Add MOM6 mini-app section for GPU work

documentation/docs/pages/season2.md

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 # Season 2
+
+## Navigating MOM6 as a non-oceanographer: a MOM6 mini-app for GPU work.
+
+Date: 7/05/2026.
+
+Presenter: Jorge Gálvez Vallejo (@JorgeG94).
+
+Link to repo: [hackathon_mom6_miniapp](https://github.com/JorgeG94/hackathon_mom6_miniapp)
+
+### Brief Intro
+
+Joining a new project in a field you did not study can be extremely daunting! But fear not, for 
+fortune favors the brave. I'd say there are three options here:
+
+- You are an oceanographer that has little knowledge of high performance computing 
+- You are a high performance computing person that has no knowledge of oceanography 
+- You are a new student and don't know either
+
+The third one naturally has the most to overcome, but they also have the most time. The first one
+is simply "we have to learn how to code", the second one is "I have to learn oceanography". However, 
+the second one might not need to learn a lot of oceanography since their contributions don't depend 
+on them understanding the physics of the ocean dynamics. 
+
+I am a stubborn person that doesn't like to write code I don't understand, so I basically like to 
+create more work for myself.  
+
+### Detailed notes (flow of consciousness) 
+
+As an HPC person whose goal is to either optimize code or port it to different architectures the key 
+aspect to understand is *what are the bottlenecks?* in the current code. In ocean simulations, to my 
+annoyance, there is no _one_ routine that dominates 80% of the time. This makes my work harder, usually
+one can quickly say "ah yes, the calculation of this physical thing takes most of the time" so one spends
+the most time there. Then naturally you go ask the people that work on the codebase about the bottlenecks and
+because everyone is using it for a different thing you will hear different things, this is where the oceanography
+knowledge becomes useful! 
+
+What is the best way to understand a gigantic codebase with thousands of lines of code? Simplify it! I.e. the creation of a mini-app. 
+This is also the best thing to do for a hackathon, because you can capture algorithmic complexity, main pain points, and you 
+end up with a smaller application that is easy to build, easy to verify, and low stakes if you completely break it! 
+
+How does one create a mini-app? First, ask the oceanographers what are the pain points! They'll quickly tell you about the 
+"dynamical core", which is where the basic physics are solved, i.e. the fluid mechanics part of the code. The crucial bit 
+here is to adopt a "how hard can it be?" mentality, be positive. I was quickly pointed to the file `MOM_dyn_split_RK2.F90`, 
+which contains the main RK2 timestepping procedure. Fortran is our friend here, there is not a lot of object orientation 
+shenanigans happening, i.e. what you read is what you get (most of the time). The RK2 step can be summarized as:
+
+```fortran 
+!! The split RK2 scheme:
+!!   1. Predictor phase:
+!!      - Compute horizontal viscosity
+!!      - Compute Coriolis/momentum advection (CAu, CAv)
+!!      - Apply vertical viscosity
+!!      - Advance barotropic mode (fast 2D dynamics)
+!!      - Update layer thicknesses via continuity
+!!   2. Corrector phase:
+!!      - Recompute tendencies with updated state
+!!      - Apply vertical viscosity
+!!      - Final barotropic step
+!!      - Final continuity update
+!!
+```
+
+Don't get too distracted by initialization procedures, those might look ugly but once you pay attention they are simply setting arrays
+to something. The above algorithm has done most of the work for us now! We now know what routines we need to look for:
+
+- Horizontal/Vertical viscosities
+- Coriolis 
+- Barotropic solver 
+- Continuity
+
+A key concept here can be extracted from MOM, the first M means "modular". Each physics engine should be a module, i.e. it should be able to 
+be run as standalone. Why? Because if I only want to optimize the Coriolis routines, why should I have to run everything else? So when creating a mini-app
+always try to have a separation of concerns. 
+
+We go into the magical place that is `MOM6/src/core`, which is where most of the routines we're interested in are. The viscosities are _parametrizations_, i.e. 
+approximations to extremely annoying physics. If you're feeling adventurous code up a non-hydrostatic solver that tries to resolve the vertical physics. It is
+_ a w f u l_. Here we have:
+
+```
+MOM_barotropic.F90
+MOM_continuity_PPM.F90
+MOM_CoriolisAdv.F90
+```
+
+So then we follow the `MOM_dyn_split_RK2.F90` to find the function names that are the most interesting, for simplicity we will do the `call btstep(..)`. Inside
+a MOM6 subroutine, we can think of them like:
+
+```fortran 
+subroutine btstep(....)
+real :: x
+integer :: y
+logical :: a 
+
+! indices mapping 
+is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = GV%ke 
+
+! bookkeeping (timing, profiling) 
+
+if(OBC) then 
+
+endif 
+
+! halo updates (look for do_group_pass)
+call create_group_pass(...)
+
+! begin real work 
+...
+
+end subroutine btstep
+```
+This is not the rule everywhere, especially in helper functions and subroutines. But realizing that _most_ do some bookkeeping, accounting at the start, and then 
+they check for configs, such as `OBCs` etc. will make your life less overwhelming. Once in, the magic is just realizing the loops are just loops! 
+
+```fortran 
+      do j=js,je ; do I=is-1,ie
+        uhbt0(I,j) = uhbt(I,j) - find_uhbt(dt*ubt(I,j), BTCL_u(I,j)) * Idt
+      enddo ; enddo
+```
+
+As you go into the routine you'll realize that there are patterns. Certain routines loop over certain indices, there's `u`s and `v`s and you start quickly 
+noticing how the algorithms are structured. This is the way, you simply just continue doing this _with a lot of patience_. 
+
+The mini-app is a work of hackathon and obsession, trying to compare lots of stuff (serial, openmp, openacc, cuda-fortran) just to get knowledge about the 
+advantages and disadvantages of each approach. Testing performance without having to worry too much about breaking MOM6. 
+
+
+
+
 ## Navier Stokes -> stacked shallow water (adiabatic)
 ## Generalised vertical coordinates
 ## Vertical Lagrangian remapping