Set up BGC case with CESM2.1

Set up BGC case with CESM2.1#

1: Check out a sandbox of the most recent version of CESM2.1#

Caveat: Support for coupled biogeochemistry in CESM3 is still under development. So this content describes biogeochemical features in the context of CESM2. For example, experiments use CESM2 resolutions.#

Run the following commands in the parent directory of where you have checked out versions of CESM3.#

Note that CESM2 manages versions of components of CESM with a tool called manage_externals, not git-fleximod, so the commands below differ from what you’ve used in CESM3.#

cd /glade/u/home/$USER/code
git clone https://github.com/ESCOMP/CESM.git cesm2.1.5
cd /glade/u/home/$USER/code/cesm2.1.5
git checkout cesm2.1.5
./manage_externals/checkout_externals

2: Set up a BGC case#

We will create two different cases and compare the case directories. We want to check if the differences make sense. You will NOT run the model in this challenge exercise.

Exercise: Set up a BGC control case

Create a case called b.e21.B1850.f19_g17.001 using the compset B1850 at f19_g17 resolution.

cd /glade/u/home/$USER/code/cesm2.1.5/cime/scripts
./create_newcase --case /glade/u/home/$USER/cases/b.e21.B1850.f19_g17.001 --compset B1850 --res f19_g17

Create a case called b.e21.B1850_BPRP.f19_g17.001 using the compset B1850_BPRP at f19_g17 resolution.

cd /glade/u/home/$USER/code/cesm2.1.5/cime/scripts
./create_newcase --case /glade/u/home/$USER/cases/b.e21.B1850_BPRP.f19_g17.001 --compset B1850 --res f19_g17

  • What happens when you run create_newcase? Follow the instructions to get this working, but don’t do it for real unless you know what you’re doing.

Run case.setup and preview_namelists for each case.

  • What changes occur when the carbon cycle is made prognostic?

POP BGC Specific Output#

ocn/hist/$CASE.pop.h.ecosys.nday1.????-??-??.nc

  • selected ocean ecosys variables at daily resolution

  • surface flux related, productivity, and functional group vertical integrals.

ocn/hist/$CASE.pop.h.ecosys.nyear1.????.nc

  • selected three dimensional ocean ecosys tracer budget terms.

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