Bug 1610996

I am getting exactly the same error when I try to rebuild pygrib on s390x.
The same code builds fine on f28 and for all architecture except s390x on rawhide.

I used this build command:
   fedpkg scratch-build --arches s390x --target rawhide
and get this output in build.log:
(see https://koji.fedoraproject.org/koji/taskinfo?taskID=28793934)

+ /usr/bin/python2 setup.py build
Traceback (most recent call last):
  File "setup.py", line 2, in <module>
    import os, glob, numpy, sys
  File "/usr/lib64/python2.7/site-packages/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/usr/lib64/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/usr/lib64/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/usr/lib64/python2.7/site-packages/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError: 
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.
Original error was: /usr/lib64/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: LogBase2_128
error: Bad exit status from /var/tmp/rpm-tmp.5XhzdD (%build)
RPM build errors:
    Bad exit status from /var/tmp/rpm-tmp.5XhzdD (%build)
Child return code was: 1

I see the same with python3-numpy when trying to build astropy (therefore I also modify title as it is not Python 2 specific):


Traceback (most recent call last):
  File "/usr/lib64/python3.7/site-packages/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: /usr/lib64/python3.7/site-packages/numpy/core/multiarray.cpython-37m-s390x-linux-gnu.so: undefined symbol: LogBase2_128
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "setup.py", line 128, in <module>
    **package_info
  File "/usr/lib/python3.7/site-packages/setuptools/__init__.py", line 129, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib64/python3.7/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/lib64/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/lib64/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib64/python3.7/distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "/usr/lib64/python3.7/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/lib64/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/builddir/build/BUILD/astropy-3.0.3/astropy_helpers/astropy_helpers/setup_helpers.py", line 242, in run
    orig_run(self)
  File "/builddir/build/BUILD/astropy-3.0.3/astropy_helpers/astropy_helpers/commands/build_ext.py", line 292, in run
    np_include = get_numpy_include_path()
  File "/builddir/build/BUILD/astropy-3.0.3/astropy_helpers/astropy_helpers/utils.py", line 72, in get_numpy_include_path
    import numpy
  File "/usr/lib64/python3.7/site-packages/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/usr/lib64/python3.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python3.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/usr/lib64/python3.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/usr/lib64/python3.7/site-packages/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError: 
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.

This may be caused by an incorrect fix I applied to get this to build:

%ifnarch s390x
%{python2_sitearch}/numpy/__pycache__/*
%endif


On s390x, it wasn't being created.

If not, it might be a large Python s390x issue.

I don't think this is the reason, as this does not affect the also broken python3-numpy.

BTW: I see that you also skip tests on s390x, is numpy so broken on that architecture?

Can be reporduced in mock:

$ sudo dnf install qemu-user-static
$ mock -r fedora-rawhide-s390x --forcearch s390x --install python3-numpy
$ mock -r fedora-rawhide-s390x --forcearch s390x shell
<mock-chroot> sh-4.4# python3
Python 3.7.0 (default, Jul 23 2018, 08:49:45) 
[GCC 8.1.1 20180712 (Red Hat 8.1.1-5)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from numpy import multiarray
Traceback (most recent call last):
  File "/usr/lib64/python3.7/site-packages/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: /usr/lib64/python3.7/site-packages/numpy/core/multiarray.cpython-37m-s390x-linux-gnu.so: undefined symbol: LogBase2_128

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib64/python3.7/site-packages/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/usr/lib64/python3.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python3.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/usr/lib64/python3.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/usr/lib64/python3.7/site-packages/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError: 
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: /usr/lib64/python3.7/site-packages/numpy/core/multiarray.cpython-37m-s390x-linux-gnu.so: undefined symbol: LogBase2_128

<mock-chroot> sh-4.4# rpm -q python3-numpy
python3-numpy-1.15.0-1.fc29.s390x

See this upstream comment [1], as I believe that is the cause of the issue.

[1] https://github.com/numpy/numpy/pull/11568#issuecomment-412252038

(In reply to Gwyn Ciesla from comment #3)
> This may be caused by an incorrect fix I applied to get this to build:
> 
> %ifnarch s390x
> %{python2_sitearch}/numpy/__pycache__/*
> %endif

Why does this directory exist at all? Python 2 does not create a __pycache__ directory; that's something from Python 3. It looks like a pytest artifact; they should not actually be packaged.

PR: https://src.fedoraproject.org/rpms/numpy/pull-request/6

May or may not work yet; will have to see how the build goes.

*** Bug 1615407 has been marked as a duplicate of this bug. ***