Use Scratch for Bathymetry (#95)

* Use Scratch for Bathymetry * add scratch for JRA55 * small bugfix * bugfix * updating Oceananigans and ClimaSeaIce * typo * another typo * differentiate scratch names * bugfix * last test fix --------- Co-authored-by: Simone Silvestri <[email protected]> Co-authored-by: Simone Silvestri <[email protected]>
CliMA · Jul 4, 2024 · f52a6d6 · f52a6d6
1 parent dc7a775
commit f52a6d6
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diff --git a/.gitignore b/.gitignore
@@ -34,3 +34,8 @@ docs/src/literated/
 *.DS_Store
 *.swp
 *.zip
+
+# outputs of NVIDIA profiling tools
+*.qdrep
+*.nsys-rep
+*.ncu-rep
diff --git a/Manifest.toml b/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.10.4"
 manifest_format = "2.0"
-project_hash = "b259754f5c46aa5209342e33ffe472cc48d8cee9"
+project_hash = "086b5c52c3f2a61f133762647db63128f8714c56"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -97,15 +97,15 @@ version = "0.5.0"
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[deps.BitFlags]]
-git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b"
+git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
 uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
-version = "0.1.8"
+version = "0.1.9"
 
 [[deps.BitTwiddlingConvenienceFunctions]]
 deps = ["Static"]
-git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b"
+git-tree-sha1 = "f21cfd4950cb9f0587d5067e69405ad2acd27b87"
 uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b"
-version = "0.1.5"
+version = "0.1.6"
 
 [[deps.Blosc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"]
@@ -132,9 +132,9 @@ version = "0.1.3"
 
 [[deps.CPUSummary]]
 deps = ["CpuId", "IfElse", "PrecompileTools", "Static"]
-git-tree-sha1 = "585a387a490f1c4bd88be67eea15b93da5e85db7"
+git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec"
 uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
-version = "0.2.5"
+version = "0.2.6"
 
 [[deps.CUDA]]
 deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "Crayons", "DataFrames", "ExprTools", "GPUArrays", "GPUCompiler", "KernelAbstractions", "LLVM", "LLVMLoopInfo", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "NVTX", "Preferences", "PrettyTables", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics"]
@@ -160,9 +160,9 @@ version = "0.9.0+0"
 
 [[deps.CUDA_Runtime_Discovery]]
 deps = ["Libdl"]
-git-tree-sha1 = "5db9da5fdeaa708c22ba86b82c49528f402497f2"
+git-tree-sha1 = "f3b237289a5a77c759b2dd5d4c2ff641d67c4030"
 uuid = "1af6417a-86b4-443c-805f-a4643ffb695f"
-version = "0.3.3"
+version = "0.3.4"
 
 [[deps.CUDA_Runtime_jll]]
 deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
@@ -182,23 +182,21 @@ weakdeps = ["SparseArrays"]
 
 [[deps.ClimaSeaIce]]
 deps = ["Adapt", "KernelAbstractions", "Oceananigans", "RootSolvers", "Roots", "SeawaterPolynomials"]
-git-tree-sha1 = "0ac8d2566e8f4887896c8a03ee87050fcbbf6599"
-repo-rev = "ss/new-oceananigans"
-repo-url = "https://github.com/CliMA/ClimaSeaIce.jl.git"
+git-tree-sha1 = "36752a8f020c7f1c959fea0e5a98b113d54fc74f"
 uuid = "6ba0ff68-24e6-4315-936c-2e99227c95a4"
-version = "0.1.0"
+version = "0.1.1"
 
 [[deps.CloseOpenIntervals]]
 deps = ["Static", "StaticArrayInterface"]
-git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1"
+git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581"
 uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9"
-version = "0.1.12"
+version = "0.1.13"
 
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
-git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73"
+git-tree-sha1 = "b8fe8546d52ca154ac556809e10c75e6e7430ac8"
 uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
-version = "0.7.4"
+version = "0.7.5"
 
 [[deps.ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
@@ -239,6 +237,11 @@ git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7"
 uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
 version = "0.3.0"
 
+[[deps.CommonWorldInvalidations]]
+git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0"
+uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8"
+version = "1.0.0"
+
 [[deps.Compat]]
 deps = ["TOML", "UUIDs"]
 git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248"
@@ -446,9 +449,9 @@ version = "6.2.1+6"
 
 [[deps.GPUArrays]]
 deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"]
-git-tree-sha1 = "38cb19b8a3e600e509dc36a6396ac74266d108c1"
+git-tree-sha1 = "5c9de6d5af87acd2cf719e214ed7d51e14017b7a"
 uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "10.1.1"
+version = "10.2.2"
 
 [[deps.GPUArraysCore]]
 deps = ["Adapt"]
@@ -487,15 +490,15 @@ version = "1.10.8"
 
 [[deps.HostCPUFeatures]]
 deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"]
-git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2"
+git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293"
 uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0"
-version = "0.1.16"
+version = "0.1.17"
 
 [[deps.Hwloc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "ca0f6bf568b4bfc807e7537f081c81e35ceca114"
+git-tree-sha1 = "1d334207121865ac8c1c97eb7f42d0339e4635bf"
 uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
-version = "2.10.0+0"
+version = "2.11.0+0"
 
 [[deps.IfElse]]
 git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1"
@@ -522,9 +525,15 @@ version = "0.2.1"
 
 [[deps.InlineStrings]]
 deps = ["Parsers"]
-git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461"
+git-tree-sha1 = "86356004f30f8e737eff143d57d41bd580e437aa"
 uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
-version = "1.4.0"
+version = "1.4.1"
+
+    [deps.InlineStrings.extensions]
+    ArrowTypesExt = "ArrowTypes"
+
+    [deps.InlineStrings.weakdeps]
+    ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
 
 [[deps.IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -599,9 +608,9 @@ version = "0.2.1+0"
 
 [[deps.KernelAbstractions]]
 deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
-git-tree-sha1 = "8e5a339882cc401688d79b811d923a38ba77d50a"
+git-tree-sha1 = "d0448cebd5919e06ca5edc7a264631790de810ec"
 uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
-version = "0.9.20"
+version = "0.9.22"
 
     [deps.KernelAbstractions.extensions]
     EnzymeExt = "EnzymeCore"
@@ -652,9 +661,9 @@ version = "1.3.1"
 
 [[deps.LayoutPointers]]
 deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"]
-git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277"
+git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c"
 uuid = "10f19ff3-798f-405d-979b-55457f8fc047"
-version = "0.1.15"
+version = "0.1.17"
 
 [[deps.LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
@@ -724,9 +733,9 @@ version = "1.0.3"
 
 [[deps.LoopVectorization]]
 deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"]
-git-tree-sha1 = "8f6786d8b2b3248d79db3ad359ce95382d5a6df8"
+git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd"
 uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
-version = "0.12.170"
+version = "0.12.171"
 weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"]
 
     [deps.LoopVectorization.extensions]
@@ -875,9 +884,9 @@ version = "1.2.0"
 
 [[deps.Oceananigans]]
 deps = ["Adapt", "CUDA", "Crayons", "CubedSphere", "Dates", "Distances", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilArrays", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays"]
-git-tree-sha1 = "994ae77f4f232940822770d8ce7c2f84e373156e"
+git-tree-sha1 = "745b1c19221e09886cae331450a2a4ea73708a38"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.91.1"
+version = "0.91.3"
 
     [deps.Oceananigans.extensions]
     OceananigansEnzymeExt = "Enzyme"
@@ -959,15 +968,17 @@ version = "2.8.1"
 
 [[deps.PencilArrays]]
 deps = ["Adapt", "JSON3", "LinearAlgebra", "MPI", "OffsetArrays", "Random", "Reexport", "StaticArrayInterface", "StaticArrays", "StaticPermutations", "Strided", "TimerOutputs", "VersionParsing"]
-git-tree-sha1 = "8c5b9251650cb0ac77911f7e8a9e8f7c15bd5c99"
+git-tree-sha1 = "fa85ac32172d96cfdb91dbc53e8e57007e5a2b5a"
 uuid = "0e08944d-e94e-41b1-9406-dcf66b6a9d2e"
-version = "0.19.4"
+version = "0.19.5"
 
     [deps.PencilArrays.extensions]
+    PencilArraysAMDGPUExt = ["AMDGPU"]
     PencilArraysDiffEqExt = ["DiffEqBase"]
     PencilArraysHDF5Ext = ["HDF5"]
 
     [deps.PencilArrays.weakdeps]
+    AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e"
     DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
     HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 
@@ -990,9 +1001,9 @@ version = "0.3.3"
 
 [[deps.PolyesterWeave]]
 deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"]
-git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6"
+git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd"
 uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad"
-version = "0.2.1"
+version = "0.2.2"
 
 [[deps.PooledArrays]]
 deps = ["DataAPI", "Future"]
@@ -1122,9 +1133,9 @@ version = "0.1.0"
 
 [[deps.SLEEFPirates]]
 deps = ["IfElse", "Static", "VectorizationBase"]
-git-tree-sha1 = "3aac6d68c5e57449f5b9b865c9ba50ac2970c4cf"
+git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0"
 uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa"
-version = "0.6.42"
+version = "0.6.43"
 
 [[deps.Scratch]]
 deps = ["Dates"]
@@ -1182,16 +1193,16 @@ uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15"
 version = "0.1.1"
 
 [[deps.Static]]
-deps = ["IfElse"]
-git-tree-sha1 = "d2fdac9ff3906e27f7a618d47b676941baa6c80c"
+deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"]
+git-tree-sha1 = "0bbff21027dd8a107551847528127b62a35f7594"
 uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "0.8.10"
+version = "1.1.0"
 
 [[deps.StaticArrayInterface]]
 deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"]
-git-tree-sha1 = "5d66818a39bb04bf328e92bc933ec5b4ee88e436"
+git-tree-sha1 = "8963e5a083c837531298fc41599182a759a87a6d"
 uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718"
-version = "1.5.0"
+version = "1.5.1"
 weakdeps = ["OffsetArrays", "StaticArrays"]
 
     [deps.StaticArrayInterface.extensions]
@@ -1200,9 +1211,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"]
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "6e00379a24597be4ae1ee6b2d882e15392040132"
+git-tree-sha1 = "20833c5b7f7edf0e5026f23db7f268e4f23ec577"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.5"
+version = "1.9.6"
 weakdeps = ["ChainRulesCore", "Statistics"]
 
     [deps.StaticArrays.extensions]
@@ -1232,15 +1243,15 @@ version = "1.7.0"
 
 [[deps.Strided]]
 deps = ["LinearAlgebra", "StridedViews", "TupleTools"]
-git-tree-sha1 = "40c69be0e1b72ee2f42923b7d1ff13e0b04e675c"
+git-tree-sha1 = "bd9bd1c70cfc115cc3a30213fc725125a6b43652"
 uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67"
-version = "2.0.4"
+version = "2.1.0"
 
 [[deps.StridedViews]]
 deps = ["LinearAlgebra", "PackageExtensionCompat"]
-git-tree-sha1 = "5b765c4e401693ab08981989f74a36a010aa1d8e"
+git-tree-sha1 = "2917996ce0fa6b8a3a85240a5e9ff930e2aeaa43"
 uuid = "4db3bf67-4bd7-4b4e-b153-31dc3fb37143"
-version = "0.2.2"
+version = "0.3.1"
 weakdeps = ["CUDA"]
 
     [deps.StridedViews.extensions]
@@ -1367,9 +1378,9 @@ uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 version = "0.5.24"
 
 [[deps.TranscodingStreams]]
-git-tree-sha1 = "a947ea21087caba0a798c5e494d0bb78e3a1a3a0"
+git-tree-sha1 = "d73336d81cafdc277ff45558bb7eaa2b04a8e472"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.10.9"
+version = "0.10.10"
 weakdeps = ["Random", "Test"]
 
     [deps.TranscodingStreams.extensions]
@@ -1404,15 +1415,15 @@ version = "0.2.1"
 
 [[deps.UnsafeAtomicsLLVM]]
 deps = ["LLVM", "UnsafeAtomics"]
-git-tree-sha1 = "d9f5962fecd5ccece07db1ff006fb0b5271bdfdd"
+git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5"
 uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249"
-version = "0.1.4"
+version = "0.1.5"
 
 [[deps.VectorizationBase]]
 deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"]
-git-tree-sha1 = "e863582a41c5731f51fd050563ae91eb33cf09be"
+git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5"
 uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
-version = "0.21.68"
+version = "0.21.70"
 
 [[deps.VersionParsing]]
 git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868"
@@ -1421,9 +1432,9 @@ version = "1.3.0"
 
 [[deps.XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
-git-tree-sha1 = "52ff2af32e591541550bd753c0da8b9bc92bb9d9"
+git-tree-sha1 = "d9717ce3518dc68a99e6b96300813760d887a01d"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
-version = "2.12.7+0"
+version = "2.13.1+0"
 
 [[deps.XZ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]

diff --git a/Project.toml b/Project.toml
@@ -18,6 +18,7 @@ KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 Oceananigans = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Scratch = "6c6a2e73-6563-6170-7368-637461726353"
 SeawaterPolynomials = "d496a93d-167e-4197-9f49-d3af4ff8fe40"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -36,6 +37,7 @@ JLD2 = "0.4"
 KernelAbstractions = "0.9"
 NCDatasets = "0.12, 0.13, 0.14"
 Oceananigans = "0.90, 0.91"
+Scratch = "1"
 SeawaterPolynomials = "0.3.4"
 StaticArrays = "1"
 Statistics = "1.9"

diff --git a/src/Bathymetry.jl b/src/Bathymetry.jl
@@ -19,13 +19,19 @@ using JLD2
 using NCDatasets
 using Downloads
 using Printf
+using Scratch
+
+download_bathymetry_cache::String = ""
+function __init__()
+    global download_bathymetry_cache = @get_scratch!("Bathymetry")
+end
 
 """
     regrid_bathymetry(target_grid;
                       url = "https://www.ngdc.noaa.gov/thredds/fileServer/global/ETOPO2022/60s/60s_surface_elev_netcdf", 
                       height_above_water = <none>,
                       minimum_depth = 0,
-                      dir = joinpath(@__DIR__, "..", "data"),
+                      dir = download_cache,
                       filename = "ETOPO_2022_v1_60s_N90W180_surface.nc")
 
 Regrid bathymetry associated with the NetCDF file at `path = joinpath(dir, filename)` to `target_grid`.
@@ -73,7 +79,7 @@ Keyword Arguments:
 function regrid_bathymetry(target_grid;
                            height_above_water = nothing,
                            minimum_depth = 0,
-                           dir = joinpath(@__DIR__, "..", "data"),
+                           dir = download_bathymetry_cache,
                            url = "https://www.ngdc.noaa.gov/thredds/fileServer/global/ETOPO2022/60s/60s_surface_elev_netcdf", 
                            filename = "ETOPO_2022_v1_60s_N90W180_surface.nc",
                            interpolation_passes = 1,