Just a hypothesis.

During these off-peak hours some other applications are actively running
(maintenance etc.), and as java is not intensively used, its memory is swapped
to the hard disks.

Thus, when it awakens and does the GC, it takes so much time to wake up
the memory walking through it to collect the garbage.


What is memory consumption at night time? Are there memory-intensive
tasks being performed at that time?

May be restarting the tomcat can be scheduled after all those are
done? (Or a forced GC, or filling memory with a bunch of dummy
objects, up to Runtime.freeMemory()?)

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