Hi, I appreciate the help. I really want to figure this out.
I was wondering if tiling was an issue. I tried NtileI = 1, NtileJ = 8 with the same ocean_ini.nc file and the model output appears to be the same.
The 2dx-noise appears when a larger scale mode structure develops after about 1.5 years. When I turn up the horizontal mixing, I can suppress the noise and this structure too but I'd like to see the instability develop. Yes, the noise does appear to arise first in the southern part of the domain. I have NS walls and EW periodic.
I tried turning off the ana_sst so that the surface heat flux is zero but that didn't help.
The last couple days, I've been going to finer x-resolution, dx = .14 deg, dy = .28 deg. and ramping up the horizontal mixing with the hope of damping this grid noise without damping the larger scale structure. Even VISC4 = 10^13 m^4/s, which seems quite large, and TNU4 = 10^10 m^4/s still is unable to remove it.
For one of the runs with LMD and convection on in the y-z plane at an x-grid point, there are alternating secondary cells (v,w) within the surface mixed layer. At one x-grid point over, these secondary cells have the same magnitude and similar structure but rotate in the opposite direction. From the surface, it appears as 2dx grid-noise in the surface v-field. I'm just not sure why these circulations would alternate direction every x-grid point. I'm not sure if it's related to the cells seen in this post:
https://www.myroms.org/forum/viewtopic.php?f=14&t=917.
I'm going to try Smagorinsky as well and see if that helps.