lib/libcompiler_rt/ builds llvm-project/compiler-rt including atomics (for arm there is additional sys/arm/arm/stdatomic.c).
Many packages have a dependency on lib/libcompiler_rt. lib/libcompiler_rt is installed to /usr/lib/libcompiler_rt.a. 
The symbols are hidden, which usually lead to benign ODR violations if both an executable and its DT_NEEDED get a copy of libcompiler_rt.a. 

However, atomic.o has a global lock pool, and having different lock pools would lead to non-synchronized atomic operations.

Prepare input files as attached at the end of this post.

% zsh a.sh
/tmp/b-9aaa82.o: reference to __atomic_compare_exchange
/usr/lib/libcompiler_rt.a(atomic.o): definition of __atomic_compare_exchange
/tmp/a-864004.o: reference to __atomic_compare_exchange
/usr/lib/libcompiler_rt.a(atomic.o): definition of __atomic_compare_exchange
9470401
/tmp/b-28139a.o: reference to __atomic_compare_exchange
/usr/lib/libgcc.a(atomic.o): definition of __atomic_compare_exchange
/tmp/a-1dceb9.o: reference to __atomic_compare_exchange
/usr/lib/libgcc.a(atomic.o): definition of __atomic_compare_exchange
9481088

The expected result is 10000000. libgcc.a has the same issue.
In practice it is extremely rare when two pieces of code operating on the same atomic lives in different link units.

---

cat > a.cc <<'eof'
#include <cstdint>
#include <iostream>
#include <thread>
#include <vector>
using namespace std;

#define REP(i, n) for (int i = 0; i < (n); i++)

constexpr int kIterations = 500'000;
__int128_t g;

void loop_b();
void loop_a() {
  REP(i, kIterations) {
    for(;;) {
      auto e = __atomic_load_n(&g, __ATOMIC_RELAXED), desired = e+1;
      if (__atomic_compare_exchange_n(&g, &e, desired, 0, __ATOMIC_RELAXED, __ATOMIC_RELAXED))
        break;
    }
  }
}

int main() {
  vector<thread> ts;
  REP(i, 10) ts.emplace_back(loop_a), ts.emplace_back(loop_b);
  for (auto &t : ts) t.join();
  cout << (int64_t)g << '\n';
}
eof
cat > a.sh <<'eof'
clang++ -O1 -fpic -Wno-atomic-alignment b.cc -shared -lcompiler_rt -o b.so -Wl,-y,__atomic_compare_exchange
clang++ -O1 -Wno-atomic-alignment a.cc ./b.so -lcompiler_rt -pthread -o a -Wl,-y,__atomic_compare_exchange
./a

clang++ -O1 -fpic -Wno-atomic-alignment b.cc -shared -o b.gcc.so -Wl,-y,__atomic_compare_exchange
clang++ -O1 -Wno-atomic-alignment a.cc ./b.gcc.so -pthread -o a.gcc -Wl,-y,__atomic_compare_exchange
./a.gcc
eof
cat > b.cc <<'eof'
#define REP(i, n) for (int i = 0; i < (n); i++)
extern __int128_t g;
constexpr int kIterations = 500'000;
void loop_b() {
  REP(i, kIterations) {
    for(;;) {
      auto e = __atomic_load_n(&g, __ATOMIC_RELAXED);
      auto desired = e + 1;
      if (__atomic_compare_exchange_n(&g, &e, desired, 0, __ATOMIC_RELAXED, __ATOMIC_RELAXED))
        break;
    }
  }
}
eof