[Numpy-discussion] Problem with libgfortran installed with pip install numpy

David Grote dpgrote at lbl.gov
Fri Nov 9 18:00:01 EST 2018

Hi Matthew - Do you have any comment in this?

On Wed, Sep 5, 2018 at 5:01 PM Charles R Harris <charlesr.harris at gmail.com>

> On Wed, Sep 5, 2018 at 5:38 PM David Grote <dpgrote at lbl.gov> wrote:
>> Hi - I have recently come across this problem. On my mac, I build a
>> Fortran code, producing a shared object, that I import into Python along
>> with numpy. This had been working fine until recently when I started seeing
>> sag faults deep inside the Fortran code, usually in Fortran print
>> statements. I tracked this down to a gfortran version issue.
>> I use the brew installation of Python and gcc (using the most recent
>> version, 8.2.0). gcc of course installs a version of libgfortran.dylib.
>> Doing a lsof of a running Python, I see that it finds that copy of
>> libgfortran, and also a copy that was downloaded with numpy
>> (/usr/local/lib/python3.7/site-packages/numpy/.dylibs/libgfortran.3.dylib).
>> Looking at numpy's copy of libgfortran, I see that it is version 4.9.0,
>> much older. Since my code is importing numpy first, the OS seems be using
>> numpy's version of libgfortran to link when importing my code. I know from
>> other experience that older versions of libgfortran are not compatible with
>> code compiled using a new version of gfortran and so therefore segfaults
>> happen.
>> If I download the numpy source and do python setup.py install, I don't
>> have this problem.
>> After this long description, my question is why is such an old version of
>> gcc used to build the distribution of numpy that gets installed from pypi?
>> gcc version 4.9.0 is from 2014. Can a newer version be used?
> The library came in with the use of OpenBLAS, I don't think there is a
> fundamental reason that a newer version of gfortran couldn't be used, but I
> have little experience with the Mac. Note that we have also given up on 32
> bit Python on Mac for library related reasons. Matthew Brett would be the
> guy to discuss this with.
> Chuck
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