From bb9d6d150c805c72267618fd627cb0009dfca557 Mon Sep 17 00:00:00 2001 From: nefrathenrici Date: Tue, 9 Apr 2024 14:03:52 -0700 Subject: [PATCH] Add calibration framework, perfectmodel experiment --- .buildkite/pipeline.yml | 13 + .github/workflows/calibration_test.yml | 22 + .github/workflows/ci.yml | 6 +- .gitignore | 2 + Artifacts.toml | 7 + Project.toml | 2 +- calibration/README.md | 23 + .../Artifacts.toml | 6 + .../Manifest.toml | 2873 +++++++++++++++++ .../Project.toml | 14 + .../model_config.yml | 18 + .../model_interface.jl | 54 + .../observation_map.jl | 34 + .../pipeline.sbatch | 33 + .../postprocessing.jl | 91 + .../prior.toml | 5 + calibration/model_interface.jl | 69 + calibration/test/Manifest.toml | 2792 ++++++++++++++++ calibration/test/Project.toml | 12 + calibration/test/e2e_test.jl | 170 + calibration/test/interface.jl | 33 + calibration/test/model_config.yml | 15 + calibration/test/prior.toml | 3 + 23 files changed, 6295 insertions(+), 2 deletions(-) create mode 100644 .github/workflows/calibration_test.yml create mode 100644 calibration/README.md create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Artifacts.toml create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Manifest.toml create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Project.toml create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/model_config.yml create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/model_interface.jl create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/observation_map.jl create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/pipeline.sbatch create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/postprocessing.jl create mode 100644 calibration/experiments/sphere_held_suarez_rhoe_equilmoist/prior.toml create mode 100644 calibration/model_interface.jl create mode 100644 calibration/test/Manifest.toml create mode 100644 calibration/test/Project.toml create mode 100644 calibration/test/e2e_test.jl create mode 100644 calibration/test/interface.jl create mode 100644 calibration/test/model_config.yml create mode 100644 calibration/test/prior.toml diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index f06bbf26d14..4054e7a3670 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -39,6 +39,11 @@ steps: - "julia --project=perf -e 'using Pkg; Pkg.precompile()'" - "julia --project=perf -e 'using Pkg; Pkg.status()'" + - echo "--- Instantiate calibration/test" + - "julia --project=calibration/test -e 'using Pkg; Pkg.instantiate(;verbose=true)'" + - "julia --project=calibration/test -e 'using Pkg; Pkg.precompile()'" + - "julia --project=calibration/test -e 'using Pkg; Pkg.status()'" + - echo "--- Download artifacts" - "julia --project=examples artifacts/download_artifacts.jl" @@ -487,6 +492,14 @@ steps: agents: slurm_mem: 20GB + - group: "Calibration" + steps: + - label: "Calibration interface unit tests" + command: julia --project=calibration/test calibration/test/interface.jl + - label: "end to end test" + command: julia --project=calibration/test calibration/test/e2e_test.jl + artifact_paths: "calibration_end_to_end_test/*" + - group: "Diagnostic EDMFX" steps: diff --git a/.github/workflows/calibration_test.yml b/.github/workflows/calibration_test.yml new file mode 100644 index 00000000000..a71f58a730c --- /dev/null +++ b/.github/workflows/calibration_test.yml @@ -0,0 +1,22 @@ +name: Calibration +on: + push: + tags: '*' + pull_request: + merge_group: + +jobs: + test: + name: ClimaCalibrate E2E Test + runs-on: ubuntu-latest + timeout-minutes: 30 + steps: + - uses: julia-actions/cache@v2 + - uses: julia-actions/julia-buildpkg@v1 + - uses: actions/checkout@v4 + - uses: julia-actions/setup-julia@v2 + with: + version: '1.10' + - run: | + julia --project=calibration/test -e 'using Pkg; Pkg.instantiate(;verbose=true)' + julia --project=calibration/test calibration/test/e2e_test.jl diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b2198798c63..9517dca9170 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -18,7 +18,7 @@ jobs: test: name: ci ${{ matrix.version }} - ${{ matrix.os }} runs-on: ${{ matrix.os }} - timeout-minutes: 30 + timeout-minutes: 45 strategy: fail-fast: false matrix: @@ -38,6 +38,10 @@ jobs: version: ${{ matrix.version }} arch: ${{ matrix.arch }} - uses: julia-actions/julia-buildpkg@v1 + - name: Calibration E2E Test + run: | + julia --project=calibration/test -e 'using Pkg; Pkg.instantiate(;verbose=true)' + julia --project=calibration/test calibration/test/e2e_test.jl - uses: julia-actions/julia-runtest@v1 - uses: julia-actions/julia-processcoverage@v1 - uses: codecov/codecov-action@v4 diff --git a/.gitignore b/.gitignore index d59f15fdb9f..a8505b54376 100644 --- a/.gitignore +++ b/.gitignore @@ -43,6 +43,8 @@ test/Manifest.toml *.hdf5 *.h5 *.g +*.lock +*.loc # misc .DS_Store diff --git a/Artifacts.toml b/Artifacts.toml index 81a5be8599a..0417c41197d 100644 --- a/Artifacts.toml +++ b/Artifacts.toml @@ -4,3 +4,10 @@ git-tree-sha1 = "9da4af348af2606764e5e2c94d9439714221dff1" [[aerosol2005.download]] sha256 = "952d723b8462439c266dc0df79d0d4e71f774559edb941e03b7979e8ad743f56" url = "https://caltech.box.com/shared/static/chmel1vdthfvfac0yl61ayw2jqnjzr2c.gz" + +[atmos_held_suarez_obs] +git-tree-sha1 = "d93ff2958e12d6bba6e8343bfa73554390df52e4" + + [[atmos_held_suarez_obs.download]] + sha256 = "f5d63df2bab849632bd2fcd5a4e3165465d1898e1a5fbee6e5fe07f5b3e57fc3" + url = "https://caltech.box.com/shared/static/sbn6afsgn2xzxi5n0ffs928otstshjvi.gz" diff --git a/Project.toml b/Project.toml index f73f396987e..ecf9e60c9de 100644 --- a/Project.toml +++ b/Project.toml @@ -52,7 +52,7 @@ AtmosphericProfilesLibrary = "0.1" ClimaComms = "0.6.2" ClimaCore = "0.14.6" ClimaDiagnostics = "0.2" -ClimaParams = "0.10.4" +ClimaParams = "0.10.8" ClimaTimeSteppers = "0.7.32" ClimaUtilities = "0.1.3" CloudMicrophysics = "0.18, 0.19, 0.20" diff --git a/calibration/README.md b/calibration/README.md new file mode 100644 index 00000000000..2246e2db3d1 --- /dev/null +++ b/calibration/README.md @@ -0,0 +1,23 @@ +# ClimaAtmos Calibration Experiments + +This directory contains the model interface (`model_interface.jl`) for ClimaCalibrate and folders (within `experiments/`) for reproducing calibration experiments. + +## Current Experiments + +### sphere_held_suarez_rhoe_equilmoist + +A perfect-model calibration, using ClimaAtmos v0.24.0. + +- Configuration: 0-moment microphysics scheme, spherical with Held-Suarez forcing. +- Observational data: zonal and 60-day time average air temperature at 242m altitude. Provided by [ClimaArtifacts](https://github.com/CliMA/ClimaArtifacts/tree/main/atmos_held_suarez_obs). +- Parameter being calibrated: `equator_pole_temperature_gradient_wet` + +For more details, see the experiment directory. + +To reproduce the results, on the Caltech central cluster run + +```sbatch calibration/experiments/sphere_held_suarez_rhoe_equilmoist/pipeline.sbatch``` + +## New Experiments + +To set up your own experiment, please follow the [setup guide](https://clima.github.io/ClimaCalibrate.jl/dev/atmos_setup_guide/). diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Artifacts.toml b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Artifacts.toml new file mode 100644 index 00000000000..c57306fc7eb --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Artifacts.toml @@ -0,0 +1,6 @@ +[atmos_held_suarez_obs] +git-tree-sha1 = "d93ff2958e12d6bba6e8343bfa73554390df52e4" + + [[atmos_held_suarez_obs.download]] + sha256 = "f5d63df2bab849632bd2fcd5a4e3165465d1898e1a5fbee6e5fe07f5b3e57fc3" + url = "https://caltech.box.com/shared/static/sbn6afsgn2xzxi5n0ffs928otstshjvi.gz" diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Manifest.toml b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Manifest.toml new file mode 100644 index 00000000000..7c03b1fe0b8 --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Manifest.toml @@ -0,0 +1,2873 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.4" +manifest_format = "2.0" +project_hash = "61d99b62ba82ddc58dc08a505b8e349985ee11cf" + +[[deps.ADTypes]] +git-tree-sha1 = "2314e58e823f0fd6ee02dbbecb997370f501dd4a" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "1.5.0" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesEnzymeCoreExt = "EnzymeCore" + +[[deps.AMD]] +deps = 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"3.5.0+0" diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Project.toml b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Project.toml new file mode 100644 index 00000000000..ee61aa211d5 --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/Project.toml @@ -0,0 +1,14 @@ +[deps] +CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" +ClimaAnalysis = "29b5916a-a76c-4e73-9657-3c8fd22e65e6" +ClimaAtmos = "b2c96348-7fb7-4fe0-8da9-78d88439e717" +ClimaCalibrate = "4347a170-ebd6-470c-89d3-5c705c0cacc2" +ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" +ClimaUtilities = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +EnsembleKalmanProcesses = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d" +JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819" +YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" + +[compat] +ClimaAtmos = "=0.24.0" diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/model_config.yml b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/model_config.yml new file mode 100644 index 00000000000..0977e66f8f2 --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/model_config.yml @@ -0,0 +1,18 @@ +dt: 500secs +t_end: 560days +ode_algo: ARS343 +moist: equil +forcing: held_suarez +precip_model: 0M +job_id: sphere_held_suarez_rhoe_equilmoist +output_dir: output/sphere_held_suarez_rhoe_equilmoist +# This filepath is only valid on the Caltech central cluster, to reproduce this path run: +# using ClimaUtilities.ClimaArtifacts; artifact = @clima_artifact("atmos_held_suarez_obs") +# restart_file = joinpath(artifact, "day200.0.hdf5") +restart_file: /groups/esm/ClimaArtifacts/artifacts/atmos_held_suarez_obs/day200.0.hdf5 +output_default_diagnostics: false +diagnostics: + - reduction_time: average + short_name: ta + period: 60days + writer: nc diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/model_interface.jl b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/model_interface.jl new file mode 100644 index 00000000000..ad52f3ae30f --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/model_interface.jl @@ -0,0 +1,54 @@ +import ClimaAtmos as CA +import YAML +import ClimaComms +@static pkgversion(ClimaComms) >= v"0.6" && ClimaComms.@import_required_backends +using ClimaUtilities.ClimaArtifacts +import ClimaCalibrate: + set_up_forward_model, run_forward_model, path_to_ensemble_member + +""" + set_up_forward_model(member, iteration, experiment_dir::AbstractString) + set_up_forward_model(member, iteration, config_dict::AbstractDict) + +Return an AtmosConfig object for the given member and iteration. + +Turns off default diagnostics and sets the TOML parameter file to the member's path. +This assumes that the config dictionary has an `output_dir` key. +""" +function set_up_forward_model(member, iteration, experiment_dir::AbstractString) + config_dict = YAML.load_file(joinpath(experiment_dir, "model_config.yml")) + set_up_forward_model(member, iteration, config_dict::AbstractDict) +end + +function set_up_forward_model(member, iteration, config_dict::AbstractDict) + output_dir = config_dict["output_dir"] + member_path = path_to_ensemble_member(output_dir, iteration, member) + config_dict["output_dir"] = member_path + parameter_path = joinpath(member_path, "parameters.toml") + if haskey(config_dict, "toml") + push!(config_dict["toml"], parameter_path) + else + config_dict["toml"] = [parameter_path] + end + + # Turn off default diagnostics + config_dict["output_default_diagnostics"] = false + return CA.AtmosConfig(config_dict) +end + +""" + run_forward_model(atmos_config::CA.AtmosConfig) + +Run the atmosphere model with the given an AtmosConfig object. +Currently only has basic error handling. +""" +function run_forward_model(atmos_config::CA.AtmosConfig) + simulation = CA.get_simulation(atmos_config) + sol_res = CA.solve_atmos!(simulation) + if sol_res.ret_code == :simulation_crashed + !isnothing(sol_res.sol) && sol_res.sol .= eltype(sol_res.sol)(NaN) + error( + "The ClimaAtmos simulation has crashed. See the stack trace for details.", + ) + end +end diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/observation_map.jl b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/observation_map.jl new file mode 100644 index 00000000000..937eadb178e --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/observation_map.jl @@ -0,0 +1,34 @@ +import EnsembleKalmanProcesses: TOMLInterface +import ClimaCalibrate: observation_map, ExperimentConfig +import ClimaAnalysis: SimDir, get, slice, average_lat, average_lon + +function observation_map(iteration) + ensemble_size = 10 + output_dir = joinpath("output", "sphere_held_suarez_rhoe_equilmoist") + single_member_dims = (1,) + G_ensemble = Array{Float64}(undef, single_member_dims..., ensemble_size) + + for m in 1:ensemble_size + member_path = + TOMLInterface.path_to_ensemble_member(output_dir, iteration, m) + simdir_path = joinpath(member_path, "output_active") + if isdir(simdir_path) + simdir = SimDir(simdir_path) + G_ensemble[:, m] .= process_member_data(simdir) + else + G_ensemble[:, m] .= NaN + end + end + return G_ensemble +end + +const meters = 1.0 +const days = 86400.0 +# Cut off first 120 day to get equilibrium, take second level slice +function process_member_data(simdir::SimDir) + isempty(simdir.vars) && return NaN + ta = get(simdir; short_name = "ta", reduction = "average", period = "60d") + zonal_avg_temp_observations = + slice(average_lat(average_lon(ta)), z = 242meters) + return slice(zonal_avg_temp_observations, time = 240days).data +end diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/pipeline.sbatch b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/pipeline.sbatch new file mode 100644 index 00000000000..d254b0763df --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/pipeline.sbatch @@ -0,0 +1,33 @@ +#!/bin/bash +#SBATCH --time=3:00:00 +#SBATCH --output=sphere_held_suarez_rhoe_equilmoist_calibration.txt + +julia --project=calibration/experiments/sphere_held_suarez_rhoe_equilmoist -e ' +import Pkg; Pkg.instantiate(;verbose=true) +import JLD2 +using ClimaUtilities.ClimaArtifacts +import ClimaCalibrate: calibrate, ExperimentConfig, CaltechHPCBackend, get_prior, kwargs + +experiment_dir = dirname(Base.active_project()) +include(joinpath(experiment_dir, "observation_map.jl")) +artifact_path = @clima_artifact("atmos_held_suarez_obs") +model_interface = joinpath(experiment_dir, "model_interface.jl") + +# Load data and configurations +n_iterations = 2 +ensemble_size = 10 +observations = JLD2.load_object(joinpath(artifact_path, "obs_mean.jld2")) +noise = JLD2.load_object(joinpath(artifact_path, "obs_noise_cov.jld2")) +prior = get_prior(joinpath(experiment_dir, "prior.toml")) +output_dir = joinpath("output", "sphere_held_suarez_rhoe_equilmoist") + +experiment_config = ExperimentConfig(; n_iterations, ensemble_size, + observations, noise, output_dir, prior) +slurm_kwargs = kwargs(time = 50, ntasks = 16) +eki = calibrate(CaltechHPCBackend, experiment_config; model_interface, slurm_kwargs, verbose=true) + +include(joinpath(experiment_dir, "postprocessing.jl")) +prior = get_prior(joinpath(experiment_dir, "prior.toml")) +convergence_plot(eki, prior) +scatter_plot(eki) +' diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/postprocessing.jl b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/postprocessing.jl new file mode 100644 index 00000000000..2832dc7f052 --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/postprocessing.jl @@ -0,0 +1,91 @@ +import EnsembleKalmanProcesses as EKP +using EnsembleKalmanProcesses.ParameterDistributions +using EnsembleKalmanProcesses.TOMLInterface +using Distributions +import Statistics: mean +import CairoMakie: Makie +import ClimaCalibrate + +function convergence_plot( + eki::EKP.EnsembleKalmanProcess, + prior::ParameterDistribution; + theta_star = 65.0, + output = joinpath("output", "sphere_held_suarez_rhoe_equilmoist"), +) + u_vec = EKP.get_u(eki) + meanabsdiff²(x, e) = sum(i -> abs(i - x)^2, e) / length(e) + error_vec = map(ensemble -> meanabsdiff²(theta_star, ensemble), u_vec) + error_vec = map(ensemble -> meanabsdiff²(mean(ensemble), ensemble), u_vec) + phi_vec = transform_unconstrained_to_constrained(prior, u_vec) + u_series = eachcol(reduce(vcat, u_vec)) + phi_series = eachcol(reduce(vcat, phi_vec)) + + f = Makie.Figure(title = "Convergence Plot", resolution = (800, 800)) + + ax = Makie.Axis( + f[1, 1], + xlabel = "Iteration", + ylabel = "Error", + xticks = 0:50, + ) + Makie.lines!(ax, 0.0:(length(error_vec) - 1), error_vec) + + ax = Makie.Axis( + f[1, 2], + xlabel = "Iteration", + ylabel = "Spread", + xticks = 0:50, + ) + Makie.lines!(ax, 0.0:(length(spread_vec) - 1), spread_vec) + + ax = Makie.Axis( + f[2, 1], + xlabel = "Iteration", + ylabel = "Unconstrained Parameters", + xticks = 0:50, + ) + Makie.lines!.(ax, tuple(0.0:(length(u_series[1]) - 1)), u_series) + + ax = Makie.Axis( + f[2, 2], + xlabel = "Iteration", + ylabel = "Constrained Parameters", + xticks = 0:50, + ) + Makie.lines!.(ax, tuple(0.0:(length(phi_series[1]) - 1)), phi_series) + Makie.hlines!(ax, [theta_star], color = :red, linestyle = :dash) + Makie.save(joinpath(output, "convergence.png"), f) +end + +function scatter_plot( + eki, + output = joinpath("output", "sphere_held_suarez_rhoe_equilmoist"), +) + # Define figure with explicit size + f = Makie.Figure(resolution = (800, 600)) + a = Makie.Axis( + f[1, 1], + title = "60-Day Zonal Avg Temp at 242m versus Unconstrained Equator-Pole Temp Gradient", + ylabel = "Parameter Value", + xlabel = "Temperature (K)", + ) + + g = vec.(EKP.get_g(eki; return_array = true)) + u = vec.(EKP.get_u(eki; return_array = true)) + + for (gg, uu) in zip(g, u) + Makie.scatter!(a, gg, uu) + end + + # Save the figure + Makie.save(joinpath(output, "scatter.png"), f) +end + +# Uncomment for easy plotting +# import JLD2 +# iteration = 2 +# output_dir = joinpath("output", "sphere_held_suarez_rhoe_equilmoist") +# eki_filepath = joinpath(ClimaCalibrate.path_to_iteration(output_dir, iteration), "eki_file.jld2") +# eki = JLD2.load_object(eki_filepath) +# prior_path = joinpath("calibration", "experiments", "sphere_held_suarez_rhoe_equilmoist", "prior.toml") +# prior = ClimaCalibrate.get_prior(prior_path) diff --git a/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/prior.toml b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/prior.toml new file mode 100644 index 00000000000..cda6b7b2106 --- /dev/null +++ b/calibration/experiments/sphere_held_suarez_rhoe_equilmoist/prior.toml @@ -0,0 +1,5 @@ +["equator_pole_temperature_gradient_wet"] +prior = "Parameterized(Normal(4.779568,0.31223328))" +constraint = "[bounded_below(0)]" +# EKP.ParameterDistributions.constrained_gaussian("name", 125, 40, 0, Inf) +type = "float" diff --git a/calibration/model_interface.jl b/calibration/model_interface.jl new file mode 100644 index 00000000000..6acf50fb3d8 --- /dev/null +++ b/calibration/model_interface.jl @@ -0,0 +1,69 @@ +import ClimaAtmos as CA +import YAML +import ClimaComms +@static pkgversion(ClimaComms) >= v"0.6" && ClimaComms.@import_required_backends +using ClimaUtilities.ClimaArtifacts +import ClimaCalibrate: + set_up_forward_model, + run_forward_model, + path_to_ensemble_member, + ExperimentConfig + +""" + set_up_forward_model(member, iteration, experiment_dir::AbstractString) + set_up_forward_model(member, iteration, ::ExperimentConfig; experiment_dir) + set_up_forward_model(member, iteration, config_dict::AbstractDict) + +Return an AtmosConfig object for the given member and iteration. + +Turns off default diagnostics and sets the TOML parameter file to the member's path. +This assumes that the config dictionary has an `output_dir` key. +""" +function set_up_forward_model( + member, + iteration, + ::ExperimentConfig; + experiment_dir = dirname(Base.active_project()), +) + # Assume experiment_dir is project dir + config_dict = YAML.load_file(joinpath(experiment_dir, "model_config.yml")) + set_up_forward_model(member, iteration, config_dict::AbstractDict) +end + +function set_up_forward_model(member, iteration, experiment_dir::AbstractString) + config_dict = YAML.load_file(joinpath(experiment_dir, "model_config.yml")) + set_up_forward_model(member, iteration, config_dict::AbstractDict) +end + +function set_up_forward_model(member, iteration, config_dict::AbstractDict) + output_dir = config_dict["output_dir"] + member_path = path_to_ensemble_member(output_dir, iteration, member) + config_dict["output_dir"] = member_path + parameter_path = joinpath(member_path, "parameters.toml") + if haskey(config_dict, "toml") + push!(config_dict["toml"], parameter_path) + else + config_dict["toml"] = [parameter_path] + end + + # Turn off default diagnostics + config_dict["output_default_diagnostics"] = false + return CA.AtmosConfig(config_dict) +end + +""" + run_forward_model(atmos_config::CA.AtmosConfig) + +Run the atmosphere model with the given an AtmosConfig object. +Currently only has basic error handling. +""" +function run_forward_model(atmos_config::CA.AtmosConfig) + simulation = CA.get_simulation(atmos_config) + sol_res = CA.solve_atmos!(simulation) + if sol_res.ret_code == :simulation_crashed + !isnothing(sol_res.sol) && sol_res.sol .= eltype(sol_res.sol)(NaN) + error( + "The ClimaAtmos simulation has crashed. See the stack trace for details.", + ) + end +end diff --git a/calibration/test/Manifest.toml b/calibration/test/Manifest.toml new file mode 100644 index 00000000000..e1995559853 --- /dev/null +++ b/calibration/test/Manifest.toml @@ -0,0 +1,2792 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.4" +manifest_format = "2.0" +project_hash = "89884ed7a225cc54d4e13a752a3036d05d402c43" + +[[deps.ADTypes]] +git-tree-sha1 = "3a6511b6e54550bcbc986c560921a8cd7761fcd8" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "1.5.1" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesEnzymeCoreExt = "EnzymeCore" + +[[deps.AMD]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] +git-tree-sha1 = "45a1272e3f809d36431e57ab22703c6896b8908f" +uuid = "14f7f29c-3bd6-536c-9a0b-7339e30b5a3e" +version = "0.5.3" + +[[deps.AbstractFFTs]] +deps = ["LinearAlgebra"] 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+[[deps.x264_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +version = "2021.5.5+0" + +[[deps.x265_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +version = "3.5.0+0" diff --git a/calibration/test/Project.toml b/calibration/test/Project.toml new file mode 100644 index 00000000000..6af14a27dca --- /dev/null +++ b/calibration/test/Project.toml @@ -0,0 +1,12 @@ +[deps] +CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" +ClimaAnalysis = "29b5916a-a76c-4e73-9657-3c8fd22e65e6" +ClimaAtmos = "b2c96348-7fb7-4fe0-8da9-78d88439e717" +ClimaCalibrate = "4347a170-ebd6-470c-89d3-5c705c0cacc2" +ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" +ClimaUtilities = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +EnsembleKalmanProcesses = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d" +JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819" +MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" +YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" diff --git a/calibration/test/e2e_test.jl b/calibration/test/e2e_test.jl new file mode 100644 index 00000000000..ae5aed23c77 --- /dev/null +++ b/calibration/test/e2e_test.jl @@ -0,0 +1,170 @@ +#= End-to-end test +Runs a perfect model calibration, calibrating on the parameter `astronomical_unit` +with top-of-atmosphere radiative shortwave flux in the loss function. + +The calibration is run twice, once on the backend obtained via `get_backend()` +and once on the `JuliaBackend`. The output of each calibration is tested individually +and compared to ensure reproducibility. +=# +import ClimaCalibrate as CAL +import ClimaAtmos as CA +import ClimaAnalysis: SimDir, get, slice, average_xy +import CairoMakie +import JLD2 +import LinearAlgebra: I +import EnsembleKalmanProcesses as EKP +import Statistics: var, mean +using Test + +# Paths and setup +experiment_dir = joinpath(pkgdir(CA), "calibration", "test") +model_interface = joinpath(pkgdir(CA), "calibration", "model_interface.jl") +include(model_interface) + +# Observation map +function CAL.observation_map(iteration) + ensemble_size = 10 + output_dir = "calibration_end_to_end_test" + single_member_dims = (1,) + G_ensemble = Array{Float64}(undef, single_member_dims..., ensemble_size) + + for m in 1:ensemble_size + member_path = CAL.path_to_ensemble_member(output_dir, iteration, m) + simdir_path = joinpath(member_path, "output_active") + if isdir(simdir_path) + simdir = SimDir(simdir_path) + G_ensemble[:, m] .= process_member_data(simdir) + else + G_ensemble[:, m] .= NaN + end + end + return G_ensemble +end + +function process_member_data(simdir::SimDir) + isempty(simdir.vars) && return NaN + rsut = + get(simdir; short_name = "rsut", reduction = "average", period = "30d") + return slice(average_xy(rsut); time = 30).data +end + +# Generate observations +obs_path = joinpath(experiment_dir, "observations.jld2") +if !isfile(obs_path) + @info "Generating observations" + config = CA.AtmosConfig(joinpath(experiment_dir, "model_config.yml")) + simulation = CA.get_simulation(config) + CA.solve_atmos!(simulation) + observations = Vector{Float64}(undef, 1) + observations .= process_member_data(SimDir(simulation.output_dir)) + JLD2.save_object(obs_path, observations) +end + +# Initialize experiment data +astronomical_unit = 149_597_870_000 +observations = JLD2.load_object(obs_path) +noise = 0.1 * I +n_iterations = 3 +ensemble_size = 10 +prior = CAL.get_prior(joinpath(experiment_dir, "prior.toml")) +output_dir = "calibration_end_to_end_test" +experiment_config = CAL.ExperimentConfig(; + n_iterations, + ensemble_size, + observations, + noise, + output_dir, + prior, +) + +# Minimal EKI test +function minimal_eki_test(eki) + params = EKP.get_u(eki) + spread = map(x -> var(abs.(x)), params) + + # Spread should be heavily decreased as particles have converged + @test last(spread) / first(spread) < 0.1 + # Parameter should be close to true value + @test mean(last(params)) ≈ astronomical_unit rtol = 0.02 +end + +# Caltech HPC backend +if !(@isdefined backend) + backend = CAL.get_backend() +end +@info "Running Calibration E2E test on $backend" +if backend <: CAL.SlurmBackend + slurm_kwargs = CAL.kwargs(time = 10) + test_eki = CAL.calibrate( + backend, + experiment_config; + slurm_kwargs, + model_interface, + verbose = true, + ) +else + test_eki = CAL.calibrate(backend, experiment_config) +end +@testset "Test Calibration on $backend" begin + minimal_eki_test(test_eki) +end + +# Run calibration +julia_eki = CAL.calibrate(CAL.JuliaBackend, experiment_config) + +@testset "Julia-only comparison calibration" begin + minimal_eki_test(julia_eki) +end + +@testset "Compare $backend output to JuliaBackend" begin + for (uu, slurm_uu) in zip(EKP.get_u(julia_eki), EKP.get_u(test_eki)) + @test uu ≈ slurm_uu rtol = 0.02 + end +end + +# Debug plots +function scatter_plot(eki::EKP.EnsembleKalmanProcess) + f = CairoMakie.Figure(resolution = (800, 600)) + ax = CairoMakie.Axis( + f[1, 1], + ylabel = "Absolute Parameter Value", + xlabel = "Top of atmosphere radiative SW flux", + ) + + g = vec.(EKP.get_g(eki; return_array = true)) + params = map(x -> abs.(x), vec.((EKP.get_u(eki)))) + + for (gg, uu) in zip(g, params) + CairoMakie.scatter!(ax, gg, uu) + end + + CairoMakie.hlines!(ax, [astronomical_unit], linestyle = :dash) + CairoMakie.vlines!(ax, observations, linestyle = :dash) + + output = joinpath(output_dir, "scatter.png") + CairoMakie.save(output, f) + return output +end + +scatter_plot(test_eki) + +function param_versus_iter_plot(eki::EKP.EnsembleKalmanProcess) + f = CairoMakie.Figure(resolution = (800, 600)) + ax = CairoMakie.Axis( + f[1, 1], + ylabel = "Parameter Value", + xlabel = "Iteration", + ) + params = EKP.get_u(eki) + for (i, param) in enumerate(params) + CairoMakie.scatter!(ax, fill(i, length(param)), vec(param)) + end + + CairoMakie.hlines!(ax, [astronomical_unit]; color = :red, linestyle = :dash) + + output = joinpath(output_dir, "param_vs_iter.png") + CairoMakie.save(output, f) + return output +end + +param_versus_iter_plot(test_eki) diff --git a/calibration/test/interface.jl b/calibration/test/interface.jl new file mode 100644 index 00000000000..1f4ebbff1d4 --- /dev/null +++ b/calibration/test/interface.jl @@ -0,0 +1,33 @@ +# Tests for ensuring that the calibration/model interface sets the AtmosConfig correctly. +import ClimaAtmos as CA +import ClimaCalibrate +using Test + +include(joinpath(pkgdir(CA), "calibration", "model_interface.jl")) + +member = 1 +iter = 0 + +mktempdir() do output_dir + member_path = + ClimaCalibrate.path_to_ensemble_member(output_dir, iter, member) + mkpath(member_path) + # We need to check that a "base" TOML is support alongside the TOML sampled from the prior + base_toml_file = touch(joinpath(output_dir, "default_parameters.toml")) + sampled_toml_file = touch(joinpath(member_path, "parameters.toml")) + config_dict = Dict( + "output_default_diagnostics" => true, + "moist" => "equil", + "toml" => [base_toml_file], + "output_dir" => output_dir, + ) + (; parsed_args) = + ClimaCalibrate.set_up_forward_model(member, iter, config_dict) + + @testset "Atmos Configuration" begin + @test parsed_args["moist"] == "equil" + @test parsed_args["output_dir"] == member_path + @test parsed_args["output_default_diagnostics"] == false + @test parsed_args["toml"] == [base_toml_file, sampled_toml_file] + end +end diff --git a/calibration/test/model_config.yml b/calibration/test/model_config.yml new file mode 100644 index 00000000000..d36b49d5162 --- /dev/null +++ b/calibration/test/model_config.yml @@ -0,0 +1,15 @@ +dt: 2000secs +t_end: 30days +config: column +h_elem: 1 +insolation: timevarying +job_id: calibration_end_to_end_test +output_dir: calibration_end_to_end_test +output_default_diagnostics: false +dt_rad: 6hours +rad: clearsky +diagnostics: + - reduction_time: average + short_name: rsut + period: 30days + writer: nc diff --git a/calibration/test/prior.toml b/calibration/test/prior.toml new file mode 100644 index 00000000000..af6e0b31891 --- /dev/null +++ b/calibration/test/prior.toml @@ -0,0 +1,3 @@ +[astronomical_unit] +prior = "constrained_gaussian(astronomical_unit, 200_000, 100597870000, -Inf, Inf)" +type = "float"