Add diagnostic module

.buildkite/pipeline.yml

@@ -1023,6 +1023,14 @@ steps:
         agents:
           slurm_mem: 20GB
 
+      - label: ":fire: Flame graph: perf target (diagnostics)"
+        command: >
+          julia --color=yes --project=perf perf/flame.jl
+          --config_file $PERF_CONFIG_PATH/flame/diagnostics.yml
+        artifact_paths: "flame_perf_diagnostics/*"
+        agents:
+          slurm_mem: 20GB
+
       # Inference
       - label: ":rocket: JET n-failures (inference)"
         command: >

.gitignore

@@ -22,6 +22,9 @@ deps/src/
 docs/build/
 docs/site/
 
+# File generated by make_available_diagnostics.jl
+docs/src/available_diagnostics.md
+
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be
 # committed for packages, but should be committed for applications that require a static

config/default_configs/default_config.yml

@@ -249,3 +249,6 @@ override_τ_precip:
 log_params:
   help: "Log parameters to file [`false` (default), `true`]"
   value: false
+output_default_diagnostics:
+  help: "Output the default diagnostics associated to the selected atmospheric model"
+  value: false

config/model_configs/sphere_baroclinic_wave_rhoe.yml

@@ -1,6 +1,6 @@
 dt_save_to_disk: "2days"
 regression_test: true
 initial_condition: "DryBaroclinicWave"
-dt: "580secs"
+dt: "400secs"
 t_end: "10days"
 job_id: "sphere_baroclinic_wave_rhoe"

config/model_configs/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.yml

@@ -13,3 +13,4 @@ viscous_sponge: true
 job_id: "sphere_held_suarez_rhoe_equilmoist_hightop_sponge"
 moist: "equil"
 toml: [toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml]
+output_default_diagnostics: true

config/model_configs/sphere_held_suarez_rhoe_hightop.yml

@@ -3,7 +3,7 @@ dt_save_to_disk: "4days"
 regression_test: true
 t_end: "8days"
 forcing: "held_suarez"
-dt: "500secs"
+dt: "400secs"
 z_elem: 25
 job_id: "sphere_held_suarez_rhoe_hightop"
 z_max: 45000.0

config/model_configs/sphere_held_suarez_rhotheta.yml

@@ -3,5 +3,5 @@ dt_save_to_disk: "10days"
 regression_test: true
 t_end: "20days"
 forcing: "held_suarez"
-dt: "500secs"
+dt: "400secs"
 job_id: "sphere_held_suarez_rhotheta"

config/model_configs/sphere_zalesak_upwind_tracer_energy_ssp_baroclinic_wave_rhoe_equilmoist.yml

@@ -1,7 +1,7 @@
 dt_save_to_disk: "5days"
 initial_condition: "MoistBaroclinicWave"
 max_newton_iters_ode: 4
-dt: "500secs"
+dt: "400secs"
 tracer_upwinding: zalesak
 t_end: "5days"
 ode_algo: "SSP333"

config/perf_configs/flame/diagnostics.yml

@@ -0,0 +1,11 @@
+job_id: "flame_perf_diagnostics"
+diagnostics:
+  - short_name: ua
+    period: 1secs
+    reduction_time: average
+  - short_name: va
+    period: 1secs
+    reduction_time: max
+  - short_name: ta
+    period: 1secs
+    reduction_time: max

config/perf_configs/gpu_baroclinic_wave_rhoe.yml

@@ -1,5 +1,5 @@
 job_id: "gpu_baroclinic_wave_rhoe" 
-dt: "580secs" 
+dt: "400secs"
 t_end: "10days" 
 dt_save_to_disk: "2days" 
 initial_condition: "DryBaroclinicWave" 

config/perf_configs/gpu_held_suarez_rhoe_hightop.yml

@@ -3,6 +3,6 @@ z_elem: 25
 dz_bottom: 300 
 forcing: "held_suarez" 
 job_id: "gpu_held_suarez_rhoe_hightop" 
-dt: "500secs" 
+dt: "400secs"
 t_end: "8days" 
 dt_save_to_disk: "4days"

docs/make.jl

@@ -8,6 +8,8 @@ disable_logging(Base.CoreLogging.Info) # Hide doctest's `@info` printing
 doctest(ClimaAtmos)
 disable_logging(Base.CoreLogging.BelowMinLevel) # Re-enable all logging
 
+include("make_diagnostic_table.jl")
+
 makedocs(
     CitationBibliography(joinpath(@__DIR__, "bibliography.bib")),
     modules = [ClimaAtmos],
@@ -26,6 +28,8 @@ makedocs(
         "Contributor Guide" => "contributor_guide.md",
         "Equations" => "equations.md",
         "EDMF Equations" => "edmf_equations.md",
+        "Diagnostics" => "diagnostics.md",
+        "Available Diagnostics" => "available_diagnostics.md",
         "Diagnostic EDMF Equations" => "diagnostic_edmf_equations.md",
         "Gravity Wave Drag Parameterizations" => "gravity_wave.md",
         "Radiative Equilibrium" => "radiative_equilibrium.md",

docs/make_diagnostic_table.jl

@@ -0,0 +1,32 @@
+import ClimaAtmos as CA
+
+# Read all the diagnostics we know how to compute, and print them into a
+# markdown table that is later compiled into the docs
+
+# basename(pwd()) if the code is run from inside the docs folder. If we don't
+# have that, we will assume that we are running from the project root. If this
+# code is run from anywhere but these two places, mkdocs will fail to find
+# availbale_diagnostics.md
+prefix = basename(pwd()) == "docs" ? "" : "docs/"
+
+out_path = "$(prefix)src/available_diagnostics.md"
+
+open(out_path, "w") do file
+
+    write(file, "# Available diagnostic variables\n\n")
+
+    write(
+        file,
+        "| Short name | Long name | Standard name | Units | Comments |\n",
+    )
+    write(file, "|---|---|---|---|---|\n")
+
+    for d in values(CA.Diagnostics.ALL_DIAGNOSTICS)
+        write(file, "| `$(d.short_name)` ")
+        write(file, "| $(d.long_name) ")
+        write(file, "| `$(d.standard_name)` ")
+        write(file, "| $(d.units) ")
+        write(file, "| $(d.comments)|\n")
+    end
+end
+@info "Written $out_path"