Comment (by Roland Haas):

I started to look into this. I certainly still happens, and can be reproduced with a slightly simplified partfile (2 reflevels, 1 mpi rank, euler instead of rk4 time stepping, 0 timesteps) and shows nan in the prolongation region of reflevel 1 on timelevel 1 (but not tl 2 it seems so really only when interpolation in time is required). I will poke around a bit more.

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Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2554/init_3_timelevels-produces-nans-on-past