Intel® Fortran Compiler
Build applications that can scale for the future with optimized code designed for Intel® Xeon® and compatible processors.
29279 Discussions

Scipy 15.1 still fails test with -O2 or -O3 flag

Jonah_M_
Beginner
‎09-15-2015 12:37 PM
351 Views

Hello,

I am compiling numpy and scipy with the intel compiler and with MKL. I am following this guide: https://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl

I am posting to confirm that the bug that plagued older versions of scipy is still present and that optimizations still prevent scipy from passing all tests. (See, e.g., https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/507583)

Numpy passes all self tests. But scipy has the following failures:

======================================================================
FAIL: test_definition (test_basic.TestIfftnSingle)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/fftpack/tests/test_basic.py", line 657, in test_definition
    assert_array_almost_equal_nulp(y,direct_idftn(x),self.maxnlp)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 1358, in assert_array_almost_equal_nulp
    raise AssertionError(msg)
AssertionError: X and Y are not equal to 3500 ULP

======================================================================
FAIL: test_lorentz (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/odr/tests/test_odr.py", line 293, in test_lorentz
    3.7798193600109009e+00]),
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 842, in assert_array_almost_equal
    precision=decimal)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 665, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 6 decimals

(mismatch 100.0%)
 x: array([  1.000000e+03,   1.000000e-01,   3.800000e+00])
 y: array([  1.430678e+03,   1.339051e-01,   3.779819e+00])

======================================================================
FAIL: test_multi (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/odr/tests/test_odr.py", line 190, in test_multi
    0.5101147161764654, 0.5173902330489161]),
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 842, in assert_array_almost_equal
    precision=decimal)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 665, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 6 decimals

(mismatch 100.0%)
 x: array([ 4. ,  2. ,  7. ,  0.4,  0.5])
 y: array([ 4.379988,  2.433306,  8.002885,  0.510115,  0.51739 ])

======================================================================
FAIL: test_pearson (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/odr/tests/test_odr.py", line 236, in test_pearson
    np.array([5.4767400299231674, -0.4796082367610305]),
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 842, in assert_array_almost_equal
    precision=decimal)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 665, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 6 decimals

(mismatch 100.0%)
 x: array([ 1.,  1.])
 y: array([ 5.47674 , -0.479608])

======================================================================
FAIL: test_qhull.TestDelaunay.test_incremental('pathological-1-chunk-1',)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/spatial/tests/test_qhull.py", line 507, in check
    np.arange(points.shape[0]))
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 739, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 620, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

(shapes (79,), (81,) mismatch)
 x: array([ 0,  2,  3,  4,  5,  6,  7,  8,  9, 11, 12, 13, 14, 15, 16, 17, 18,
       19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
       36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,...
 y: array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16,
       17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
       34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,...

======================================================================
FAIL: test_qhull.TestUtilities.test_degenerate_barycentric_transforms
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/decorators.py", line 146, in skipper_func
    return f(*args, **kwargs)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/spatial/tests/test_qhull.py", line 296, in test_degenerate_barycentric_transforms
    assert_(bad_count < 20, bad_count)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 53, in assert_
    raise AssertionError(smsg)
AssertionError: 26

======================================================================
FAIL: test_bdtrc (test_basic.TestCephes)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/tests/test_basic.py", line 118, in test_bdtrc
    assert_equal(cephes.bdtrc(1,3,0.5),0.5)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 334, in assert_equal
    raise AssertionError(msg)
AssertionError: 
Items are not equal:
 ACTUAL: 0.50000000000000011
 DESIRED: 0.5

======================================================================
FAIL: test_bdtri (test_basic.TestCephes)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/tests/test_basic.py", line 115, in test_bdtri
    assert_equal(cephes.bdtri(1,3,0.5),0.5)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 334, in assert_equal
    raise AssertionError(msg)
AssertionError: 
Items are not equal:
 ACTUAL: 0.49999999999999994
 DESIRED: 0.5

======================================================================
FAIL: test_cosm1 (test_basic.TestCephes)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/tests/test_basic.py", line 214, in test_cosm1
    assert_equal(cephes.cosm1(0),0.0)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 326, in assert_equal
    raise AssertionError(msg)
AssertionError: 
Items are not equal:
 ACTUAL: -0.0
 DESIRED: 0.0

======================================================================
FAIL: test_data.test_boost(<Data for eval_legendre_ld: legendre_p_ipp-legendre_p>,)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/tests/test_data.py", line 481, in _test_factory
    test.check(dtype=dtype)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/_testutils.py", line 292, in check
    assert_(False, "\n".join(msg))
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 53, in assert_
    raise AssertionError(smsg)
AssertionError: 
Max |adiff|: 7.49401e-16
Max |rdiff|: 7.92476e-14
Bad results (1 out of 140) for the following points (in output 0):
                          18.0             -0.8049191832542419 =>          -0.009106206044325216 !=          -0.009106206044324494  (rdiff          7.924759910919454e-14)

======================================================================
FAIL: test_data.test_boost(<Data for gammaincc: igamma_int_data_ipp-igamma_int_data>,)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/tests/test_data.py", line 481, in _test_factory
    test.check(dtype=dtype)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/_testutils.py", line 292, in check
    assert_(False, "\n".join(msg))
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 53, in assert_
    raise AssertionError(smsg)
AssertionError: 
Max |adiff|: 1.21569e-14
Max |rdiff|: 4.27465e-14
Bad results (1 out of 140) for the following points (in output 0):
                          36.5                            73.0 =>          8.570090512692315e-07 !=          8.570090512692681e-07  (rdiff          4.274654382528594e-14)

======================================================================
FAIL: test_data.test_boost(<Data for gdtrc_: igamma_int_data_ipp-igamma_int_data>,)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/tests/test_data.py", line 481, in _test_factory
    test.check(dtype=dtype)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/_testutils.py", line 292, in check
    assert_(False, "\n".join(msg))
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 53, in assert_
    raise AssertionError(smsg)
AssertionError: 
Max |adiff|: 1.21569e-14
Max |rdiff|: 4.27465e-14
Bad results (1 out of 140) for the following points (in output 0):
                          36.5                            73.0 =>          8.570090512692315e-07 !=          8.570090512692681e-07  (rdiff          4.274654382528594e-14)

======================================================================
FAIL: test_orthogonal.test_js_roots
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/tests/test_orthogonal.py", line 371, in test_js_roots
    verify_gauss_quad(roots(68.9, 2.25), evalf(68.9, 2.25), 5, atol=2e-14)
  File "/nfs/galaxy/unixhome/jmiller/scipy-test/lib/python2.7/site-packages/scipy/special/tests/test_orthogonal.py", line 283, in verify_gauss_quad
    assert_allclose(vv, np.eye(N), rtol, atol)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 1297, in assert_allclose
    verbose=verbose, header=header)
  File "/nfs/galaxy/unixhome/jmiller/numpy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 665, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=1e-15, atol=2e-14

(mismatch 100.0%)
 x: array([[  1.000000e+00,  -2.932083e-14,   1.628550e-14,  -5.973276e-15,
         -1.360751e-15],
       [ -2.932083e-14,   1.000000e+00,  -1.985946e-14,   1.119072e-14,...
 y: array([[ 1.,  0.,  0.,  0.,  0.],
       [ 0.,  1.,  0.,  0.,  0.],
       [ 0.,  0.,  1.,  0.,  0.],...

----------------------------------------------------------------------
Ran 17005 tests in 117.640s

FAILED (KNOWNFAIL=97, SKIP=1181, failures=13)
<nose.result.TextTestResult run=17005 errors=0 failures=13>

However if I change "-O3" flag to "-O1" in both in both "numpy/distutils/intelcompiler.py" and "numpy/distutils/fcompiler/intel.py",  both libraries pass all tests.

Scipy is mostly written in fortran. So the issue is with the fortran compiler.

Thanks.

0 Kudos

Link Copied

0 Replies
Reply

Community support is provided Monday to Friday. Other contact methods are available here.

Intel does not verify all solutions, including but not limited to any file transfers that may appear in this community. Accordingly, Intel disclaims all express and implied warranties, including without limitation, the implied warranties of merchantability, fitness for a particular purpose, and non-infringement, as well as any warranty arising from course of performance, course of dealing, or usage in trade.

For more complete information about compiler optimizations, see our Optimization Notice.