[yt-users] install/compile error

Alexander Heger alexander.heger at monash.edu
Mon Sep 14 16:42:25 PDT 2015


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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