[Scipy-tickets] [SciPy] #678: scipy.test failure with mkl/cdft

SciPy Trac scipy-tickets@scipy....
Fri Apr 22 12:50:22 CDT 2011


#678: scipy.test failure with mkl/cdft
------------------------+---------------------------------------------------
  Reporter:  dstuebe    |       Owner:  cdavid     
      Type:  defect     |      Status:  closed     
  Priority:  normal     |   Milestone:  Unscheduled
 Component:  scipy.lib  |     Version:             
Resolution:  fixed      |    Keywords:             
------------------------+---------------------------------------------------
Changes (by rgommers):

  * status:  accepted => closed
  * resolution:  => fixed


Old description:

> Hello SciPy
>
> I am setting up scipy on a ROCKS5.0 cluster using the rocks rolls intel
> package. The code builds beautifully. Thank you for you hard work. It
> seems however that maybe the optimization in ifort/mkl is not compatible
> with the methods in scipy. Please let me know if you have any experience
> with these issues - is there some way to fix the problem?
>
> Thanks so much
>
> David
>

> site.cfg for Numpy:
> [DEFAULT]
> library_dirs = /usr/local/lib
> include_dirs = /usr/local/include
>
> [mkl]
> library_dirs = /opt/intel/mkl/10.0.1.014/lib/em64t
> include_dirs = /opt/intel/mkl/10.0.1.014/include
> lapack_libs = mkl_lapack
> mkl_libs = mkl, guide
>
> [fftw3]
> library_dirs = /opt/intel/mkl/10.0.1.014/lib/em64t
> fftw3_libs = mkl_cdft
>

> Error in scipy.test:
> ======================================================================
> FAIL: check_syevr (scipy.lib.lapack.tests.test_lapack.test_flapack_float)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/scipy/lib/lapack/tests/esv_tests.py", line 41, in check_syevr
>     assert_array_almost_equal(w,exact_w)
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
>     header='Arrays are not almost equal')
>   File "/usr/local/install/python/2.5.2/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 33.3333333333%)
>  x: array([-0.66992444,  0.48769474,  9.18222618], dtype=float32)
>  y: array([-0.66992434,  0.48769389,  9.18223045])
>
> ======================================================================
> FAIL: check_syevr_irange
> (scipy.lib.lapack.tests.test_lapack.test_flapack_float)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/scipy/lib/lapack/tests/esv_tests.py", line 66, in
> check_syevr_irange
>     assert_array_almost_equal(w,exact_w[rslice])
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
>     header='Arrays are not almost equal')
>   File "/usr/local/install/python/2.5.2/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 33.3333333333%)
>  x: array([-0.66992444,  0.48769474,  9.18222618], dtype=float32)
>  y: array([-0.66992434,  0.48769389,  9.18223045])
>
> ======================================================================
> FAIL: test_explicit (scipy.odr.tests.test_odr.test_odr)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/scipy/odr/tests/test_odr.py", line 50, in test_explicit
>     -8.7849712165253724e-02]),
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
>     header='Arrays are not almost equal')
>   File "/usr/local/install/python/2.5.2/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 100.0%)
>  x: array([  1.26462971e+03,  -5.42545890e+01,  -8.64250389e-02])
>  y: array([  1.26465481e+03,  -5.40184100e+01,  -8.78497122e-02])
>
> ======================================================================
> FAIL: test_lorentz (scipy.odr.tests.test_odr.test_odr)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/scipy/odr/tests/test_odr.py", line 295, in test_lorentz
>     3.7798193600109009e+00]),
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
>     header='Arrays are not almost equal')
>   File "/usr/local/install/python/2.5.2/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 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 (scipy.odr.tests.test_odr.test_odr)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/scipy/odr/tests/test_odr.py", line 191, in test_multi
>     0.5101147161764654,  0.5173902330489161]),
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
>     header='Arrays are not almost equal')
>   File "/usr/local/install/python/2.5.2/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 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 (scipy.odr.tests.test_odr.test_odr)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/scipy/odr/tests/test_odr.py", line 238, in test_pearson
>     np.array([ 5.4767400299231674, -0.4796082367610305]),
>   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
> packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
>     header='Arrays are not almost equal')
>   File "/usr/local/install/python/2.5.2/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 100.0%)
>  x: array([ 1.,  1.])
>  y: array([ 5.47674003, -0.47960824])
>
> ----------------------------------------------------------------------
> Ran 1848 tests in 8.429s
>
> FAILED (failures=6)

New description:

 Hello SciPy

 I am setting up scipy on a ROCKS5.0 cluster using the rocks rolls intel
 package. The code builds beautifully. Thank you for you hard work. It
 seems however that maybe the optimization in ifort/mkl is not compatible
 with the methods in scipy. Please let me know if you have any experience
 with these issues - is there some way to fix the problem?

 Thanks so much

 David


 site.cfg for Numpy:
 [DEFAULT]
 library_dirs = /usr/local/lib
 include_dirs = /usr/local/include

 [mkl]
 library_dirs = /opt/intel/mkl/10.0.1.014/lib/em64t
 include_dirs = /opt/intel/mkl/10.0.1.014/include
 lapack_libs = mkl_lapack
 mkl_libs = mkl, guide

 [fftw3]
 library_dirs = /opt/intel/mkl/10.0.1.014/lib/em64t
 fftw3_libs = mkl_cdft


 Error in scipy.test:
 ======================================================================
 FAIL: check_syevr (scipy.lib.lapack.tests.test_lapack.test_flapack_float)
 ----------------------------------------------------------------------
 Traceback (most recent call last):
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/scipy/lib/lapack/tests/esv_tests.py", line 41, in check_syevr
     assert_array_almost_equal(w,exact_w)
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "/usr/local/install/python/2.5.2/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 33.3333333333%)
  x: array([-0.66992444,  0.48769474,  9.18222618], dtype=float32)
  y: array([-0.66992434,  0.48769389,  9.18223045])

 ======================================================================
 FAIL: check_syevr_irange
 (scipy.lib.lapack.tests.test_lapack.test_flapack_float)
 ----------------------------------------------------------------------
 Traceback (most recent call last):
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/scipy/lib/lapack/tests/esv_tests.py", line 66, in
 check_syevr_irange
     assert_array_almost_equal(w,exact_w[rslice])
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "/usr/local/install/python/2.5.2/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 33.3333333333%)
  x: array([-0.66992444,  0.48769474,  9.18222618], dtype=float32)
  y: array([-0.66992434,  0.48769389,  9.18223045])

 ======================================================================
 FAIL: test_explicit (scipy.odr.tests.test_odr.test_odr)
 ----------------------------------------------------------------------
 Traceback (most recent call last):
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/scipy/odr/tests/test_odr.py", line 50, in test_explicit
     -8.7849712165253724e-02]),
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "/usr/local/install/python/2.5.2/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 100.0%)
  x: array([  1.26462971e+03,  -5.42545890e+01,  -8.64250389e-02])
  y: array([  1.26465481e+03,  -5.40184100e+01,  -8.78497122e-02])

 ======================================================================
 FAIL: test_lorentz (scipy.odr.tests.test_odr.test_odr)
 ----------------------------------------------------------------------
 Traceback (most recent call last):
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/scipy/odr/tests/test_odr.py", line 295, in test_lorentz
     3.7798193600109009e+00]),
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "/usr/local/install/python/2.5.2/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 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 (scipy.odr.tests.test_odr.test_odr)
 ----------------------------------------------------------------------
 Traceback (most recent call last):
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/scipy/odr/tests/test_odr.py", line 191, in test_multi
     0.5101147161764654,  0.5173902330489161]),
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "/usr/local/install/python/2.5.2/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 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 (scipy.odr.tests.test_odr.test_odr)
 ----------------------------------------------------------------------
 Traceback (most recent call last):
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/scipy/odr/tests/test_odr.py", line 238, in test_pearson
     np.array([ 5.4767400299231674, -0.4796082367610305]),
   File "/usr/local/install/python/2.5.2/lib/python2.5/site-
 packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "/usr/local/install/python/2.5.2/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 100.0%)
  x: array([ 1.,  1.])
  y: array([ 5.47674003, -0.47960824])

 ----------------------------------------------------------------------
 Ran 1848 tests in 8.429s

 FAILED (failures=6)

--

Comment:

 ifort default changed to -O1 for numpy 1.6.0, so this should be fixed.
 Thanks Christoph.

-- 
Ticket URL: <http://projects.scipy.org/scipy/ticket/678#comment:7>
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