[yt-users] install/compile error

[Alexander Heger]

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.

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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