trying to install the yt package, most recent version 3.2.1 on python 3.5.0 using pip

pip3 install -U yt

error output attached. The same package installs fine with python 3.4.3, same compiler and also build from scratch, so the suspicion is that it is related to the new 3.5.0 version. The system installed is the current Fedora 22, gcc 5.1.1-4.

It looks like the problem is that yt uses OpenMP whereas OpenMP doesn't support atomic operations:

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;
 ^

I'm not sure that Include/pyatomic.h should be included by the main Include/Python.h header. We already skipped Include/pyatomic.h on C++ because this header is incompatible with C++.

When I just comment out the

#include "pyatomic.h" 

line, python 3.5.0 will no longer compile

gcc -pthread -c -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Werror=declaration-after-statement -I. -IInclude -I./Include -DPy_BUILD_CORE -o Programs/python.o ./Programs/python.c
In file included from Include/traceback.h:8:0,
from Include/Python.h:97,
from ./Programs/python.c:3:
Include/pystate.h:186:8: error: unknown type name ‘_Py_atomic_address’
PyAPI_DATA(_Py_atomic_address) _PyThreadState_Current;
^
Makefile:747: recipe for target 'Programs/python.o' failed
make: *** [Programs/python.o] Error 1

pystate.h:

/* Assuming the current thread holds the GIL, this is the
PyThreadState for the current thread.

   Issue python/cpython#67832: pyatomic.h is incompatible with C++ (yet). Disable
   PyThreadState_GET() optimization: declare it as an alias to
   PyThreadState_Get(), as done for limited API. */
#if !defined(Py_LIMITED_API) && !defined(__cplusplus)
PyAPI_DATA(_Py_atomic_address) _PyThreadState_Current;
#endif

"When I just comment out the << #include "pyatomic.h" >> line, python 3.5.0 will no longer compile"

Sure. My idea is to "disable" the header with we are not building Python itself. There is a nice define for that: Py_BUILD_CORE. See attached patch.

Since all symbols in pyatomic.h are prefixed by _Py, this header is fully part of the Python private API and so it's fine to modify it in a bugfix release (3.5.0 => 3.5.1).

If everything in the header is a _Py definition then I agree we should hide it in Python.h from the public.

if I just include this patch, some modules don't build:

(...)

gcc -pthread -fPIC -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Werror=declaration-after-statement -Ibuild/temp.linux-x86_64-3.5/libffi/include -Ibuild/temp.linux-x86_64-3.5/libffi -I/home/alex/Python-3.5.0/Modules/_ctypes/libffi/src -I./Include -I/home/alex/Python/include -I. -IInclude -I/usr/local/include -I/home/alex/Python-3.5.0/Include -I/home/alex/Python-3.5.0 -c /home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c -o build/temp.linux-x86_64-3.5/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.o -Wall -fexceptions
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c: In function ‘PyCSimpleType_from_param’:
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2062:15: error: ‘_PyThreadState_Current’ undeclared (first use in this function)
         if (Py_EnterRecursiveCall("while processing _as_parameter_")) {
               ^
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2062:15: note: each undeclared identifier is reported only once for each function it appears in
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2062:28: error: ‘__atomic_load_ptr’ undeclared (first use in this function)
         if (Py_EnterRecursiveCall("while processing _as_parameter_")) {
                            ^
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2062:66: error: argument 1 of ‘__atomic_load’ must be a non-void pointer type
         if (Py_EnterRecursiveCall("while processing _as_parameter_")) {
                                                                  ^
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2062:19: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
         if (Py_EnterRecursiveCall("while processing _as_parameter_")) {
                   ^
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2067:62: error: argument 1 of ‘__atomic_load’ must be a non-void pointer type
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2067:21: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
         Py_LeaveRecursiveCall();
                     ^
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2067:62: error: argument 1 of ‘__atomic_load’ must be a non-void pointer type
/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2067:139: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]

Failed to build these modules:
_ctypes _decimal _json
_pickle

So, apparently, more than just one spot needs to be fixed. I also tried just modifying the Python.h after install, but that does not do the trick either.

/home/alex/Python-3.5.0/Modules/_ctypes/_ctypes.c:2062:15: error: ‘_PyThreadState_Current’ undeclared (first use in this function)
         if (Py_EnterRecursiveCall("while processing _as_parameter_")) {
               ^

Ah yes, if you check the fix for C++ (changeset cb05b6d7aacd), I also had to modify pystate.h.

Please try pyatomic-2.patch which hides more CPython internals in public headers.

I created a venv with a Python patched with pyatomic-2.patch: I successfully installed yt. yt depends on numpy & Cython: good news, numpy & Cython were compiled correctly. These two libraries are well known users of the Python C API. It's not enough to check if this change breaks modules on PyPI, but it's still a good news :-)

Would there be a way to expose these internals rather than hiding them?

Would there be a way to expose these internals rather than hiding them?

Here is the issue is that pyatomic.h cannot be compiled on OpenMP. We had the same issue with C++. In fact, it doesn't make sense to compile pyatomic.h differently to access an atomic variable from an extension module. We must always use exactly the same implementation, otherwise bad things will happen.

A solution for that is to hide the implementation details and only expose high level APIs.

For example, pyatomic.h must be completly hidden.

A consequence is that the _PyThreadState_Current variable must be hidden to. _PyThreadState_Current is an implementation detail, you must not access it directly.

The PyThreadState_GET() macro uses directly the _PyThreadState_Current variable. So the solution to expose the "PyThreadState_GET" symbol (not necessary as a macro) is to define it as an alias to the PyThreadState_Get() *function*.

The advantage of using a function is that we don't expose implementation details to third-party extensions, it avoids the risk of ABI incompatibilies.

Understood and agreed. Second patch looks good to me.

Cython calls PyThreadState_GET() in pretty much every helper function that deals with exceptions, but I doubt that the potential speed difference is going to be relevant in the real world. And we target CPython's API level anyway, not the ABI, so the C code will just adapt at compile time.

New changeset d4fcb362f7c6 by Victor Stinner in branch '3.5':
Issue bpo-25150: Hide the private _Py_atomic_xxx symbols from the public
https://hg.python.org/cpython/rev/d4fcb362f7c6

I pushed my fix pyatomic-2.patch to Python 3.5 and 3.6.

Thanks for the bug report Alexander Heger!

Dear Victor,

yes, you patch seems to fix the yt install. Thank you very much!

I hope this can be included in 3.5.1.

Best wishes,
Alexander

Yes my fix will be part of Python 3.5.1 release.

Should it work with /configure '--with-cxx-main=g++' && make?

Because currently it doesn't:

g++ -c -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Werror=declaration-after-statement -I. -IInclude -I./Include -DPy_BUILD_CORE -o Programs/python.o ./Programs/python.c
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from Include/pyatomic.h:10:0,
from Include/Python.h:53,
from ./Programs/python.c:3:
/usr/lib64/gcc/x86_64-pld-linux/5.2.0/include/stdatomic.h:40:9: error: ‘_Atomic’ does not name a type
[...]

(testing 3.5.0 + patch for this issue from hg)

Same for 3.5 branch from hg (git mirror actually).

Hi,
Just a few words to tell you that I had the same problem to compile scipy 0.16.0 with mkl libraries under python 3.5 and linux fedora 22. Pyatomic-2.patch solved the problem.
Thanks

"Pyatomic-2.patch solved the problem."

Great! The good news is that the Python 3.5.1 release has now a schedule: https://www.python.org/dev/peps/pep-0478/

"3.5.1 final: December 6, 2015"

seems to work now with 3.5.1rc1

On 5 November 2015 at 23:01, STINNER Victor <report@bugs.python.org> wrote:

STINNER Victor added the comment:

"Pyatomic-2.patch solved the problem."

Great! The good news is that the Python 3.5.1 release has now a schedule: https://www.python.org/dev/peps/pep-0478/

"3.5.1 final: December 6, 2015"

----------

---

Python tracker <report@bugs.python.org>
<http://bugs.python.org/issue25150\>

---

cool

2015-11-23 22:19 GMT+01:00 Alexander Heger <report@bugs.python.org>:

Alexander Heger added the comment:

seems to work now with 3.5.1rc1

On 5 November 2015 at 23:01, STINNER Victor <report@bugs.python.org> wrote:
>
> STINNER Victor added the comment:
>
> "Pyatomic-2.patch solved the problem."
>
> Great! The good news is that the Python 3.5.1 release has now a schedule: https://www.python.org/dev/peps/pep-0478/
>
> "3.5.1 final: December 6, 2015"
>
> ----------
>
> _______________________________________
> Python tracker <report@bugs.python.org>
> <http://bugs.python.org/issue25150\>
> _______________________________________

----------

---

Python tracker <report@bugs.python.org>
<http://bugs.python.org/issue25150\>

---

I think this should be reconsidered. I understand the desire to compile Python with OpenMP. But the resolution here is hiding _Py_atomic symbols all the time, even when OpenMP isn't involved, and even when building a standard extension module.

Case in point: if I want to include "internal/pystate.h" from _pickle.c, I get the following error:

"""
In file included from ./Include/internal/pystate.h:12:0,
from /home/antoine/cpython/default/Modules/_pickle.c:10:
./Include/internal/ceval.h:14:5: error: unknown type name ‘_Py_atomic_int’
_Py_atomic_int calls_to_do;
^
"""

(see bpo-34128 for context)

This issue is closed. Would you mind to either reopen it or create a new issue?

Yes, why not fix this by putting the offending code under "#ifndef _OPENMP"?

What would be even better if is pyatomic.h wasn't included in Python.h, which should be fine since pyatomic.h doesn't have any public APIs. Maybe we can do that for 3.8.

(Ah, Benjamin restarted the discussion, so I reopen this issue.)

I understand the desire to compile Python with OpenMP.

I'm not sure that I understood the use case. Do you want to only compile Python core ("python3" binary") or just stdlib C extensions, or both?

But the resolution here is hiding _Py_atomic symbols all the time, even when OpenMP isn't involved, and even when building a standard extension module.

Sorry, but I don't understand the problem. Why is it an issue to hide _Py_atomic symbols?

This issue is very specific to *third party* extensions, not C extensions which are part of the standard library. That's why I asked if it wouldn't be better to open a new issue, if your use case concerns the stdlib and/or Python core.

Python.h does not include pyatomic.h in Python 3.8: the header file moved to the internal C API. The initial issue is fixed, so I close again the issue.