, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
 x: array([ 4. ,  2. ,  7. ,  0.4,  0.5])
 y: array([ 4.37998803,  2.43330576,  8.00288459,  0.51011472,  0.51739023])

======================================================================
FAIL: test_pearson (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py",
line 235, in test_pearson
    np.array([ 5.4767400299231674, -0.4796082367610305]),
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 537, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 395, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
 x: array([ 1.,  1.])
 y: array([ 5.47674003, -0.47960824])

======================================================================
FAIL: test_jv_cephes_vs_amos (test_basic.TestBessel)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 1678, in test_jv_cephes_vs_amos
    self.check_cephes_vs_amos(jv, jn, rtol=1e-10, atol=1e-305)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 1672, in check_cephes_vs_amos
    assert_tol_equal(c1, c2, err_msg=(v, z), rtol=rtol, atol=atol)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 38, in assert_tol_equal
    verbose=verbose, header=header)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 395, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=1e-10, atol=1e-305
(-100.3, -1300)
(mismatch 100.0%)
 x: array(0.0)
 y: array((-0.012756553055739306+0.017557888993457362j))

======================================================================
FAIL: Real-valued Bessel I overflow
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 1787, in test_ticket_503
    assert_tol_equal(iv(1, 700), 1.528500390233901e302)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 38, in assert_tol_equal
    verbose=verbose, header=header)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 395, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=1e-07, atol=0

(mismatch 100.0%)
 x: array(1.5306870843952584e+302)
 y: array(1.528500390233901e+302)

======================================================================
FAIL: Real-valued Bessel domains
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 1770, in test_ticket_854
    assert isnan(jv(0.5, -1))
AssertionError

======================================================================
FAIL: test_yv_cephes_vs_amos_only_small_orders (test_basic.TestBessel)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 1688, in test_yv_cephes_vs_amos_only_small_orders
    self.check_cephes_vs_amos(yv, yn, rtol=1e-11, atol=1e-305, skip=skipper)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 1672, in check_cephes_vs_amos
    assert_tol_equal(c1, c2, err_msg=(v, z), rtol=rtol, atol=atol)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 38, in assert_tol_equal
    verbose=verbose, header=header)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/numpy/testing/utils.py",
line 395, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=1e-11, atol=1e-305
(-20.0, -1300)
(mismatch 100.0%)
 x: array(0.0)
 y: array((-0.021008635623302012+0.013914406061324559j))

======================================================================
FAIL: test_basic.TestStruve.test_some_values
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/nose/case.py",
line 182, in runTest
    self.test(*self.arg)
  File "/data/pau112/INNO/local/x86_64/lib/python2.5/site-packages/scipy/special/tests/test_basic.py",
line 2295, in test_some_values
    assert isnan(struve(-7.1, -1))
AssertionError

----------------------------------------------------------------------
Ran 3574 tests in 44.545s

FAILED (KNOWNFAIL=6, SKIP=31, errors=5, failures=8)

Matthieu

2009/6/8 Matthieu Brucher <matthieu.brucher@gmail.com>:
> OK, I'm stuck with #946 with the MKL as well (finally managed to
> compile and use it with only the static library safe for libguide).
>
> I'm trying to download the trunk at the moment to check if the
> segmentation fault is still there.
>
> Matthieu
>
> 2009/6/8 Matthieu Brucher <matthieu.brucher@gmail.com>:
>> Good luck with fixing this then :|
>>
>> I've tried to build scipy with the MKL and ATLAS, and I have in both
>> cases a segmentation fault. With the MKL, it is the same as in a
>> previous mail, and for ATLAS it is there:
>> Regression test for #946. ... Segmentation fault
>>
>> A bad ATLAS compilation?
>>
>> Matthieu
>>
>>>> It could be simply enhanced by refactoring only mconf.h with proper
>>>> compiler flags, and fix yn.c to remove the NAN detection (as it should
>>>> be in the mconf.h).
>>>
>>> NAN and co definition should be dealt with the portable definitions we
>>> have now in numpy - I just have to find a way to reuse the
>>> corresponding code outside numpy (distutils currently does not handle
>>> proper installation of libraries built through build_clib), it is on
>>> my TODO list for scipy 0.8.
>>>
>>> Unfortunately, this is only the tip of the iceberg. A lot of code in
>>> cephes uses #ifdef on platform specificities, and let's not forget it
>>> is pre-ANSI C code (K&R declarations), with a lot of hidden bugs.\
>>>
>>> cheers,
>>>
>>> David
>>> _______________________________________________
>>> Numpy-discussion mailing list
>>> Numpy-discussion@scipy.org
>>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>>
>>
>>
>>
>> --
>> Information System Engineer, Ph.D.
>> Website: http://matthieu-brucher.developpez.com/
>> Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92
>> LinkedIn: http://www.linkedin.com/in/matthieubrucher
>>
>
>
>
> --
> Information System Engineer, Ph.D.
> Website: http://matthieu-brucher.developpez.com/
> Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92
> LinkedIn: http://www.linkedin.com/in/matthieubrucher
>



-- 
Information System Engineer, Ph.D.
Website: http://matthieu-brucher.developpez.com/
Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92
LinkedIn: http://www.linkedin.com/in/matthieubrucher


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