Hello Andrea,
As told a few times in other posts, if a segmentation fault or a NaN (Not a Number) occurs, you should use a debug configuration with debug options to investigate.
See e.g. the S11.gfortran.debug configuration in the $HOMETEL/configs/systel.edf.cfg configuration file, in particular the flag fflags_debug_gfo for gfortran compiler.
fflags_debug_gfo: -g -Wall -fcheck=all -fbacktrace -fbounds-check -finit-integer=-1 -finit-real=nan -ffpe-trap=invalid,zero,overflow
It will show in which subroutine the issue/nan/segfault occurs, the first suspicious line and may help you to change something in your computation.
In your case, I have seen that you have negative depths in sources/khione/source_hydro_icover.f:
IF( H%R(I).LT.EPS ) SP_EAU =
& MAX( SP_EAU, SQRT(GRAV*(EPS-H%R(I))*H%R(I)/EPS) )
which is not good.
You should better user TREATMENT OF NEGATIVE DEPTHS = 2 rather than 1 which allows negative depths (even slightly negative). You should then use SUPG OPTION = 0;0
Just after, I have seen that you use SCHEME FOR ADVECTION OF TRACERS = 1 (i.e. method of characteristics which is not conservative and shoud not be used for tracers). You can try scheme = 13 e.g. which works with tidal flats (but is quite diffusive).
Using 16 cores for only 7783 triangles in your mesh may be useless. I would be surprised that you get the best performances with so many cores.
Anyway, I would suggest you to use recommended option for the hydrodynamics part, described in the TELEMAC-2D user manual. I have not read your whole steering file carefully but you may use other not recommended options.
Hope this helps,
Chi-Tuan