[yt-users] install/compile error

Matthew Turk matthewturk at gmail.com
Mon Sep 14 16:19:48 PDT 2015


On Mon, Sep 14, 2015 at 6:19 PM, Alexander Heger <alexander.heger at monash.edu
> wrote:

> Dear Nathan,
>
> the gcc 5.1 comes by default with Fedora 22 - I probably would have to
> re-compile the entire python 3.5 with the older gcc.  The link you
> sent does not seem promising that has been fixed, not sure the current
> gcc 5.2 (bugfix release) would do better.  So best easiest for now may
> be to go with Matt's suggestion, I agree.
>
> I this a bug in python 3.5 to rely on a broken gcc feature?  Or maybe
> never meant to be be compiled with gcc 5.x?  Fedora's python 3.4 is
> also compiled with gcc 5.1.1
>
> ~>/bin/python3.4
> Python 3.4.2 (default, Jul  9 2015, 17:24:30)
> [GCC 5.1.1 20150618 (Red Hat 5.1.1-4)] on linux
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
>
> btw, yt is the only package that broke, all others compiled fine.
>

None of the others use OpenMP.


>
> Best wishes,
> Alexander
>
>
> On 15 September 2015 at 01:52, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
> > So the most important lines in the file you attached are here:
> >
> > In file included from
> /home/alex/Python/include/python3.5m/pyatomic.h:12:0,
> >                      from
> /home/alex/Python/include/python3.5m/Python.h:53,
> >                      from
> > build/src.linux-x86_64-3.5/yt/utilities/lib/geometry_utils.c:4:
> >     /usr/lib/gcc/x86_64-redhat-linux/5.1.1/include/stdatomic.h:40:1:
> sorry,
> > unimplemented: ‘_Atomic’ with OpenMP
> >      typedef _Atomic _Bool atomic_bool;
> >
> >
> > So python.h is bringing in pyatomic.h, which is looking for stdatomic.h,
> > which in turn prints "sorrry, unimplemented" and breaks the build. See
> the
> > following gcc bug:
> >
> > https://gcc.gnu.org/bugzilla/show_bug.cgi?id=65467
> >
> > I believe downgrading to an older gcc release (before gcc 5.0) will
> likely
> > fix this. An alternative would be to manually disable openmp support in
> yt's
> > setup.py script as Matt suggested.
> >
> >
> > On Mon, Sep 14, 2015 at 10:25 AM, Matthew Turk <matthewturk at gmail.com>
> > wrote:
> >>
> >> Hi Alex,
> >>
> >> Looks like you have some weird stuff going on with OpenMP.  Probably
> best
> >> to manually disable it in yt/utilities/lib/setup.py by having it return
> >> false for the detection.
> >>
> >> On Sun, Sep 13, 2015 at 10:10 PM, Alexander Heger
> >> <alexander.heger at monash.edu> wrote:
> >>>
> >>> I know you don't yet quite support prime-time use of python 3.x.
> >>> But since this is in progress, I provide some feedback.
> >>>
> >>> When doing a pip3 install yt I get the attached error message.
> >>>
> >>> Best wishes,
> >>> Alexander
> >>>
> >>>
> >>>
> >>>
> >>>
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> >>
> >>
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> >
> >
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