Using std::atomic_uint64_t leads to "error: no type named 'atomic_uint64_t' in namespace 'std'"
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The issue may just be that <atomic> is not included. But not using these atomic aliases appears to be more common.
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clang -v of the failing command:
clang -cc1 version 11.0.0 based upon LLVM 11.0.0git default target
x86_64-unknown-linux-gnu
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I added #include <atomic> to bolt/include/bolt/Passes/ShrinkWrapping.h which may have fixed the issue.