Merge branch 'main' into glw/density-example

.buildkite/pipeline.yml

@@ -1,10 +1,10 @@
 agents:
   queue: central
   slurm_mem: 8G
-  modules: julia/1.9.3 cuda/12.2
+  modules: julia/1.10.0 cuda/12.2
 
 env:
-  JULIA_VERSION: "1.9.3"
+  JULIA_VERSION: "1.10.0"
   OPENBLAS_NUM_THREADS: 1
   CUDA_VERSION: "12.2"
   OMPI_MCA_opal_warn_on_missing_libcuda: 0
@@ -58,12 +58,12 @@ steps:
       slurm_ntasks: 1
     timeout_in_minutes: 60
 
-  - label: ":mag::rocket: Constructor flop measurements"
-    command:
-      - "julia --project=perf perf/flops.jl"
-    agents:
-      slurm_ntasks: 1
-    timeout_in_minutes: 60
+  # - label: ":mag::rocket: Constructor flop measurements"
+  #   command:
+  #     - "julia --project=perf perf/flops.jl"
+  #   agents:
+  #     slurm_ntasks: 1
+  #   timeout_in_minutes: 60
 
   - label: ":mag::rocket: JET tests"
     command:
@@ -87,3 +87,20 @@ steps:
       slurm_ntasks: 1
       slurm_gpus: 1
     timeout_in_minutes: 60
+
+  - label: "KernelAbstraction GPU kernel benchmarks"
+    command:
+      - "julia --project=gpuenv perf/kernel_bm.jl CuArray"
+    agents:
+      slurm_ntasks: 1
+      slurm_gpus: 1
+    timeout_in_minutes: 60
+
+  - label: "KernelAbstraction CPU kernel benchmarks"
+    command:
+      - "julia --project=gpuenv perf/kernel_bm.jl"
+    agents:
+      slurm_ntasks: 1
+      slurm_gpus: 1
+    timeout_in_minutes: 60
+

.github/workflows/CodeCov.yml

@@ -13,12 +13,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2.2.0
+    - uses: actions/checkout@v4
 
     - name: Set up Julia
       uses: julia-actions/setup-julia@latest
       with:
-        version: 1.9
+        version: '1.10'
 
     - name: Test with coverage
       env:
@@ -36,7 +36,7 @@ jobs:
       if: success()
 
     - name: Submit coverage
-      uses: codecov/codecov-action@v1.0.7
+      uses: codecov/codecov-action@v3
       with:
         token: ${{secrets.CODECOV_TOKEN}}
       if: success()

.github/workflows/DocCleanUp.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
 

.github/workflows/JuliaFormatter.yml

@@ -18,9 +18,9 @@ jobs:
       with:
         access_token: ${{ github.token }}
 
-    - uses: actions/checkout@v2.2.0
+    - uses: actions/checkout@v4
 
-    - uses: dorny/paths-filter@v2.9.1
+    - uses: dorny/paths-filter@v2
       id: filter
       with:
         filters: |
@@ -30,7 +30,7 @@ jobs:
     - uses: julia-actions/setup-julia@latest
       if: steps.filter.outputs.julia_file_change == 'true'
       with:
-        version: 1.9
+        version: '1.10'
 
     - name: Apply JuliaFormatter
       if: steps.filter.outputs.julia_file_change == 'true'

.github/workflows/ci.yml

@@ -15,18 +15,18 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
           - '1.7'
           - '1.8'
           - '1.9'
+          - '1.10'
         os:
           - ubuntu-latest
           - macOS-latest
           - windows-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}

.github/workflows/docs.yml

@@ -12,10 +12,10 @@ jobs:
   docbuild:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
-          version: 1.9
+          version: '1.10'
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

.github/workflows/invalidations.yml

@@ -19,12 +19,12 @@ jobs:
     - uses: julia-actions/setup-julia@v1
       with:
         version: '1'
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: julia-actions/julia-buildpkg@v1
     - uses: julia-actions/julia-invalidations@v1
       id: invs_pr
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.event.repository.default_branch }}
     - uses: julia-actions/julia-buildpkg@v1

Project.toml

@@ -1,16 +1,26 @@
 name = "Thermodynamics"
 uuid = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 authors = ["Climate Modeling Alliance"]
-version = "0.11.2"
+version = "0.11.4"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RootSolvers = "7181ea78-2dcb-4de3-ab41-2b8ab5a31e74"
+# Required for backwards compatibility with Julia <1.9
+CLIMAParameters = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
+
+[weakdeps]
+CLIMAParameters = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
+
+[extensions]
+CreateParametersExt = "CLIMAParameters"
 
 [compat]
 DocStringExtensions = "0.8.1, 0.9"
-KernelAbstractions = "0.7, 0.8, 0.9"
+KernelAbstractions = "0.9"
+Random = "1"
 RootSolvers = "0.4"
 julia = "1.6"
+CLIMAParameters = "0.8"

docs/Project.toml

@@ -8,7 +8,6 @@ KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 RootSolvers = "7181ea78-2dcb-4de3-ab41-2b8ab5a31e74"
 Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
-UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
 julia = "1.7"

docs/src/Clausius_Clapeyron.jl

@@ -4,23 +4,10 @@ import CLIMAParameters as CP
 using Thermodynamics.TestedProfiles
 import Thermodynamics.Parameters as TP
 
-function get_parameter_set(::Type{FT}) where {FT}
-    toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
-    aliases = string.(fieldnames(TP.ThermodynamicsParameters))
-    param_pairs = CP.get_parameter_values!(toml_dict, aliases, "Thermodynamics")
-    param_set = TP.ThermodynamicsParameters{FT}(; param_pairs...)
-    logfilepath = joinpath(@__DIR__, "logfilepath_$FT.toml")
-    CP.log_parameter_information(toml_dict, logfilepath)
-    return param_set
-end
-const param_set_Float64 = get_parameter_set(Float64)
-const param_set_Float32 = get_parameter_set(Float32)
-parameter_set(::Type{Float64}) = param_set_Float64
-parameter_set(::Type{Float32}) = param_set_Float32
 ArrayType = Array{Float64}
-
 FT = eltype(ArrayType)
-param_set = parameter_set(FT)
+
+param_set = TP.ThermodynamicsParameters(FT)
 profiles = TestedProfiles.PhaseEquilProfiles(param_set, ArrayType)
 (; T, p, e_int, ρ, θ_liq_ice, phase_type) = profiles
 (; q_tot, q_liq, q_ice, q_pt, RH, e_kin, e_pot) = profiles

docs/src/Formulation.md

@@ -376,7 +376,7 @@ A virtual potential temperature can be defined analogously:
 \end{equation}
 ```
 
-!!! note
+!!! note "Relationship between virtual temperature and 'density temperature'"
     Some texts distinguish a "(condensate-ignoring) virtual temperature" and a "density temperature", and an analogous condensate-ignoring virtual potential temperature and density potential temperature.
     In those texts, the definition of density temperature incorporates condensate mass but their "condensate-ignoring virtual temperature" does not.
     We always take the mass of any condensate into account in the thermodynamics of moist air, so this distinction is irrelevant here.
@@ -420,6 +420,7 @@ TODO: there was a commented equation here, do we need it?
 This expression for temperature as a function of liquid-ice potential temperature is obtained from \eqref{e:TempFromThetaLiGivenP} by substituting for pressure in the Exner function ``\Pi`` from the ideal gas law, ``p=ρ R_m T``, solving for temperature using a second-order Taylor expansion around ``T_u`` for small condensate specific humidities, and using the relation ``1-κ = c_{vm}/c_{pm}``, which follows from ``c_{pm} - R_m = c_{vm}``. The relation for temperature \eqref{e:TempFromThetaLiGivenRho} holds to second order in condensate specific humidities ``q_l`` and ``q_i``. That is, the inversion relation \eqref{e:TempFromThetaLiGivenRho} holds to one higher order of accuracy than the definition of the liquid-ice potential temperature \eqref{e:liquid_ice_pottemp} itself, which is only first-order accurate in the condensate specific humidities ``q_l`` and ``q_i``.
 
 ### Speed of Sound
+
 The speed of sound in (moist) unstratified air is
 ```math
 \begin{equation}

docs/src/TemperatureProfiles.md

@@ -22,11 +22,8 @@ import Thermodynamics as TD
 import Plots
 import CLIMAParameters as CP
 import Thermodynamics.Parameters as TP
-FT = Float64;
-toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
-aliases = string.(fieldnames(TP.ThermodynamicsParameters))
-param_pairs = CP.get_parameter_values!(toml_dict, aliases, "Thermodynamics")
-param_set = TP.ThermodynamicsParameters{FT}(; param_pairs...)
+FT = Float64
+param_set = TP.ThermodynamicsParameters(FT)
 z = range(FT(0), stop = FT(2.5e4), length = 50);
 
 isothermal = TD.TemperatureProfiles.IsothermalProfile(param_set, FT);
@@ -49,11 +46,8 @@ import Thermodynamics as TD
 import Plots
 import CLIMAParameters as CP
 import Thermodynamics.Parameters as TP
-FT = Float64;
-toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
-aliases = string.(fieldnames(TP.ThermodynamicsParameters))
-param_pairs = CP.get_parameter_values!(toml_dict, aliases, "Thermodynamics")
-param_set = TP.ThermodynamicsParameters{FT}(; param_pairs...)
+FT = Float64
+param_set = TP.ThermodynamicsParameters(FT)
 z = range(FT(0), stop = FT(2.5e4), length = 50);
 
 decaying = TD.TemperatureProfiles.DecayingTemperatureProfile{FT}(param_set);
@@ -75,11 +69,8 @@ import Thermodynamics as TD
 import Plots
 import CLIMAParameters as CP
 import Thermodynamics.Parameters as TP
-FT = Float64;
-toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
-aliases = string.(fieldnames(TP.ThermodynamicsParameters))
-param_pairs = CP.get_parameter_values!(toml_dict, aliases, "Thermodynamics")
-param_set = TP.ThermodynamicsParameters{FT}(; param_pairs...)
+FT = Float64
+param_set = TP.ThermodynamicsParameters(FT)
 z = range(FT(0), stop = FT(2.5e4), length = 50);
 
 dry_adiabatic = TD.TemperatureProfiles.DryAdiabaticProfile{FT}(param_set);

docs/src/TestedProfiles.md

@@ -9,11 +9,8 @@ import Thermodynamics as TD
 import Plots
 import CLIMAParameters as CP
 import Thermodynamics.Parameters as TP
-FT = Float64;
-toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
-aliases = string.(fieldnames(TP.ThermodynamicsParameters))
-param_pairs = CP.get_parameter_values!(toml_dict, aliases, "Thermodynamics")
-param_set = TP.ThermodynamicsParameters{FT}(; param_pairs...)
+FT = Float64
+param_set = TP.ThermodynamicsParameters(FT)
 
 profiles = TD.TestedProfiles.PhaseDryProfiles(param_set, Array{FT});
 (;T, ρ, z) = profiles
@@ -31,11 +28,8 @@ import Thermodynamics as TD
 import Plots
 import CLIMAParameters as CP
 import Thermodynamics.Parameters as TP
-FT = Float64;
-toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
-aliases = string.(fieldnames(TP.ThermodynamicsParameters))
-param_pairs = CP.get_parameter_values!(toml_dict, aliases, "Thermodynamics")
-param_set = TP.ThermodynamicsParameters{FT}(; param_pairs...)
+FT = Float64
+param_set = TP.ThermodynamicsParameters(FT)
 
 profiles = TD.TestedProfiles.PhaseEquilProfiles(param_set, Array{FT});
 (;T, ρ, q_tot, z) = profiles

docs/src/saturation_adjustment.jl

@@ -1,17 +1,13 @@
-import RootSolvers
-const RS = RootSolvers
+import RootSolvers as RS
 import Plots
 
-FT = Float64;
 import Thermodynamics as TD
-const TP = TD.Parameters
+import Thermodynamics.Parameters as TP
 import CLIMAParameters as CP
 
-TD.print_warning() = false
-toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
-aliases = string.(fieldnames(TP.ThermodynamicsParameters))
-param_pairs = CP.get_parameter_values!(toml_dict, aliases, "Thermodynamics")
-const param_set = TP.ThermodynamicsParameters{FT}(; param_pairs...)
+FT = Float64
+
+const param_set = TP.ThermodynamicsParameters(FT)
 
 profiles = TD.TestedProfiles.PhaseEquilProfiles(param_set, Array{FT});
 (; ρ, q_tot) = profiles

ext/CreateParametersExt.jl

@@ -0,0 +1,42 @@
+module CreateParametersExt
+
+import Thermodynamics.Parameters.ThermodynamicsParameters
+import CLIMAParameters as CP
+
+ThermodynamicsParameters(::Type{FT}) where {FT <: AbstractFloat} =
+    ThermodynamicsParameters(CP.create_toml_dict(FT))
+
+function ThermodynamicsParameters(toml_dict::CP.AbstractTOMLDict)
+    name_map = (;
+        :temperature_min_at_reference => :T_min_ref,
+        :entropy_water_vapor => :entropy_water_vapor,
+        :entropy_dry_air => :entropy_dry_air,
+        :potential_temperature_reference_pressure => :p_ref_theta,
+        :entropy_reference_temperature => :entropy_reference_temperature,
+        :temperature_saturation_adjustment_max => :T_max,
+        :molar_mass_dry_air => :molmass_dryair,
+        :pow_icenuc => :pow_icenuc,
+        :temperature_triple_point => :T_triple,
+        :adiabatic_exponent_dry_air => :kappa_d,
+        :pressure_triple_point => :press_triple,
+        :thermodynamics_temperature_reference => :T_0,
+        :temperature_water_freeze => :T_freeze,
+        :isobaric_specific_heat_ice => :cp_i,
+        :latent_heat_sublimation_at_reference => :LH_s0,
+        :isobaric_specific_heat_vapor => :cp_v,
+        :molar_mass_water => :molmass_water,
+        :mean_sea_level_pressure => :MSLP,
+        :isobaric_specific_heat_liquid => :cp_l,
+        :latent_heat_vaporization_at_reference => :LH_v0,
+        :temperature_saturation_adjustment_min => :T_min,
+        :gas_constant => :gas_constant,
+        :temperature_mean_at_reference => :T_surf_ref,
+        :gravitational_acceleration => :grav,
+        :temperature_homogenous_nucleation => :T_icenuc,
+    )
+    parameters = CP.get_parameter_values(toml_dict, name_map, "Thermodynamics")
+    FT = CP.float_type(toml_dict)
+    return ThermodynamicsParameters{FT}(; parameters...)
+end
+
+end

gpuenv/Project.toml

@@ -1,19 +1,17 @@
 [deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 CLIMAParameters = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
-CUDAKernels = "72cfdca4-0801-4ab0-bf6a-d52aa10adc57"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RootSolvers = "7181ea78-2dcb-4de3-ab41-2b8ab5a31e74"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
+Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 
 [compat]
-CLIMAParameters = "0.6, 0.7"
-CUDA = "3.5"
-CUDAKernels = "0.3, 0.4"
-KernelAbstractions = "0.7, 0.8"
+CLIMAParameters = "0.8"
+CUDA = "3.5, 4, 5"
+KernelAbstractions = "0.9"
 RootSolvers = "0.4"
-UnPack = "1.0"
 julia = "1.7"