[SciPy-User] how critical are testing errors in Scipy under Lion?

Angel Yanguas-Gil angel.yanguas@gmail....
Sat Jun 9 21:33:38 CDT 2012


Hi, My OS is Lion. I compiled from source following the instructions
in Scipy docs under python.org's 2.7.3 and I got errors when running
scipy.test().

I know there is a previous thread on this topic that lead to a ticket
to look into the problem, but what I am trying to do is understand the
impact of these errors on the day-to-day work with scipy. How do they
affect Scipy's reliability under Lion? I know it is related to simple
precision, but I don't know how big of an issue is. I've been using
scipy for almost five years, and since moving to Lion last fall I have
been reluctant to base my more serious work on Scipy+Lion for that
reason, to the point that I am using Scipy mostly under Ubuntu these
days. But it would be great to know if I am overreacting.

Any clues? (relevant part from nose test results are included below).

Thanks,

ay


Running unit tests for scipy
NumPy version 1.6.1
NumPy is installed in
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
SciPy version 0.10.1
SciPy is installed in
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy
Python version 2.7.3 (v2.7.3:70274d53c1dd, Apr  9 2012, 20:52:43) [GCC
4.2.1 (Apple Inc. build 5666) (dot 3)]
nose version 1.1.2


======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py",
line 58, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 12

======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py",
line 67, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: -9

======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py",
line 78, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

======================================================================
FAIL: test_basic.TestNorm.test_overflow
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py",
line 581, in test_overflow
    assert_almost_equal(norm(a), a)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 452, in assert_almost_equal
    return assert_array_almost_equal(actual, desired, decimal, err_msg)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 800, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals

(mismatch 100.0%)
 x: array(-0.0)
 y: array([  1.00000002e+20], dtype=float32)

======================================================================
FAIL: test_basic.TestNorm.test_stable
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py",
line 586, in test_stable
    assert_almost_equal(norm(a) - 1e4, 0.5)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
 ACTUAL: -10000.0
 DESIRED: 0.5

======================================================================
FAIL: test_basic.TestNorm.test_types
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py",
line 568, in test_types
    assert_allclose(norm(x), np.sqrt(14), rtol=tol)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1168, in assert_allclose
    verbose=verbose, header=header)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=2.38419e-06, atol=0

(mismatch 100.0%)
 x: array(1.0842021724855044e-19)
 y: array(3.7416573867739413)

======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py",
line 99, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 12


======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py",
line 109, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: -9

======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py",
line 127, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py",
line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

Bummer.


More information about the SciPy-User mailing list