Skip to content

Commit

Permalink
Merge pull request #188 from OceanBioME/jsw/fix-box-model-speedy-save
Browse files Browse the repository at this point in the history 
Fixs box model `SpeedyOutput` + adds tests for `BoxModel`
  • Loading branch information
@jagoosw
jagoosw authored Jul 26, 2024
2 parents 33b611a + 19e8b7c commit 4bcaf29
Show file tree
Hide file tree
Showing 14 changed files with 188 additions and 87 deletions.
77 changes: 39 additions & 38 deletions Manifest.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@ weakdeps = ["ChainRulesCore", "Test"]

[[deps.Accessors]]
deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"]
git-tree-sha1 = "c0d491ef0b135fd7d63cbc6404286bc633329425"
git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a"
uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
version = "0.1.36"
version = "0.1.37"

[deps.Accessors.extensions]
AccessorsAxisKeysExt = "AxisKeys"
Expand Down Expand Up @@ -52,9 +52,9 @@ version = "1.1.1"

[[deps.ArrayInterface]]
deps = ["Adapt", "LinearAlgebra", "SparseArrays", "SuiteSparse"]
git-tree-sha1 = "ed2ec3c9b483842ae59cd273834e5b46206d6dda"
git-tree-sha1 = "5c9b74c973181571deb6442d41e5c902e6b9f38e"
uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
version = "7.11.0"
version = "7.12.0"

[deps.ArrayInterface.extensions]
ArrayInterfaceBandedMatricesExt = "BandedMatrices"
Expand Down Expand Up @@ -137,9 +137,9 @@ version = "5.4.2"

[[deps.CUDA_Driver_jll]]
deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
git-tree-sha1 = "c48f9da18efd43b6b7adb7ee1f93fe5f2926c339"
git-tree-sha1 = "97df9d4d6be8ac6270cb8fd3b8fc413690820cbd"
uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc"
version = "0.9.0+0"
version = "0.9.1+1"

[[deps.CUDA_Runtime_Discovery]]
deps = ["Libdl"]
Expand All @@ -149,9 +149,9 @@ version = "0.3.4"

[[deps.CUDA_Runtime_jll]]
deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
git-tree-sha1 = "bcba305388e16aa5c879e896726db9e71b4942c6"
git-tree-sha1 = "afea94249b821dc754a8ca6695d3daed851e1f5a"
uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2"
version = "0.14.0+1"
version = "0.14.1+0"

[[deps.ChainRulesCore]]
deps = ["Compat", "LinearAlgebra"]
Expand Down Expand Up @@ -217,9 +217,9 @@ weakdeps = ["InverseFunctions"]

[[deps.ConstructionBase]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2"
git-tree-sha1 = "d8a9c0b6ac2d9081bf76324b39c78ca3ce4f0c98"
uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
version = "1.5.5"
version = "1.5.6"

[deps.ConstructionBase.extensions]
ConstructionBaseIntervalSetsExt = "IntervalSets"
Expand Down Expand Up @@ -346,9 +346,9 @@ version = "6.2.1+6"

[[deps.GPUArrays]]
deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"]
git-tree-sha1 = "5c9de6d5af87acd2cf719e214ed7d51e14017b7a"
git-tree-sha1 = "a74c3f1cf56a3dfcdef0605f8cdb7015926aae30"
uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
version = "10.2.2"
version = "10.3.0"

[[deps.GPUArraysCore]]
deps = ["Adapt"]
Expand Down Expand Up @@ -381,9 +381,9 @@ version = "1.14.2+1"

[[deps.Hwloc_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "1d334207121865ac8c1c97eb7f42d0339e4635bf"
git-tree-sha1 = "5e19e1e4fa3e71b774ce746274364aef0234634e"
uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
version = "2.11.0+0"
version = "2.11.1+0"

[[deps.IfElse]]
git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1"
Expand All @@ -397,32 +397,33 @@ uuid = "40713840-3770-5561-ab4c-a76e7d0d7895"
version = "0.2.1"

[[deps.InlineStrings]]
deps = ["Parsers"]
git-tree-sha1 = "86356004f30f8e737eff143d57d41bd580e437aa"
git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d"
uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
version = "1.4.1"
version = "1.4.2"

[deps.InlineStrings.extensions]
ArrowTypesExt = "ArrowTypes"
ParsersExt = "Parsers"

[deps.InlineStrings.weakdeps]
ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"

[[deps.IntelOpenMP_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4"
git-tree-sha1 = "14eb2b542e748570b56446f4c50fbfb2306ebc45"
uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0"
version = "2024.1.0+0"
version = "2024.2.0+0"

[[deps.InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[deps.InverseFunctions]]
deps = ["Test"]
git-tree-sha1 = "e7cbed5032c4c397a6ac23d1493f3289e01231c4"
git-tree-sha1 = "18c59411ece4838b18cd7f537e56cf5e41ce5bfd"
uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
version = "0.1.14"
version = "0.1.15"
weakdeps = ["Dates"]

[deps.InverseFunctions.extensions]
Expand Down Expand Up @@ -600,9 +601,9 @@ version = "1.9.4+0"

[[deps.MKL_jll]]
deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"]
git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b"
git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f"
uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
version = "2024.1.0+0"
version = "2024.2.0+0"

[[deps.MPI]]
deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "PkgVersion", "PrecompileTools", "Requires", "Serialization", "Sockets"]
Expand All @@ -620,9 +621,9 @@ version = "0.20.16"

[[deps.MPICH_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
git-tree-sha1 = "4099bb6809ac109bfc17d521dad33763bcf026b7"
git-tree-sha1 = "19d4bd098928a3263693991500d05d74dbdc2004"
uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
version = "4.2.1+1"
version = "4.2.2+0"

[[deps.MPIPreferences]]
deps = ["Libdl", "Preferences"]
Expand Down Expand Up @@ -717,9 +718,9 @@ version = "0.91.3"
Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"

[[deps.OffsetArrays]]
git-tree-sha1 = "e64b4f5ea6b7389f6f046d13d4896a8f9c1ba71e"
git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e"
uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
version = "1.14.0"
version = "1.14.1"
weakdeps = ["Adapt"]

[deps.OffsetArrays.extensions]
Expand All @@ -737,9 +738,9 @@ version = "0.8.1+2"

[[deps.OpenMPI_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
git-tree-sha1 = "a9de2f1fc98b92f8856c640bf4aec1ac9b2a0d86"
git-tree-sha1 = "2f0a1d8c79bc385ec3fcda12830c9d0e72b30e71"
uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
version = "5.0.3+0"
version = "5.0.4+0"

[[deps.OpenSSL_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
Expand Down Expand Up @@ -937,9 +938,9 @@ version = "0.3.4"

[[deps.SentinelArrays]]
deps = ["Dates", "Random"]
git-tree-sha1 = "90b4f68892337554d31cdcdbe19e48989f26c7e6"
git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a"
uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
version = "1.4.3"
version = "1.4.5"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
Expand Down Expand Up @@ -970,9 +971,9 @@ weakdeps = ["ChainRulesCore"]

[[deps.Static]]
deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"]
git-tree-sha1 = "0bbff21027dd8a107551847528127b62a35f7594"
git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603"
uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
version = "1.1.0"
version = "1.1.1"

[[deps.StaticArrayInterface]]
deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"]
Expand All @@ -987,9 +988,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"]

[[deps.StaticArrays]]
deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
git-tree-sha1 = "20833c5b7f7edf0e5026f23db7f268e4f23ec577"
git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.9.6"
version = "1.9.7"
weakdeps = ["ChainRulesCore", "Statistics"]

[deps.StaticArrays.extensions]
Expand Down Expand Up @@ -1079,10 +1080,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.1"

[[deps.Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"]
git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d"
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"]
git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.11.1"
version = "1.12.0"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
Expand Down
2 changes: 1 addition & 1 deletion Project.toml
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "OceanBioME"
uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
authors = ["Jago Strong-Wright <[email protected]> and contributors"]
version = "0.10.4"
version = "0.10.5"

[deps]
Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
Expand Down
31 changes: 13 additions & 18 deletions benchmark/box_model.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
# ```

using OceanBioME, Oceananigans.Units, Oceananigans, BenchmarkTools
using Oceananigans.Fields: FunctionField

const year = years = 365day

Expand All @@ -25,13 +26,20 @@ const year = years = 365day
@inline PAR⁰(t) = 60 * (1 - cos((t + 15days) * 2π / year)) * (1 / (1 + 0.2 * exp(-((mod(t, year) - 200days) / 50days)^2))) + 2

z = -10 # nominal depth of the box for the PAR profile
@inline PAR(t)::Float64 = PAR⁰(t) * exp(0.2z) # Modify the PAR based on the nominal depth and exponential decay
@inline PAR_func(t)::Float64 = PAR⁰(t) * exp(0.2z) # Modify the PAR based on the nominal depth and exponential decay

function run_box_simulation()
biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid = BoxModelGrid,
light_attenuation_model = nothing)

model = BoxModel(; biogeochemistry, forcing = (; PAR))
clock = Clock(time = Float64(0))

grid = BoxModelGrid()

PAR = FunctionField{Center, Center, Center}(PAR_func, grid; clock)

biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid,
light_attenuation_model = PrescribedPhotosyntheticallyActiveRadiation(PAR))

model = BoxModel(; biogeochemistry, clock)

set!(model, N = 10.0, P = 0.1, Z = 0.01)

Expand All @@ -41,25 +49,12 @@ function run_box_simulation()

fast_output = SpeedyOutput("box_benchmarking.jld2")

simulation.callbacks[:output] = Callback(fast_output, IterationInterval(20);)
simulation.callbacks[:output] = Callback(fast_output, IterationInterval(20))

@info "Running the model..."
run!(simulation)
end

function fast_output(sim, fname)
file = jldopen(fname, "w+")

model = sim.model

t = time(sim)

file["fields/$t"] = model.field_values

close(file)

return nothing
end
#####
##### results
#####
Expand Down
8 changes: 4 additions & 4 deletions docs/make.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,12 +52,12 @@ example_pages = [ title => "generated/$(filename).md" for (title, filename) in e

if !isdir(OUTPUT_DIR) mkdir(OUTPUT_DIR) end

model_parameters = (LOBSTER(; grid = BoxModelGrid, light_attenuation_model = nothing).underlying_biogeochemistry,
NutrientPhytoplanktonZooplanktonDetritus(; grid = BoxModelGrid, light_attenuation_model = nothing).underlying_biogeochemistry,
model_parameters = (LOBSTER(; grid = BoxModelGrid(), light_attenuation_model = nothing).underlying_biogeochemistry,
NutrientPhytoplanktonZooplanktonDetritus(; grid = BoxModelGrid(), light_attenuation_model = nothing).underlying_biogeochemistry,
SLatissima(),
TwoBandPhotosyntheticallyActiveRadiation(; grid = RectilinearGrid(size=(1, 1, 1), extent=(1, 1, 1))),
SimpleMultiG(; grid = BoxModelGrid),
InstantRemineralisation(; grid = BoxModelGrid),
SimpleMultiG(; grid = BoxModelGrid()),
InstantRemineralisation(; grid = BoxModelGrid()),
OCMIP_default,
GasExchange(; gas = :CO₂).condition.func,
GasExchange(; gas = :O₂).condition.func)
Expand Down
2 changes: 1 addition & 1 deletion examples/box.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ using Oceananigans.Fields: FunctionField

const year = years = 365day

grid = BoxModelGrid
grid = BoxModelGrid()
clock = Clock(time = zero(grid))

nothing #hide
Expand Down
2 changes: 1 addition & 1 deletion examples/data_assimilation.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ function run_box_simulation(initial_photosynthetic_slope,
phyto_base_mortality_rate,
j)

biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid = BoxModelGrid,
biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid = BoxModelGrid(),
initial_photosynthetic_slope,
base_maximum_growth,
nutrient_half_saturation,
Expand Down
Loading

2 comments on commit 4bcaf29

@jagoosw
Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@JuliaRegistrator register

@JuliaRegistrator
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Registration pull request created: JuliaRegistries/General/111818

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.10.5 -m "<description of version>" 4bcaf29797abcb7c7293a299c2e1c549e3d3d7eb
git push origin v0.10.5

Please sign in to comment.