<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Sep 14, 2015 at 6:19 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">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></blockquote><div><br></div><div>None of the others use OpenMP.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Best wishes,<br>
Alexander<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
On 15 September 2015 at 01:52, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>> wrote:<br>
> So the most important lines in the file you attached are here:<br>
><br>
> In file included from /home/alex/Python/include/python3.5m/pyatomic.h:12:0,<br>
> from /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: 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 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 likely<br>
> fix this. An alternative would be to manually disable openmp support in 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 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>
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