Hello Vassilios,
as mentioned earlier in the ET phone call, i have attached the par file used in the run...
i tried checking for the nans in the output, but the last hdf5 output was too many iterations earlier and they aren't visible in 1D ascii output either
as said, the puncture tracker actually aborted the run, not the nan checker...
Thank you for the parameter file. As a unsubstantiated guess, I would try what happens if you move the outer boundary further out. Right now it sits at 50M which I would find uncomfortably close if there is any say "junk" radiation (eg from setting up a BH with spin in flat background) present. I'd move it to at least 200M (ie two more levels of mesh refinement). Not sure how likely this explanation is since your NaNs appear after many (9) light crossing times.
Yours, Roland