Use CommonSpaces/Grids

.buildkite/Manifest-v1.11.toml

@@ -1864,7 +1864,7 @@ version = "2.5.5+0"
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
-version = "0.8.5+0"
+version = "0.8.1+2"
 
 [[deps.OpenMPI_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
@@ -2210,9 +2210,9 @@ version = "0.5.1+0"
 
 [[deps.RootSolvers]]
 deps = ["ForwardDiff", "Printf"]
-git-tree-sha1 = "75b130d104fb3d9d39a5c784fad23aebc7d7d956"
+git-tree-sha1 = "769388dbf7656e70f6ee250f35bb6cbca8f43203"
 uuid = "7181ea78-2dcb-4de3-ab41-2b8ab5a31e74"
-version = "1.0.0"
+version = "0.4.6"
 
 [[deps.RoundingEmulator]]
 git-tree-sha1 = "40b9edad2e5287e05bd413a38f61a8ff55b9557b"

.buildkite/PrecompileCI/src/PrecompileCI.jl

@@ -15,33 +15,39 @@ import ClimaParams
         x_max = y_max = 1e8
         z_max = FT(30000.0)
         dz_bottom = FT(500) # other values?
-        z_stretch = Meshes.HyperbolicTangentStretching(dz_bottom) # Meshes.Uniform()
+        z_stretch = true # Meshes.Uniform()
         bubble = true # false
-        parsed_args =
-            Dict{String, Any}("topography" => "NoWarp", "topo_smoothing" => false)
-        comms_ctx = ClimaComms.context(ClimaComms.CPUSingleThreaded())
-        deep = false
-
-        # constants
-        quad = Quadratures.GLL{4}()
+        nh_poly = 3 # GLL{4} = nh_poly + 1
+        context = ClimaComms.context(ClimaComms.CPUSingleThreaded())
+        deep_atmosphere = false
+        topography = CA.NoTopography()
         params = CA.ClimaAtmosParameters(FT)
         radius = CA.Parameters.planet_radius(params)
 
-        # Sphere
-        horz_mesh = CA.cubed_sphere_mesh(; radius, h_elem)
-        h_space = CA.make_horizontal_space(horz_mesh, quad, comms_ctx, bubble)
-        CA.make_hybrid_spaces(h_space, z_max, z_elem, z_stretch; parsed_args)
-
-        # box
-        horizontal_mesh = CA.periodic_rectangle_mesh(; x_max, y_max, x_elem, y_elem)
-        h_space = CA.make_horizontal_space(horizontal_mesh, quad, comms_ctx, bubble)
-        # This is broken
-        # CA.make_hybrid_spaces(h_space, z_max, z_elem, z_stretch; parsed_args)
+        sphere_grid = CA.SphereGrid(
+            FT;
+            context, radius, h_elem, nh_poly, z_elem, z_max, z_stretch, 
+            dz_bottom, bubble, deep_atmosphere, 
+            topography,
+        )
+        box_grid = CA.BoxGrid(
+            FT; context, x_elem, x_max, y_elem, y_max, z_elem, z_max, nh_poly, 
+            z_stretch, dz_bottom, bubble, deep_atmosphere, 
+            periodic_x = true, periodic_y = true, topography,
+        )
+        plane_grid = CA.PlaneGrid(
+            FT; context, x_elem, x_max, z_elem, z_max, nh_poly, z_stretch, 
+            dz_bottom, bubble, deep_atmosphere, periodic_x = true, 
+            topography,
+        )
+        column_grid = CA.ColGrid(
+            FT; context, z_elem, z_max, z_stretch, dz_bottom,
+        )
 
-        # plane
-        horizontal_mesh = CA.periodic_line_mesh(; x_max, x_elem)
-        h_space = CA.make_horizontal_space(horizontal_mesh, quad, comms_ctx, bubble)
+        for grid in [sphere_grid, box_grid, plane_grid, column_grid]
+            CA.get_spaces(grid, context)
+        end
     end
 end
 
-end # module Precompile
+end # module PrecompileCI

.buildkite/ci_driver.jl

@@ -9,7 +9,7 @@ redirect_stderr(IOContext(stderr, :stacktrace_types_limited => Ref(false)))
 # To load in the precompiled methods, run `using PrecompileCI` before loading ClimaAtmos.
 # To see what methods are precompiled, open julia: `julia --project=.buildkite/PrecompileCI`
 # and run `using PrecompileTools; PrecompileTools.verbose[] = true; include(".buildkite/PrecompileCI/src/PrecompileCI.jl")`
-haskey(ENV, "CI") && (using PrecompileCI)
+# haskey(ENV, "CI") && (using PrecompileCI)
 
 import ClimaComms
 ClimaComms.@import_required_backends

.buildkite/pipeline.yml

@@ -28,8 +28,17 @@ steps:
       - julia --check-bounds=yes -e 'using TOML; @assert TOML.parsefile(".buildkite/Manifest-v1.11.toml")["deps"]["ClimaAtmos"][1]["path"] == ".."'
 
       - echo "--- Instantiate .buildkite"
-      - "julia --project=.buildkite -e 'using Pkg; Pkg.instantiate(;verbose=true); Pkg.precompile(;strict=true); using CUDA; CUDA.precompile_runtime(); Pkg.status()'"
-
+      - julia --project=.buildkite -e '
+
+          using Pkg;
+          Pkg.Registry.update();
+          Pkg.add(PackageSpec(name="ClimaCore",      url="https://github.com/CliMA/ClimaCore.jl",      rev="ne/fd_grid"));
+          Pkg.add(PackageSpec(name="ClimaUtilities", url="https://github.com/CliMA/ClimaUtilities.jl", rev="main"));
+          Pkg.instantiate();
+          Pkg.precompile(; strict=true);
+          using CUDA; CUDA.precompile_runtime();
+          Pkg.status()
+        '
     agents:
       slurm_cpus_per_task: 8
       slurm_gpus: 1

Project.toml

@@ -44,7 +44,7 @@ ArgParse = "1"
 Artifacts = "1"
 AtmosphericProfilesLibrary = "0.1.7"
 ClimaComms = "0.6.9"
-ClimaCore = "0.14.37"
+ClimaCore = "0.14.42"
 ClimaDiagnostics = "0.2.12"
 ClimaInterpolations = "0.1.0"
 ClimaParams = "1.0.2"

calibration/experiments/gcm_driven_scm/helper_funcs.jl

@@ -23,6 +23,7 @@ CLIMADIAGNOSTICS_LES_NAME_MAP =
 """Get z cell centers coordinates for CA run, given config. """
 function get_z_grid(atmos_config; z_max = nothing)
     params = CA.ClimaAtmosParameters(atmos_config)
+    # TODO: Update this to use the new get_spaces function
     spaces =
         CA.get_spaces(atmos_config.parsed_args, params, atmos_config.comms_ctx)
     coord = CA.Fields.coordinate_field(spaces.center_space)

docs/src/api.md

@@ -43,12 +43,21 @@ ClimaAtmos.InitialConditions.Bomex
 ClimaAtmos.InitialConditions.Soares
 ```
 
-### Helper
+## Helper
 
 ```@docs
 ClimaAtmos.InitialConditions.ColumnInterpolatableField
 ```
 
+## Grids
+
+```@docs
+ClimaAtmos.ColGrid
+ ClimaAtmos.SphereGrid
+ClimaAtmos.PlaneGrid
+ClimaAtmos.BoxGrid
+```
+
 ## Jacobian
 
 ```@docs

post_processing/ci_plots.jl

@@ -437,8 +437,6 @@ make_plots_generic(
     simulation_path,
     vars,
     time = LAST_SNAP,
-    x = 0.0, # Our columns are still 3D objects...
-    y = 0.0,
     more_kwargs = YLINEARSCALE,
 )
 ```
@@ -453,8 +451,6 @@ make_plots_generic(
     simulation_path,
     vars,
     time = LAST_SNAP,
-    x = 0.0, # Our columns are still 3D objects...
-    y = 0.0,
     more_kwargs = YLINEARSCALE,
 )
 ```
@@ -589,14 +585,23 @@ ColumnPlots = Union{
 function make_plots(::ColumnPlots, output_paths::Vector{<:AbstractString})
     simdirs = SimDir.(output_paths)
     short_names = ["ta", "wa"]
-    vars = map_comparison(get, simdirs, short_names)
+    vars = map_comparison(simdirs, short_names) do simdir, short_name
+        var = get(simdir; short_name)
+        # For vertical-only (FiniteDifferenceGrid) spaces, the data may have 
+        # extra singleton dimensions. Check and squeeze if needed.
+        if haskey(var.dims, "x") && length(var.dims["x"]) == 1
+            var = slice(var; x = var.dims["x"][1])
+        end
+        if haskey(var.dims, "y") && length(var.dims["y"]) == 1
+            var = slice(var; y = var.dims["y"][1])
+        end
+        return var
+    end
 
     make_plots_generic(
         output_paths,
         vars,
         time = LAST_SNAP,
-        x = 0.0, # Our columns are still 3D objects...
-        y = 0.0,
         MAX_NUM_COLS = length(simdirs),
         more_kwargs = YLINEARSCALE,
     )
@@ -644,7 +649,7 @@ function make_plots(
     end
 
     vars = [
-        slice(get(simdir; short_name), x = 0.0, y = 0.0) for
+        get(simdir; short_name) for
         short_name in short_names
     ]
 
@@ -689,7 +694,7 @@ function make_plots(
     surface_precip = read_var(simdir.variable_paths["pr"]["inst"]["10s"])
     viz.line_plot1D!(
         fig,
-        slice(surface_precip, x = 0.0, y = 0.0);
+        surface_precip;
         p_loc = [pr_row, 1:3],
     )
 
@@ -1371,6 +1376,12 @@ EDMFBoxPlots = Union{
     Val{:diagnostic_edmfx_dycoms_rf01_box},
     Val{:diagnostic_edmfx_trmm_box_0M},
     Val{:diagnostic_edmfx_dycoms_rf01_explicit_box},
+    Val{:prognostic_edmfx_bomex_box},
+    Val{:rcemipii_box_diagnostic_edmfx},
+    Val{:diagnostic_edmfx_trmm_stretched_box},
+}
+
+EDMFColumnPlots = Union{
     Val{:prognostic_edmfx_adv_test_column},
     Val{:prognostic_edmfx_gabls_column},
     Val{:prognostic_edmfx_gabls_column_sparse_autodiff},
@@ -1386,13 +1397,10 @@ EDMFBoxPlots = Union{
     Val{:prognostic_edmfx_simpleplume_column},
     Val{:prognostic_edmfx_gcmdriven_column},
     Val{:prognostic_edmfx_tv_era5driven_column},
-    Val{:prognostic_edmfx_bomex_box},
-    Val{:rcemipii_box_diagnostic_edmfx},
     Val{:prognostic_edmfx_soares_column},
-    Val{:diagnostic_edmfx_trmm_stretched_box},
 }
 
-EDMFBoxPlotsWithPrecip = Union{
+EDMFColumnPlotsWithPrecip = Union{
     Val{:prognostic_edmfx_rico_column},
     Val{:prognostic_edmfx_rico_implicit_column},
     Val{:prognostic_edmfx_rico_column_2M},
@@ -1485,14 +1493,99 @@ end
 function make_plots(
     sim_type::Union{
         EDMFBoxPlots,
-        EDMFBoxPlotsWithPrecip,
         DiagEDMFBoxPlotsWithPrecip,
     },
     output_paths::Vector{<:AbstractString},
 )
     simdirs = SimDir.(output_paths)
 
-    if sim_type isa EDMFBoxPlotsWithPrecip
+    if sim_type isa DiagEDMFBoxPlotsWithPrecip
+        precip_names = ("husra", "hussn", "husraup", "hussnup")
+    else
+        precip_names = ()
+    end
+
+    short_names = [
+        "wa",
+        "waup",
+        "ta",
+        "taup",
+        "hus",
+        "husup",
+        "arup",
+        "tke",
+        "ua",
+        "thetaa",
+        "thetaaup",
+        "ha",
+        "haup",
+        "hur",
+        "hurup",
+        "lmix",
+        "cl",
+        "clw",
+        "clwup",
+        "cli",
+        "cliup",
+        precip_names...,
+    ]
+    reduction = "inst"
+
+    available_periods = ClimaAnalysis.available_periods(
+        simdirs[1];
+        short_name = short_names[1],
+        reduction,
+    )
+    # choose the shortest available period
+    available_periods = collect(available_periods) # ensure vector for indexing
+    period = available_periods[argmin(CA.time_to_seconds.(available_periods))]
+
+    short_name_tuples = pair_edmf_names(short_names)
+    var_groups_zt =
+        map_comparison(simdirs, short_name_tuples) do simdir, name_tuple
+            return [
+                slice(
+                    get(simdir; short_name, reduction, period),
+                    x = 0.0,
+                    y = 0.0,
+                ) for short_name in name_tuple
+            ]
+        end
+
+    var_groups_z = [
+        ([slice(v, time = LAST_SNAP) for v in group]...,) for
+        group in var_groups_zt
+    ]
+
+    tmp_file = make_plots_generic(
+        output_paths,
+        output_name = "tmp",
+        var_groups_z;
+        plot_fn = plot_edmf_vert_profile!,
+        MAX_NUM_COLS = 2,
+        MAX_NUM_ROWS = 4,
+    )
+
+    make_plots_generic(
+        output_paths,
+        vcat(var_groups_zt...),
+        plot_fn = plot_parsed_attribute_title!,
+        summary_files = [tmp_file],
+        MAX_NUM_COLS = 2,
+        MAX_NUM_ROWS = 4,
+    )
+end
+
+function make_plots(
+    sim_type::Union{
+        EDMFColumnPlots,
+        EDMFColumnPlotsWithPrecip,
+    },
+    output_paths::Vector{<:AbstractString},
+)
+    simdirs = SimDir.(output_paths)
+
+    if sim_type isa EDMFColumnPlotsWithPrecip
         if sim_type isa Val{:prognostic_edmfx_rico_column_2M}
             precip_names = (
                 "husra",
@@ -1512,8 +1605,6 @@ function make_plots(
             precip_names =
                 ("husra", "hussn", "husraup", "hussnup", "husraen", "hussnen")
         end
-    elseif sim_type isa DiagEDMFBoxPlotsWithPrecip
-        precip_names = ("husra", "hussn", "husraup", "hussnup")
     else
         precip_names = ()
     end
@@ -1557,11 +1648,7 @@ function make_plots(
     var_groups_zt =
         map_comparison(simdirs, short_name_tuples) do simdir, name_tuple
             return [
-                slice(
-                    get(simdir; short_name, reduction, period),
-                    x = 0.0,
-                    y = 0.0,
-                ) for short_name in name_tuple
+                get(simdir; short_name, reduction, period) for short_name in name_tuple
             ]
         end
 

src/ClimaAtmos.jl

@@ -156,6 +156,7 @@ import .Diagnostics as CAD
 include(joinpath("callbacks", "get_callbacks.jl"))
 
 include(joinpath("simulation", "AtmosSimulations.jl"))
+include(joinpath("simulation", "grids.jl"))
 
 include(joinpath("solver", "model_getters.jl")) # high-level (using parsed_args) model getters
 include(joinpath("solver", "type_getters.jl"))

src/cache/temporary_quantities.jl

@@ -28,7 +28,6 @@ function temporary_quantities(Y, atmos)
     center_space, face_space = axes(Y.c), axes(Y.f)
 
     FT = Spaces.undertype(center_space)
-    CTh = CTh_vector_type(Y.c)
     uvw_vec = UVW(FT(0), FT(0), FT(0))
     return (;
         ᶠtemp_scalar = Fields.Field(FT, face_space), # ᶠp, ᶠρK_h
@@ -81,7 +80,7 @@ function temporary_quantities(Y, atmos)
         # TODO: Remove this hack
         sfc_temp_C3 = Fields.Field(C3{FT}, Spaces.level(face_space, half)), # ρ_flux_χ
         # Implicit solver cache:
-        ∂ᶜK_∂ᶜuₕ = similar(Y.c, DiagonalMatrixRow{Adjoint{FT, CTh{FT}}}),
+        ∂ᶜK_∂ᶜuₕ = similar(Y.c, DiagonalMatrixRow{Adjoint{FT, CT12{FT}}}),
         ∂ᶜK_∂ᶠu₃ = similar(Y.c, BidiagonalMatrixRow{Adjoint{FT, CT3{FT}}}),
         ᶠp_grad_matrix = similar(Y.f, BidiagonalMatrixRow{C3{FT}}),
         ᶠbidiagonal_matrix_ct3 = similar(Y.f, BidiagonalMatrixRow{CT3{FT}}),

src/callbacks/get_callbacks.jl

@@ -167,6 +167,7 @@ function get_diagnostics(parsed_args, atmos_model, Y, p, sim_info, output_dir)
                 FT(time_to_seconds(parsed_args["t_end"]) - t_start),
                 start_date;
                 output_writer = netcdf_writer,
+                topography = has_topography(axes(Y.c)),
             )...,
             diagnostics...,
         ]