[Numpy-discussion] Fwd: Multi-distribution Linux wheels - please test

[Matthew Brett]

On Mon, Feb 8, 2016 at 5:26 PM, Nathaniel Smith <njs at pobox.com> wrote:
> On Mon, Feb 8, 2016 at 4:37 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> [...]
>> I can't replicate the segfault with manylinux wheels and scipy.  On
>> the other hand, I get a new test error for numpy from manylinux, scipy
>> from manylinux, like this:
>>
>> $ python -c 'import scipy.linalg; scipy.linalg.test()'
>>
>> ======================================================================
>> FAIL: test_decomp.test_eigh('general ', 6, 'F', True, False, False, (2, 4))
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line
>> 197, in runTest
>>     self.test(*self.arg)
>>   File "/usr/local/lib/python2.7/dist-packages/scipy/linalg/tests/test_decomp.py",
>> line 658, in eigenhproblem_general
>>     assert_array_almost_equal(diag2_, ones(diag2_.shape[0]), DIGITS[dtype])
>>   File "/usr/local/lib/python2.7/dist-packages/numpy/testing/utils.py",
>> line 892, in assert_array_almost_equal
>>     precision=decimal)
>>   File "/usr/local/lib/python2.7/dist-packages/numpy/testing/utils.py",
>> line 713, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Arrays are not almost equal to 4 decimals
>>
>> (mismatch 100.0%)
>>  x: array([ 0.,  0.,  0.], dtype=float32)
>>  y: array([ 1.,  1.,  1.])
>>
>> ----------------------------------------------------------------------
>> Ran 1507 tests in 14.928s
>>
>> FAILED (KNOWNFAIL=4, SKIP=1, failures=1)
>>
>> This is a very odd error, which we don't get when running over a numpy
>> installed from source, linked to ATLAS, and doesn't happen when
>> running the tests via:
>>
>> nosetests /usr/local/lib/python2.7/dist-packages/scipy/linalg
>>
>> So, something about the copy of numpy (linked to openblas) is
>> affecting the results of scipy (also linked to openblas), and only
>> with a particular environment / test order.
>>
>> If you'd like to try and see whether y'all can do a better job of
>> debugging than me:
>>
>> # Run this script inside a docker container started with this incantation:
>> # docker run -ti --rm ubuntu:12.04 /bin/bash
>> apt-get update
>> apt-get install -y python curl
>> apt-get install libpython2.7  # this won't be necessary with next
>> iteration of manylinux wheel builds
>> curl -LO https://bootstrap.pypa.io/get-pip.py
>> python get-pip.py
>> pip install -f https://nipy.bic.berkeley.edu/manylinux numpy scipy nose
>> python -c 'import scipy.linalg; scipy.linalg.test()'
>
> I just tried this and on my laptop it completed without error.
>
> Best guess is that we're dealing with some memory corruption bug
> inside openblas, so it's getting perturbed by things like exactly what
> other calls to openblas have happened (which is different depending on
> whether numpy is linked to openblas), and which core type openblas has
> detected.
>
> On my laptop, which *doesn't* show the problem, running with
> OPENBLAS_VERBOSE=2 says "Core: Haswell".
>
> Guess the next step is checking what core type the failing machines
> use, and running valgrind... anyone have a good valgrind suppressions
> file?

My machine (which does give the failure) gives

Core: Core2

with OPENBLAS_VERBOSE=2

Matthew