Try #1487:

CliMA · Oct 25, 2023 · eb000c6 · eb000c6
2 parents d8bd661 + c48a3e9
commit eb000c6
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diff --git a/.dev/Manifest.toml b/.dev/Manifest.toml
@@ -79,9 +79,9 @@ version = "0.21.4"
 
 [[deps.JuliaFormatter]]
 deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"]
-git-tree-sha1 = "80031f6e58b09b0de4553bf63d9a36ec5db57967"
+git-tree-sha1 = "0bac3374ff3aa798148669ecb5559ba20c8b0e73"
 uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-version = "1.0.39"
+version = "1.0.40"
 
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]

diff --git a/.dev/up_deps.jl b/.dev/up_deps.jl
@@ -12,6 +12,7 @@ dirs = (
     joinpath(root, "perf"),
     joinpath(root, "docs"),
     joinpath(root, "test"),
+    joinpath(root, "benchmarks", "bickleyjet"),
     joinpath(root, "lib", "ClimaCoreMakie"),
     joinpath(root, "lib", "ClimaCorePlots"),
     joinpath(root, "lib", "ClimaCoreTempestRemap"),

diff --git a/Project.toml b/Project.toml
@@ -19,6 +19,7 @@ HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Memoize = "c03570c3-d221-55d1-a50c-7939bbd78826"
 PkgVersion = "eebad327-c553-4316-9ea0-9fa01ccd7688"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
@@ -28,6 +29,7 @@ Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
+WeakValueDicts = "897b6980-f191-5a31-bcb0-bf3c4585e0c1"
 
 [compat]
 Adapt = "3"
@@ -43,13 +45,15 @@ GaussQuadrature = "0.5"
 GilbertCurves = "0.1"
 HDF5 = "0.16, 0.17"
 IntervalSets = "0.5, 0.6, 0.7"
+Memoize = "0.4"
 PkgVersion = "0.1, 0.2, 0.3"
 RecursiveArrayTools = "2"
 Requires = "1"
 RootSolvers = "0.3, 0.4"
 Static = "0.4, 0.5, 0.6, 0.7, 0.8"
 StaticArrays = "1"
 UnPack = "1"
+WeakValueDicts = "0.1"
 julia = "1.8"
 
 [extras]

diff --git a/benchmarks/bickleyjet/Manifest.toml b/benchmarks/bickleyjet/Manifest.toml
@@ -157,7 +157,7 @@ uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 version = "0.5.5"
 
 [[deps.ClimaCore]]
-deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack"]
+deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack", "WeakValueDicts"]
 path = "../.."
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
 version = "0.10.55"
@@ -784,6 +784,12 @@ git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102"
 uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
 version = "0.3.2"
 
+[[deps.Memoize]]
+deps = ["MacroTools"]
+git-tree-sha1 = "2b1dfcba103de714d31c033b5dacc2e4a12c7caa"
+uuid = "c03570c3-d221-55d1-a50c-7939bbd78826"
+version = "0.4.4"
+
 [[deps.MicrosoftMPI_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "a7023883872e52bc29bcaac74f19adf39347d2d5"
@@ -1272,6 +1278,11 @@ git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da"
 uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91"
 version = "1.25.0+0"
 
+[[deps.WeakValueDicts]]
+git-tree-sha1 = "98528c2610a5479f091d470967a25becfd83edd0"
+uuid = "897b6980-f191-5a31-bcb0-bf3c4585e0c1"
+version = "0.1.0"
+
 [[deps.XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
 git-tree-sha1 = "24b81b59bd35b3c42ab84fa589086e19be919916"

diff --git a/docs/Manifest.toml b/docs/Manifest.toml
@@ -274,7 +274,7 @@ uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 version = "0.5.5"
 
 [[deps.ClimaCore]]
-deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack"]
+deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack", "WeakValueDicts"]
 path = ".."
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
 version = "0.10.55"
@@ -1310,9 +1310,9 @@ version = "0.1.12"
 
 [[deps.LinearSolve]]
 deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"]
-git-tree-sha1 = "158e45dd35cec1ecade0e554c0104ee89e772d82"
+git-tree-sha1 = "3196f7408f7c6014dc4ed55260e6c5e1e01c58a3"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "2.11.1"
+version = "2.12.0"
 
     [deps.LinearSolve.extensions]
     LinearSolveBandedMatricesExt = "BandedMatrices"
@@ -1477,6 +1477,12 @@ git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102"
 uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
 version = "0.3.2"
 
+[[deps.Memoize]]
+deps = ["MacroTools"]
+git-tree-sha1 = "2b1dfcba103de714d31c033b5dacc2e4a12c7caa"
+uuid = "c03570c3-d221-55d1-a50c-7939bbd78826"
+version = "0.4.4"
+
 [[deps.MicrosoftMPI_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "a7023883872e52bc29bcaac74f19adf39347d2d5"
@@ -2543,6 +2549,11 @@ git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da"
 uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91"
 version = "1.25.0+0"
 
+[[deps.WeakValueDicts]]
+git-tree-sha1 = "98528c2610a5479f091d470967a25becfd83edd0"
+uuid = "897b6980-f191-5a31-bcb0-bf3c4585e0c1"
+version = "0.1.0"
+
 [[deps.WoodburyMatrices]]
 deps = ["LinearAlgebra", "SparseArrays"]
 git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3"

diff --git a/docs/src/api.md b/docs/src/api.md
@@ -184,48 +184,46 @@ Spaces.Δz_metric_component
 ```@docs
 Spaces.SpectralElementSpace1D
 Spaces.SpectralElementSpace2D
-Spaces.SpectralElementSpace2D(topology, quadrature_style; enable_bubble)
 Spaces.SpectralElementSpaceSlab
 ```
 
 ### Quadratures
 
 
 ```@docs
-Spaces.Quadratures.QuadratureStyle
-Spaces.Quadratures.GLL
-Spaces.Quadratures.GL
-Spaces.Quadratures.Uniform
-Spaces.Quadratures.degrees_of_freedom
-Spaces.Quadratures.polynomial_degree
-Spaces.Quadratures.quadrature_points
-Spaces.Quadratures.barycentric_weights
-Spaces.Quadratures.interpolation_matrix
-Spaces.Quadratures.differentiation_matrix
-Spaces.Quadratures.orthonormal_poly
+Quadratures.QuadratureStyle
+Quadratures.GLL
+Quadratures.GL
+Quadratures.Uniform
+Quadratures.degrees_of_freedom
+Quadratures.polynomial_degree
+Quadratures.quadrature_points
+Quadratures.barycentric_weights
+Quadratures.interpolation_matrix
+Quadratures.differentiation_matrix
+Quadratures.orthonormal_poly
 ```
 
 #### Internals
 
 ```@docs
-Spaces.dss_transform
-Spaces.dss_transform!
-Spaces.dss_untransform!
-Spaces.dss_untransform
-Spaces.dss_local_vertices!
-Spaces.dss_local!
-Spaces.dss_local_ghost!
-Spaces.dss_ghost!
-Spaces.create_dss_buffer
-Spaces.fill_send_buffer!
-Spaces.DSSBuffer
-Spaces.create_ghost_buffer
-Spaces.load_from_recv_buffer!
+Topologies.dss_transform
+Topologies.dss_transform!
+Topologies.dss_untransform!
+Topologies.dss_untransform
+Topologies.dss_local_vertices!
+Topologies.dss_local!
+Topologies.dss_local_ghost!
+Topologies.dss_ghost!
+Topologies.create_dss_buffer
+Topologies.fill_send_buffer!
+Topologies.DSSBuffer
+Topologies.load_from_recv_buffer!
+Topologies.dss!
 Spaces.weighted_dss_start!
 Spaces.weighted_dss_internal!
 Spaces.weighted_dss_ghost!
 Spaces.weighted_dss!
-Spaces.dss!
 Spaces.unique_nodes
 ```
 

diff --git a/examples/Manifest.toml b/examples/Manifest.toml
@@ -238,7 +238,7 @@ uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 version = "0.5.5"
 
 [[deps.ClimaCore]]
-deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack"]
+deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack", "WeakValueDicts"]
 path = ".."
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
 version = "0.10.55"
@@ -1099,9 +1099,9 @@ version = "2.5.2"
 
 [[deps.LinearSolve]]
 deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"]
-git-tree-sha1 = "158e45dd35cec1ecade0e554c0104ee89e772d82"
+git-tree-sha1 = "3196f7408f7c6014dc4ed55260e6c5e1e01c58a3"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "2.11.1"
+version = "2.12.0"
 
     [deps.LinearSolve.extensions]
     LinearSolveBandedMatricesExt = "BandedMatrices"
@@ -1226,6 +1226,12 @@ git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102"
 uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
 version = "0.3.2"
 
+[[deps.Memoize]]
+deps = ["MacroTools"]
+git-tree-sha1 = "2b1dfcba103de714d31c033b5dacc2e4a12c7caa"
+uuid = "c03570c3-d221-55d1-a50c-7939bbd78826"
+version = "0.4.4"
+
 [[deps.MicroCollections]]
 deps = ["BangBang", "InitialValues", "Setfield"]
 git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e"
@@ -2082,6 +2088,11 @@ git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da"
 uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91"
 version = "1.25.0+0"
 
+[[deps.WeakValueDicts]]
+git-tree-sha1 = "98528c2610a5479f091d470967a25becfd83edd0"
+uuid = "897b6980-f191-5a31-bcb0-bf3c4585e0c1"
+version = "0.1.0"
+
 [[deps.WriteVTK]]
 deps = ["Base64", "CodecZlib", "FillArrays", "LightXML", "TranscodingStreams", "VTKBase"]
 git-tree-sha1 = "41f0dc2a8f6fd860c266b91fd5cdf4fead65ae69"

diff --git a/examples/bickleyjet/bickleyjet_dg.jl b/examples/bickleyjet/bickleyjet_dg.jl
@@ -208,7 +208,7 @@ function rhs!(dydt, y, (parameters, numflux), t)
     dydt_data .= RecursiveApply.rdiv.(dydt_data, space.local_geometry.WJ)
     M = Spaces.Quadratures.cutoff_filter_matrix(
         Float64,
-        space.quadrature_style,
+        Spaces.quadrature_style(space),
         3,
     )
     Operators.tensor_product!(dydt_data, M)

diff --git a/examples/hybrid/hybrid3dcs_dss.jl b/examples/hybrid/hybrid3dcs_dss.jl
@@ -85,18 +85,16 @@ function hybrid3dcubedsphere_dss_profiler(
         c = center_initial_condition(ᶜlocal_geometry),
         f = face_initial_condition(ᶠlocal_geometry),
     )
-    ghost_buffer = (
-        c = Spaces.create_ghost_buffer(Y.c),
-        f = Spaces.create_ghost_buffer(Y.f),
-    )
+    ghost_buffer =
+        (c = Spaces.create_dss_buffer(Y.c), f = Spaces.create_dss_buffer(Y.f))
     dss_buffer_f = Spaces.create_dss_buffer(Y.f)
     dss_buffer_c = Spaces.create_dss_buffer(Y.c)
     nsamples = 10000
     nsamplesprofiling = 100
 
     # precompile relevant functions
     space = axes(Y.c)
-    horizontal_topology = space.horizontal_space.topology
+    horizontal_topology = Spaces.topology(space)
     Spaces.weighted_dss_internal!(Y.c, ghost_buffer.c)
     weighted_dss_full!(Y.c, ghost_buffer.c)
     Spaces.fill_send_buffer!(

diff --git a/examples/hybrid/sphere/deformation_flow.jl b/examples/hybrid/sphere/deformation_flow.jl
@@ -216,7 +216,7 @@ function run_deformation_flow(use_limiter, fct_op)
             Geometry.LatLongZPoint(ϕ_c, λ_c1, FT(0)),
             Geometry.LatLongZPoint(ϕ_c, λ_c2, FT(0)),
         )
-        horz_geometry = horz_space.global_geometry
+        horz_geometry = Spaces.global_geometry(horz_space)
         rds = map(centers) do center
             Geometry.great_circle_distance(coord, center, horz_geometry)
         end

diff --git a/examples/hybrid/sphere/hadley_circulation.jl b/examples/hybrid/sphere/hadley_circulation.jl
@@ -250,7 +250,7 @@ end
 
 # write out our cubed sphere mesh
 meshfile_cc = remap_tmpdir * "mesh_cubedsphere.g"
-write_exodus(meshfile_cc, hv_center_space.horizontal_space.topology)
+write_exodus(meshfile_cc, Spaces.topology(hv_center_space))
 
 # write out RLL mesh
 nlat = 90

diff --git a/examples/hybrid/sphere/remap_pipeline.jl b/examples/hybrid/sphere/remap_pipeline.jl
@@ -53,7 +53,7 @@ function remap2latlon(filein, nc_dir, nlat, nlon)
     # reconstruct space, obtain Nq from space
     cspace = axes(Y.c)
     hspace = Spaces.horizontal_space(cspace)
-    Nq = Spaces.Quadratures.degrees_of_freedom(hspace.quadrature_style)
+    Nq = Spaces.Quadratures.degrees_of_freedom(Spaces.quadrature_style(hspace))
 
     # create a temporary dir for intermediate data
     remap_tmpdir = nc_dir * "remaptmp/"
@@ -97,7 +97,7 @@ function remap2latlon(filein, nc_dir, nlat, nlon)
 
     # write out our cubed sphere mesh
     meshfile_cc = remap_tmpdir * "mesh_cubedsphere.g"
-    write_exodus(meshfile_cc, hspace.topology)
+    write_exodus(meshfile_cc, Spaces.topology(hspace))
 
     meshfile_rll = remap_tmpdir * "mesh_rll.g"
     rll_mesh(meshfile_rll; nlat = nlat, nlon = nlon)

diff --git a/examples/sphere/limiters_advection.jl b/examples/sphere/limiters_advection.jl
@@ -107,13 +107,13 @@ for (k, ne) in enumerate(ne_seq)
         Spaces.SpectralElementSpace2D(grid_topology, quad; enable_bubble = true)
 
     # Initialize variables needed for limiters
-    n_elems = Topologies.nlocalelems(space.topology)
+    n_elems = Topologies.nlocalelems(Spaces.topology(space))
     min_q = zeros(n_elems)
     max_q = zeros(n_elems)
 
     coords = Fields.coordinate_field(space)
     Δh[k] = 2 * R / ne
-    global_geom = space.global_geometry
+    global_geom = Spaces.global_geometry(space)
 
     # Initialize state
     y0 = map(coords) do coord

diff --git a/examples/sphere/shallow_water_cuda.jl b/examples/sphere/shallow_water_cuda.jl
@@ -473,7 +473,7 @@ function rhs!(dYdt_fv, y_fv, parameters, t)
                     wcurl(Geometry.Covariant3Vector(curl(y.u))),
                 )
 
-            NVTX.@range "dss" Spaces.weighted_dss2!(dYdt, ghost_buffer)
+            NVTX.@range "dss" Spaces.weighted_dss!(dYdt, ghost_buffer)
         end
 
         NVTX.@range "tendency" begin
@@ -489,7 +489,7 @@ function rhs!(dYdt_fv, y_fv, parameters, t)
                 dYdt.u += -grad(g * (y.h + h_s) + norm(y.u)^2 / 2) #+
                 dYdt.u += y.u × (f + curl(y.u))
             end
-            NVTX.@range "dss" Spaces.weighted_dss2!(dYdt, ghost_buffer)
+            NVTX.@range "dss" Spaces.weighted_dss!(dYdt, ghost_buffer)
         end
     end
     return dYdt_fv

diff --git a/examples/sphere/solidbody.jl b/examples/sphere/solidbody.jl
@@ -87,7 +87,7 @@ for (k, ne) in enumerate(ne_seq)
 
     Δh[k] = 2 * R / ne
 
-    global_geom = space.global_geometry
+    global_geom = Spaces.global_geometry(space)
 
     h_init = map(coords) do coord
         rd = Geometry.great_circle_distance(coord, center, global_geom)

diff --git a/lib/ClimaCoreMakie/src/utils.jl b/lib/ClimaCoreMakie/src/utils.jl
@@ -22,7 +22,7 @@ function plot_vertices(
         space,
         ClimaCore.Geometry.Cartesian123Point.(
             ClimaCore.Fields.coordinate_field(space),
-            Ref(space.global_geometry),
+            Ref(Spaces.global_geometry(space)),
         ),
     )
 end