Update to ClimaAtmos v0.11.0 and ClimaLSM v0.2.3

[valeriabarra]

Purpose

The Purpose of this PR is to update the experiments/AMIP/modular environment to use the latest ClimaAtmos release, v0.10.0.

In order for CI integration tests to work, I also had to update the experiments/AMIP/moist_mpi_earth environment.

Closes #292 , #297 and #298

Content

• Modified compat entries in the top-level env, the experiments/AMIP/modular env, and the experiments/AMIP/moist_mpi_earth environments to be able to update using the Package manager
• Updated to the latest ClimaLSM v0.2.3 release
• Updated to the latest ClimaAtmos v0.11.0 release
• Updated the ClimaAtmos-related CLI options
• Updated to the most recent ClimaCore, ClimaLSM, and ClimaAtmos API

Review checklist

I have:

• followed the codebase contribution guide: https://clima.github.io/ClimateMachine.jl/latest/Contributing/
• followed the style guide: https://clima.github.io/ClimateMachine.jl/latest/DevDocs/CodeStyle/
• followed the documentation policy: https://github.com/CliMA/policies/wiki/Documentation-Policy
• checked that this PR does not duplicate an open PR.

In the Content, I have included

• relevant unit tests, and integration tests,

• appropriate docstrings on all functions, structs, and modules, and included relevant documentation.

• I have read and checked the items on the review checklist.

[charleskawczynski]

We'll need to add something like

      - echo "--- Instantiate amip modular env"
      - "julia --project=experiments/AMIP/modular/ -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
      - "julia --project=experiments/AMIP/modular/ -e 'using Pkg; Pkg.precompile()'"
      - "julia --project=experiments/AMIP/modular/ -e 'using Pkg; Pkg.status()'"

to the buildkite yaml for CI to work. I'm actually not sure how that environment is activated at the moment

[juliasloan25]

Looks good overall. I have one concern though - are you planning to merge this into main as is? It might be better to resolve the failing tests/CI before merging.

[valeriabarra]

Looks good overall. I have one concern though - are you planning to merge this into main as is? It might be better to resolve the failing tests/CI before merging.

Hi Julia, thank you. No, absolutely. The idea is not to merge this as is. Of course I want/need to fix CI. I am just also working on other things so I haven't back to this yet. Hopefully this afternoon.

[valeriabarra]

We'll need to add something like

      - echo "--- Instantiate amip modular env"
      - "julia --project=experiments/AMIP/modular/ -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
      - "julia --project=experiments/AMIP/modular/ -e 'using Pkg; Pkg.precompile()'"
      - "julia --project=experiments/AMIP/modular/ -e 'using Pkg; Pkg.status()'"

to the buildkite yaml for CI to work. I'm actually not sure how that environment is activated at the moment

It looks like in CI we're instantiating the other environment experiments/AMIP/moist_mpi_earth. Should I try to use this updated experiments/AMIP/modular in there instead?

[valeriabarra]

@charleskawczynski do you know what is going on with the Ubuntu-latest action?

[charleskawczynski]

@charleskawczynski do you know what is going on with the Ubuntu-latest action?

It looks like a ClimaLSM error:

home/runner/work/ClimaCoupler.jl/ClimaCoupler.jl/test/conservation_checker_tests.jl:120
  Got exception outside of a @test
  MethodError: no method matching (ClimaLSM.Parameters.LSMParameters{Float64, Float64, Float64})(::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64, ::Float64)
  Stacktrace:
    [1] macro expansion
      @ ~/work/ClimaCoupler.jl/ClimaCoupler.jl/test/conservation_checker_tests.jl:130 [inlined]
...

[charleskawczynski]

Probably the simplest thing to do, in this particular situation, would be to use their utility:

• At the top of this test directory, include(joinpath(pkgdir(ClimaLSM), "parameters", "create_parameters.jl"))
• Then use earth_param_set = create_lsm_parameters(FT) (this function is here) where it's breaking. There's probably been breaking changes to their internal parameter set.

[valeriabarra]

Probably the simplest thing to do, in this particular situation, would be to use their utility:

• At the top of this test directory, include(joinpath(pkgdir(ClimaLSM), "parameters", "create_parameters.jl"))
• Then use earth_param_set = create_lsm_parameters(FT) (this function is here) where it's breaking. There's probably been breaking changes to their internal parameter set.

I fixed it. It was a matter of updating the LSMParameters call, because its API had changed.

[valeriabarra]

This PR is ready for review!
Tests seem to be passing now.
Once approved, I'll reduce commits. Thanks all

[LenkaNovak]

Hi Valeria, thank you for this! To help with the crashing Buildkites, we’ll need to update the cli_options file by copying the Atmos CLI options here to under the ClimaAtmos flags

[valeriabarra]

Hi Valeria, thank you for this! To help with the crashing Buildkites, we’ll need to update the cli_options file by copying the Atmos CLI options here to under the ClimaAtmos flags

Yes, thank you. I realized that after I wrote my comment. I'll get to it on Monday. I think we're close!

[valeriabarra]

The issue was identified to be in the logic ClimaAtmos tries to prioritize parsed args and populate the toml file (see this line ). Once this is fixed in ClimaAtmos, I'll propagate the change here in the Coupler.

[valeriabarra]

YAY! CI finally passed.

@juliasloan25 , @charleskawczynski if you would like to give a final review, then if approved, I'll go ahead with squashing/reducing commits. Thanks everybody!

[juliasloan25]

looks good! Just a few small comments

[juliasloan25]

looks good! Just a few small comments

[valeriabarra]

bors r+

[bors]

Build failed:

• buildkite/climacoupler-ci

[valeriabarra]

Bors r+

[bors]

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