On Tue, Aug 30, 2011 at 09:04:18PM +0200, Ralf Gommers wrote:
On Tue, Aug 30, 2011 at 6:59 PM, Jack Howarth <howarth@bromo.med.uc.edu>wrote:
On Tue, Aug 30, 2011 at 01:32:09PM +0000, Pauli Virtanen wrote:
Tue, 30 Aug 2011 08:55:15 -0400, Jack Howarth wrote: [clip]
On x86_64-apple-darwin11, building scypy 0.9.0 against python2.7 using the clang compilers and gfortran from FSF gcc 4.6.1, I get the following testsuite results... [clip] ====================================================================== FAIL: test_dot (test_blas.TestFBLAS1Simple) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/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 "/sw/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
Does Numpy's test suite pass?
On x86_64-apple-darwin10, numpy passes its testsuite...
[frodo:~] howarth% python2.7 Python 2.7.2 (default, Aug 4 2011, 09:22:24) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.test() Running unit tests for numpy NumPy version 1.6.0 NumPy is installed in /sw/lib/python2.7/site-packages/numpy Python version 2.7.2 (default, Aug 4 2011, 09:22:24) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] nose version 1.1.2 ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................../sw/lib/python2.7/site-packages/numpy/core/numeric.py:1920: RuntimeWarning: invalid value encountered in absolute return all(less_equal(absolute(x-y), atol + rtol * absolute(y)))
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........................................................................................... ---------------------------------------------------------------------- Ran 3529 tests in 34.328s
OK (KNOWNFAIL=3, SKIP=1) <nose.result.TextTestResult run=3529 errors=0 failures=0>
whereas on x86_64-apple-darwin11 (building with clang), numpy fails...
None of those failures is a problem, nor is it relevant to your problem with scipy.
If anyone feels like writing a patch to disable those test_special_values on all platforms except linux, that would be appreciated.
Ralf, It seems very odd that these test_special_values tests pass in numpy on darwin10 but fail on darwin11. Doesn't that imply a possible regression in Lion? If so it might be wise to open a radar with Apple on the issue. Remember that Lion is the first darwin release built with llvm-based compilers and this change may well cause subtle regressions. For example, ppl exposed the fact that llvm-gcc silently ignores -frounding-math (while clang at least admits to doing so). Jack
Ralf
[GCC 4.2.1 Compatible Apple Clang 2.1 (tags/Apple/clang-163.7.1)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.test() Running unit tests for numpy NumPy version 1.6.0 NumPy is installed in /sw/lib/python2.7/site-packages/numpy Python version 2.7.2 (default, Jul 21 2011, 22:39:54) [GCC 4.2.1 Compatible Apple Clang 2.1 (tags/Apple/clang-163.7.1)] nose version 1.1.2
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................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ====================================================================== FAIL: Test basic arithmetic function errors ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/numpy/testing/decorators.py", line 215, in knownfailer return f(*args, **kwargs) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_numeric.py", line 321, in test_floating_exceptions lambda a,b:a/b, ft_tiny, ft_max) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_numeric.py", line 271, in assert_raises_fpe "Type %s did not raise fpe error '%s'." % (ftype, fpeerr)) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: Type <type 'numpy.complex64'> did not raise fpe error ''.
====================================================================== FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, 1, inf, inf, inf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 578, in check_complex_value assert_equal(f(z1), z2) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 605, in assert_array_compare chk_same_position(x_id, y_id, hasval='nan') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position raise AssertionError(msg) AssertionError: Arrays are not equal
x and y nan location mismatch: x: array([ nan+infj]) y: array((inf+infj))
====================================================================== FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, -1, inf, inf, inf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 578, in check_complex_value assert_equal(f(z1), z2) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 605, in assert_array_compare chk_same_position(x_id, y_id, hasval='nan') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position raise AssertionError(msg) AssertionError: Arrays are not equal
x and y nan location mismatch: x: array([ nan+infj]) y: array((inf+infj))
====================================================================== FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, 0.0, inf, inf, inf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 578, in check_complex_value assert_equal(f(z1), z2) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 605, in assert_array_compare chk_same_position(x_id, y_id, hasval='nan') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position raise AssertionError(msg) AssertionError: Arrays are not equal
x and y nan location mismatch: x: array([ nan+infj]) y: array((inf+infj))
====================================================================== FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, -0.0, inf, inf, inf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 578, in check_complex_value assert_equal(f(z1), z2) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 605, in assert_array_compare chk_same_position(x_id, y_id, hasval='nan') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position raise AssertionError(msg) AssertionError: Arrays are not equal
x and y nan location mismatch: x: array([ nan+infj]) y: array((inf+infj))
====================================================================== FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, inf, inf, inf, inf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 578, in check_complex_value assert_equal(f(z1), z2) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 605, in assert_array_compare chk_same_position(x_id, y_id, hasval='nan') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position raise AssertionError(msg) AssertionError: Arrays are not equal
x and y nan location mismatch: x: array([ nan+infj]) y: array((inf+infj))
====================================================================== FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, -inf, inf, inf, inf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 578, in check_complex_value assert_equal(f(z1), z2) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 605, in assert_array_compare chk_same_position(x_id, y_id, hasval='nan') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position raise AssertionError(msg) AssertionError: Arrays are not equal
x and y nan location mismatch: x: array([ nan+infj]) y: array((inf+infj))
====================================================================== FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, nan, inf, inf, inf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 578, in check_complex_value assert_equal(f(z1), z2) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 605, in assert_array_compare chk_same_position(x_id, y_id, hasval='nan') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position raise AssertionError(msg) AssertionError: Arrays are not equal
x and y nan location mismatch: x: array([ nan+infj]) y: array((inf+infj))
====================================================================== FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, -inf, 1, 0.0, inf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/sw/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 578, in check_complex_value assert_equal(f(z1), z2) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 605, in assert_array_compare chk_same_position(x_id, y_id, hasval='nan') File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position raise AssertionError(msg) AssertionError: Arrays are not equal
x and y nan location mismatch: x: array([ nan+infj]) y: array(infj)
---------------------------------------------------------------------- Ran 3529 tests in 38.236s
FAILED (KNOWNFAIL=3, SKIP=1, failures=9) <nose.result.TextTestResult run=3529 errors=0 failures=9>
In both cases (darwin10 and darwin11), the blas used is from /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate.
http://developer.apple.com/performance/accelerateframework.html
I doubt the system blas is at fault and more likely this is an issue with the clang compilers. I know python required an explicit addition of -fwrapv since its test for that option is confused by clang. Perhaps numpy/scipy requires -fwrapv as well? Jack
Either the BLAS you linked Scipy against is broken, or there are some compatibility problems due to compilers or mixing compiler versions.
You could check which libraries your `fblas.so` and `cblas.so` in the Scipy installation are linked against. I've never used OSX, though, so I do not know how to do this there. You can see the same information in the beginning of the build logs, though.
Maybe someone who is more familiar than me with OSX knows more.
-- Pauli Virtanen
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