STINNER Victor added the comment:

The problem is more general than Python: #include <stdatomic.h> fails in C++. 
Try to compiled atomic.cpp with g++, you will get the same error.

The following bug report in the glibc has been closed as WONTFIX:

It suggests to use the following code:

#ifdef __cplusplus
#include <atomic>
using namespace std;
#include <stdatomic.h>

I don't know if it works.

Added file:

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