[Numpy-discussion] ATLAS build errors

[Ian Henriksen]

On Sat, Mar 26, 2016 at 3:06 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> I'm workon on building manylinux wheels for numpy, and I ran into
> unexpected problems with a numpy built against the ATLAS 3.8 binaries
> supplied by CentOS 5.
>
> I'm working on the manylinux docker container [1]
>
> To get ATLAS, I'm doing `yum install atlas-devel` which gets the
> default CentOS 5 ATLAS packages.
>
> I then build numpy.  Local tests work fine, but when I test on travis,
> I get these errors [2]:
>
> ======================================================================
> ERROR: test_svd_build (test_regression.TestRegression)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/home/travis/build/matthew-brett/manylinux-testing/venv/lib/python2.7/site-packages/numpy/linalg/tests/test_regression.py",
> line 56, in test_svd_build
>     u, s, vh = linalg.svd(a)
>   File
> "/home/travis/build/matthew-brett/manylinux-testing/venv/lib/python2.7/site-packages/numpy/linalg/linalg.py",
> line 1359, in svd
>     u, s, vt = gufunc(a, signature=signature, extobj=extobj)
> ValueError: On entry to DGESDD parameter number 12 had an illegal value
>
> ======================================================================
> FAIL: test_lapack (test_build.TestF77Mismatch)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/home/travis/build/matthew-brett/manylinux-testing/venv/lib/python2.7/site-packages/numpy/testing/decorators.py",
> line 146, in skipper_func
>     return f(*args, **kwargs)
>   File
> "/home/travis/build/matthew-brett/manylinux-testing/venv/lib/python2.7/site-packages/numpy/linalg/tests/test_build.py",
> line 56, in test_lapack
>     information.""")
> AssertionError: Both g77 and gfortran runtimes linked in lapack_lite !
> This is likely to
> cause random crashes and wrong results. See numpy INSTALL.txt for more
> information.
>
>
> Sure enough, scipy built the same way segfaults or fails to import (see
> [2]).
>
> I get no errors for an openblas build.
>
> Does anyone recognize these?   How should I modify the build to avoid them?
>
> Cheers,
>
> Matthew
>
>
> [1] https://github.com/pypa/manylinux
> [2] https://travis-ci.org/matthew-brett/manylinux-testing/jobs/118712090
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The error regarding parameter 12 of dgesdd sounds a lot like
https://github.com/scipy/scipy/issues/5039 where the issue was that the
LAPACK
version was too old. CentOS 5 is pretty old, so I wouldn't be surprised if
that were
the case here too.
In general, you can't expect Linux distros to have a uniform shared object
interface
for LAPACK, so you don't gain much by using the version that ships with
CentOS 5 beyond not having to compile it all yourself. It might be better
to use a
newer LAPACK built from source with the older toolchains already there.
Best,
-Ian Henriksen
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