<div dir="ltr">I found a commit in another project that works around this issue:<div><br></div><div><a href="https://github.com/b-k/apophenia/commit/47366b7f2b99cdd2a57c17f1a0743dc2969d8ed6">https://github.com/b-k/apophenia/commit/47366b7f2b99cdd2a57c17f1a0743dc2969d8ed6</a><br></div><div><br></div><div>Perhaps we could expand our test for openmp support to also do something similar.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Sep 14, 2015 at 6:42 PM, Alexander Heger <span dir="ltr"><<a href="mailto:alexander.heger@monash.edu" target="_blank">alexander.heger@monash.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">OK, I will try to do the identical steps I did for python 3.5 install<br>
in 3.4 - but I seem to recall having had the same issues there - hence<br>
I thought to try a fresh start from scratch (in 3.5). I will keep you<br>
updated. Maybe it really is gcc 5.1.1. that is broken, as you<br>
suggest.<br>
<br>
<br>
Best wishes,<br>
Alexander<br>
<div class="HOEnZb"><div class="h5"><br>
On 15 September 2015 at 09:29, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>> wrote:<br>
><br>
><br>
> On Mon, Sep 14, 2015 at 6:19 PM, Alexander Heger<br>
> <<a href="mailto:alexander.heger@monash.edu">alexander.heger@monash.edu</a>> wrote:<br>
>><br>
>> Dear Nathan,<br>
>><br>
>> the gcc 5.1 comes by default with Fedora 22 - I probably would have to<br>
>> re-compile the entire python 3.5 with the older gcc. The link you<br>
>> sent does not seem promising that has been fixed, not sure the current<br>
>> gcc 5.2 (bugfix release) would do better. So best easiest for now may<br>
>> be to go with Matt's suggestion, I agree.<br>
>><br>
>> I this a bug in python 3.5 to rely on a broken gcc feature? Or maybe<br>
>> never meant to be be compiled with gcc 5.x? Fedora's python 3.4 is<br>
>> also compiled with gcc 5.1.1<br>
>><br>
>> ~>/bin/python3.4<br>
>> Python 3.4.2 (default, Jul 9 2015, 17:24:30)<br>
>> [GCC 5.1.1 20150618 (Red Hat 5.1.1-4)] on linux<br>
>> Type "help", "copyright", "credits" or "license" for more information.<br>
>> >>><br>
>><br>
>> btw, yt is the only package that broke, all others compiled fine.<br>
><br>
><br>
> Does yt build under python 3.4? If so I suspect it's an issue with python<br>
> 3.5. It could be an issue with the python build or a straight up bug in<br>
> Python 3.5. I don't have a test environment set up for Fedora so it's hard<br>
> for me to check.<br>
><br>
>><br>
>><br>
>> Best wishes,<br>
>> Alexander<br>
>><br>
>><br>
>> On 15 September 2015 at 01:52, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>><br>
>> wrote:<br>
>> > So the most important lines in the file you attached are here:<br>
>> ><br>
>> > In file included from<br>
>> > /home/alex/Python/include/python3.5m/pyatomic.h:12:0,<br>
>> > from<br>
>> > /home/alex/Python/include/python3.5m/Python.h:53,<br>
>> > from<br>
>> > build/src.linux-x86_64-3.5/yt/utilities/lib/geometry_utils.c:4:<br>
>> > /usr/lib/gcc/x86_64-redhat-linux/5.1.1/include/stdatomic.h:40:1:<br>
>> > sorry,<br>
>> > unimplemented: ‘_Atomic’ with OpenMP<br>
>> > typedef _Atomic _Bool atomic_bool;<br>
>> ><br>
>> ><br>
>> > So python.h is bringing in pyatomic.h, which is looking for stdatomic.h,<br>
>> > which in turn prints "sorrry, unimplemented" and breaks the build. See<br>
>> > the<br>
>> > following gcc bug:<br>
>> ><br>
>> > <a href="https://gcc.gnu.org/bugzilla/show_bug.cgi?id=65467" rel="noreferrer" target="_blank">https://gcc.gnu.org/bugzilla/show_bug.cgi?id=65467</a><br>
>> ><br>
>> > I believe downgrading to an older gcc release (before gcc 5.0) will<br>
>> > likely<br>
>> > fix this. An alternative would be to manually disable openmp support in<br>
>> > yt's<br>
>> > setup.py script as Matt suggested.<br>
>> ><br>
>> ><br>
>> > On Mon, Sep 14, 2015 at 10:25 AM, Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>><br>
>> > wrote:<br>
>> >><br>
>> >> Hi Alex,<br>
>> >><br>
>> >> Looks like you have some weird stuff going on with OpenMP. Probably<br>
>> >> best<br>
>> >> to manually disable it in yt/utilities/lib/setup.py by having it return<br>
>> >> false for the detection.<br>
>> >><br>
>> >> On Sun, Sep 13, 2015 at 10:10 PM, Alexander Heger<br>
>> >> <<a href="mailto:alexander.heger@monash.edu">alexander.heger@monash.edu</a>> wrote:<br>
>> >>><br>
>> >>> I know you don't yet quite support prime-time use of python 3.x.<br>
>> >>> But since this is in progress, I provide some feedback.<br>
>> >>><br>
>> >>> When doing a pip3 install yt I get the attached error message.<br>
>> >>><br>
>> >>> Best wishes,<br>
>> >>> Alexander<br>
>> >>><br>
>> >>><br>
>> >>><br>
>> >>><br>
>> >>><br>
>> >>> _______________________________________________<br>
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>> >>><br>
>> >><br>
>> >><br>
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</div></div></blockquote></div><br></div>