[yt-users] install/compile error

[Nathan Goldbaum]

I found a commit in another project that works around this issue:

https://github.com/b-k/apophenia/commit/47366b7f2b99cdd2a57c17f1a0743dc2969d8ed6

Perhaps we could expand our test for openmp support to also do something
similar.

On Mon, Sep 14, 2015 at 6:42 PM, Alexander Heger <alexander.heger at monash.edu
> wrote:

> OK, I will try to do the identical steps I did for python 3.5 install
> in 3.4 - but I seem to recall having had the same issues there - hence
> I thought to try a fresh start from scratch (in 3.5).  I will keep you
> updated.  Maybe it really is gcc 5.1.1. that is broken, as you
> suggest.
>
>
> Best wishes,
> Alexander
>
> On 15 September 2015 at 09:29, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
> >
> >
> > 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.
> >
> >
> > Does yt build under python 3.4? If so I suspect it's an issue with python
> > 3.5. It could be an issue with the python build or a straight up bug in
> > Python 3.5. I don't have a test environment set up for Fedora so it's
> hard
> > for me to check.
> >
> >>
> >>
> >> 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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