Project: MARBL Configuration - Plankton Time!

This project is about setting up a MARBL configuration and any nuances we might want to consider.

Download this project by either:

Running the CrocoDash CLI command: crocodash template --output marbl_case.ipynb --machine glade --notebook crocodash.projects.marbl, then filling in the paths it leaves as placeholders
Copying the file from your CrocoDash checkout: gallery/crocodash/projects/marbl.ipynb

Grid Generation¶

MARBL is integrated into MOM6, so it’s pretty straightforward to set up. Since there are so many tracers, MARBL’s initial and boundary conditions come from a previous CESM run, which carries all of them.

Since MARBL adds cost, we will pick a small domain. Let’s rip through the first steps!

from pathlib import Path

from CrocoDash.grid import Grid
from CrocoDash.vgrid import VGrid
from CrocoDash.topo import Topo
from CrocoDash.case import Case


grid = Grid(
  resolution = 0.05, # in degrees
  xstart = 278.0, # min longitude in [0, 360]
  lenx = 5.0, # longitude extent in degrees
  ystart = 7.0, # min latitude in [-90, 90]
  leny = 5.0, # latitude extent in degrees
  name = "clear_marbl",
)

topo = Topo(
    grid = grid,
    min_depth = 9.5, # in meters
)

topo.set_from_dataset(    
    bathymetry_path = "<GEBCO_LOWRES>",
    longitude_coordinate_name="lon",
    latitude_coordinate_name="lat",
    vertical_coordinate_name="elevation"
)

topo.depth.plot()
vgrid  = VGrid.hyperbolic(
    nk = 75, # number of vertical levels
    depth = topo.max_depth,
    ratio=20.0 # target ratio of top to bottom layer thicknesses
)

# CESM case (experiment) name
casename = "lost_my_marbles"

# CESM source root (Update this path accordingly!!!)
cesmroot ="<CESM>"

# Place where all your input files go 
inputdir = Path("<inputdir>") / casename
    
# CESM case directory
caseroot = Path("<casedir>") / casename


case = Case(
    cesmroot = cesmroot,
    caseroot = caseroot,
    inputdir = inputdir,
    ocn_grid = grid,
    ocn_vgrid = vgrid,
    ocn_topo = topo,
    project = '<PROJECT>',
    job_queue = "<JOB_QUEUE>", # PBS queue the run is submitted to
    job_wallclock_time = "<WALLCLOCK_1H>", # hh:mm:ss walltime requested for the run
    override = True,
    machine = "derecho",
    compset = "CR1850MARBL_JRA" )

MARBL Forcing¶

We use a global MARBL file to set up the initial condition (It is regridded as part of the model run). We generate MARBL OBCs in the same exact way as the MOM6 OBC (we’re just adding >40 more tracers).

We need to provide the path to a MARBL run or have it default to a run to generate MARBL OBCs. What we’re going to use below defaults to a FIESTY run (https://www.sciencedirect.com/science/article/abs/pii/S0079661124001204). We do not support having separate physical vs MARBL forcings. All the forcings come from one product, which in this case is CESM POP Output, the old CESM ocean model.

case.configure_forcings(
    date_range=["2000-01-01 00:00:00", "2000-02-01 00:00:00"],
    product_name="CESM_POP_OUTPUT",
    function_name="get_cesm_single_variable_data",
    marbl_ic_filepath="<MARBL_IC>",   
)

case.process_forcings()

I’d mess with the NTASKS/ROOTPEs (give more ocean PEs) and build & submit!

Feel free to iterate with process forcings! You can run it on the command line with crocodash process --caseroot YOURCASEROOT --all (or name just the pieces you changed, e.g. --bc, --cice; see crocodash process -h)!