Whenever the application is run alongside with a Java Agent (-javaagent), there is a chance that the agent can tag the objects in the heap using JVMTI tagging. Agents can use tagging for various reasons that are not in the scope of this handbook, but there is a GC-related performance issue that can start affecting the latency and throughput of your application if tagging is applied to a large subset of objects inside the heap.
The problem is hidden in the native code where JvmtiTagMap::do_weak_oops iterates over all the tags during each garbage collection event and performs a number of not-so-cheap operations for all of them. To make things worse, this operation is performed sequentially and is not parallelized.
With a large number of tags, this implies that a large part of the GC process is now carried out in a single thread and all the benefits of parallelism disappear, potentially increasing the duration of GC pauses by an order of magnitude.
To check whether or not a particular agent can be the reason for extended GC pauses, you would need to turn on the diagnostic option of –XX:+TraceJVMTIObjectTagging. Enabling the trace will allow you to get an estimate of how much native memory the tag map consumes and how much time the heap walks take.
If you are not the author of the agent yourself, fixing the problem is often out of your reach. Apart from contacting the vendor of a particular agent you cannot do much. In case you do end up in a situation like this, recommend that the vendor clean up the tags that are no longer needed.