It definitely makes sense to have a look at gc activity, but I would suggest looking at safepoints from a broader perspective. Just use -XX:+PrintGCApplicationStoppedTime to see what's going on. If it's safepoints, you could get more details with safepoint statistics.
Also, benchmark runs in java may appear undeterministic simply because compilation happens in background threads by default and some runs may exhibit a different runtime profile since the compilation threads receive their time slice in different moments throughout the benchmark.
Are the results also jittery when run entirely in interpreted mode? It may be worth to experiment with various compilation settings (ie. disable tiered compilation, employ different warmup strategies, play around with compiler control).
Are you employing any sort of affinitizing threads to cpus?
Are you running on a multi-socket setup?
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Are you benchmarking on a multi-socket/NUMA server?
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