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IIUC you sent the thread dump to Daniel privately. I doubt very much this is what he was meaning. More probably: generate that thread dump, paste it somewhere and post the link here.
Another thing wrt this: do diagnose it the first step is even to look at your gc behaviour. For that your generally enable gc logs and use a tool to analyse them and see what it gives. Looking for things like: how often does the gc chime in, how many full gc in proportion, max observed pause...
If you can generate a gc log, and post it too that could help(in that case give precise details as to when you see issues in the UI to correlate timestamps).
HTH
PS: gc logs should always be enabled, even in production.
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"Handling POST /jenkins/view/Dashboard/timeline/data/ from <ip> : http-bio-8080-exec-643" Id=40861 Group=main
BLOCKED on hudson.model.RunMap@1e73d746 owned by "Handling POST /jenkins/view/Dashboard/timeline/data/ from <ip> : http-bio-8080-exec-547" Id=40663
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