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Today, WASI does not support atomics. Support for WASI in Abseil was added in #1509 and needs to be refreshed.
Note that there is a roadmap item for wasi that will give us access to atomics via the component model's cooperative threads feature. Implementations are in progress but this may take a few months and so in the mean time, we need this fix.
I created an example with the necessary stubs that are missing from upstream abseil and validated that these can be removed with the changes in this PR: https://github.com/ricochet/wasi-protobuf/blob/main/wasi-build/wasi_stubs.cpp