[SciPy-Dev] memory corruption when running scipy 0.8 test suite

Christoph Gohlke cgohlke@uci....
Thu Jul 15 02:43:10 CDT 2010



On 7/14/2010 11:33 AM, Christoph Gohlke wrote:
>


>
> Running unit tests for scipy
> NumPy version 1.4.1
> NumPy is installed in X:\python26\lib\site-packages\numpy
> SciPy version 0.8.0.dev6609
> SciPy is installed in X:\python26\lib\site-packages\scipy
> Python version 2.6.5 (r265:79096, Mar 19 2010, 21:48:26) [MSC v.1500 32
> bit (Intel)]
> nose version 0.11.3
> ................................................................................
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> ..........................................................FFF...................
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> ...............................................................SSSSSSSSSSS.E..F.
> .........K.........F............................................................
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> .............................................................error
> removing c:\u
> sers\gohlke\appdata\local\temp\tmpaqkoypcat_test:
> c:\users\gohlke\appdata\local\
> temp\tmpaqkoypcat_test: The directory is not empty
> ................................................................................
> ..................
> ======================================================================
> ERROR: test_twodiags (test_linsolve.TestLinsolve)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>     File
> "X:\python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py",
> line 39, in test_twodiags
>       assert( norm(b - Asp*x)<  10 * cond_A * eps )
>     File "X:\python26\lib\site-packages\scipy\linalg\misc.py", line 9, in
> norm
>       return np.linalg.norm(np.asarray_chkfinite(a), ord=ord)
>     File "X:\python26\lib\site-packages\numpy\lib\function_base.py", line
> 586, inasarray_chkfinite
>       raise ValueError, "array must not contain infs or NaNs"
> ValueError: array must not contain infs or NaNs
>
> ======================================================================
> FAIL: test_lorentz (test_odr.TestODR)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>     File "X:\python26\lib\site-packages\scipy\odr\tests\test_odr.py",
> line 292, in
>    test_lorentz
>       3.7798193600109009e+00]),
>     File "X:\python26\lib\site-packages\numpy\testing\utils.py", line
> 765, in assert_array_almost_equal
>       header='Arrays are not almost equal')
>     File "X:\python26\lib\site-packages\numpy\testing\utils.py", line
> 609, 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 "X:\python26\lib\site-packages\scipy\odr\tests\test_odr.py",
> line 188, in test_multi
>       0.5101147161764654,  0.5173902330489161]),
>     File "X:\python26\lib\site-packages\numpy\testing\utils.py", line
> 765, in assert_array_almost_equal
>       header='Arrays are not almost equal')
>     File "X:\python26\lib\site-packages\numpy\testing\utils.py", line
> 609, 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 "X:\python26\lib\site-packages\scipy\odr\tests\test_odr.py",
> line 235, in test_pearson
>       np.array([ 5.4767400299231674, -0.4796082367610305]),
>     File "X:\python26\lib\site-packages\numpy\testing\utils.py", line
> 765, in assert_array_almost_equal
>       header='Arrays are not almost equal')
>     File "X:\python26\lib\site-packages\numpy\testing\utils.py", line
> 609, 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_linsolve.TestSplu.test_spilu_smoketest
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>     File "X:\python26\lib\site-packages\nose\case.py", line 186, in runTest
>       self.test(*self.arg)
>     File
> "X:\python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py",
> line 63, in test_spilu_smoketest
>       assert abs(x - r).max()<  1e-2
> AssertionError
>
> ======================================================================
> FAIL: Check that QMR works with left and right preconditioners
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>     File
> "X:\python26\lib\site-packages\scipy\sparse\linalg\isolve\tests\test_iterative.py",
> line 178, in test_leftright_precond
>       assert_equal(info,0)
>     File "X:\python26\lib\site-packages\numpy\testing\utils.py", line
> 309, in assert_equal
>       raise AssertionError(msg)
> AssertionError:
> Items are not equal:
>    ACTUAL: 1
>    DESIRED: 0
>
> ----------------------------------------------------------------------
> Ran 4399 tests in 36.788s
>
> FAILED (KNOWNFAIL=13, SKIP=35, errors=1, failures=5)
>
>
>
> On a clean 64-bit installation I also get the ndimage/dsyevr memory
> corruption (?) failure:
>
> ======================================================================
> FAIL: extrema 3
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>     File
> "X:\python26-x64\lib\site-packages\scipy\ndimage\tests\test_ndimage.py",
> line 3149, in test_extrema03
>       self.failUnless(numpy.all(output1[2]  == output4))
> AssertionError
>
>
>
> And on my 32-bit development installation I still get the airye failure,
> but only when run in the context of scipy.test():
>
> ======================================================================
> FAIL: Real-valued Bessel domains
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>     File
> "X:\python26\lib\site-packages\scipy\special\tests\test_basic.py", line
> 1691, in test_ticket_854
>       assert not isnan(airye(-1)[2:4]).any(), airye(-1)
> AssertionError: (nan, nan, nan, nan)
>
>

I opened a ticket for this artifact at 
http://projects.scipy.org/scipy/ticket/1233.

All scipy.sparse.linalg tests now pass after reworking the patch to link 
SuperLU with CBLAS instead of MKL. The patch is attached to 
http://projects.scipy.org/scipy/ticket/1225.

--
Christoph


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