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Your shader looks fine. My guess is that we're hitting some kind of performance issue related to incrementing the atomic counter. If everything needed to run the sample is in the GitHub repo you linked to, we can grab the code and run it here. We'll do that next and get back to you.
Thanks for your feedback, I included source of all deps Inside the repo, it only requires CMake to generate the visual studio solution.
(which should be located in a subfolder inside YAGF/ folder, I usually put it in YAGF/bld)