One .pdf instead of 36 .png long_runs artifacts

Long runs where producing 36 artifacts (.png files), this commit
tidy this up by gathering them into one .pdf instead.

.buildkite/Project.toml

@@ -29,6 +29,7 @@ MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Poppler_jll = "9c32591e-4766-534b-9725-b71a8799265b"
 ProfileCanvas = "efd6af41-a80b-495e-886c-e51b0c7d77a3"
 RootSolvers = "7181ea78-2dcb-4de3-ab41-2b8ab5a31e74"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"

experiments/long_runs/bucket.jl

@@ -1,7 +1,7 @@
 # # Global bucket run
 
 # The code sets up and runs the bucket model  on a spherical domain,
-# using ERA5 data. 
+# using ERA5 data.
 
 # Simulation Setup
 # Number of spatial elements: 101 in horizontal, 5 in vertical
@@ -38,6 +38,8 @@ using CairoMakie
 using Dates
 import NCDatasets
 
+using Poppler_jll: pdfunite
+
 const FT = Float64;
 time_interpolation_method = LinearInterpolation(PeriodicCalendar())
 regridder_type = :InterpolationsRegridder
@@ -167,6 +169,7 @@ setup_and_solve_problem(; greet = true);
 simdir = ClimaAnalysis.SimDir(outdir)
 short_names =
     ["swa", "rn", "tsfc", "qsfc", "lhf", "shf", "wsoil", "wsfc", "ssfc"]
+tmpdir = mktempdir(root_path)
 for short_name in short_names
     var = get(simdir; short_name)
     times = ClimaAnalysis.times(var)
@@ -182,6 +185,10 @@ for short_name in short_names
                 :mask => ClimaAnalysis.Utils.kwargs(color = :white),
             ),
         )
-        CairoMakie.save(joinpath(root_path, "$(short_name)_$t.png"), fig)
+        CairoMakie.save(joinpath(tmpdir, "$(short_name)_$t.pdf"), fig)
     end
 end
+figures = readdir(tmpdir)
+pdfunite() do unite
+    run(Cmd([unite, figures..., "figures.pdf"]))
+end

experiments/long_runs/land.jl

@@ -46,6 +46,8 @@ import GeoMakie
 using Dates
 import NCDatasets
 
+using Poppler_jll: pdfunite
+
 const FT = Float64;
 time_interpolation_method = LinearInterpolation(PeriodicCalendar())
 regridder_type = :InterpolationsRegridder
@@ -593,6 +595,7 @@ setup_and_solve_problem(; greet = true);
 #### ClimaAnalysis ####
 simdir = ClimaAnalysis.SimDir(outdir)
 short_names = ["gpp", "ct", "lai", "swc", "si", "swa", "lwu", "et", "er", "sr"]
+tmpdir = mktempdir(root_path)
 for short_name in short_names
     var = get(simdir; short_name)
     times = ClimaAnalysis.times(var)
@@ -607,6 +610,10 @@ for short_name in short_names
                 :mask => ClimaAnalysis.Utils.kwargs(color = :white),
             ),
         )
-        CairoMakie.save(joinpath(root_path, "$(short_name)_$t.png"), fig)
+        CairoMakie.save(joinpath(tmpdir, "$(short_name)_$t.pdf"), fig)
     end
 end
+figures = readdir(tmpdir)
+pdfunite() do unite
+    run(Cmd([unite, figures..., "figures.pdf"]))
+end

experiments/long_runs/land_region.jl

@@ -45,6 +45,8 @@ using CairoMakie
 using Dates
 import NCDatasets
 
+using Poppler_jll: pdfunite
+
 const FT = Float64;
 time_interpolation_method = LinearInterpolation(PeriodicCalendar())
 regridder_type = :InterpolationsRegridder
@@ -597,6 +599,7 @@ setup_and_solve_problem(; greet = true);
 #### ClimaAnalysis ####
 simdir = ClimaAnalysis.SimDir(outdir)
 short_names = ["gpp", "ct", "swc", "si"]
+tmpdir = mktempdir(root_path)
 for short_name in short_names
     var = get(simdir; short_name)
     times = ClimaAnalysis.times(var)
@@ -606,7 +609,11 @@ for short_name in short_names
         tmp = ClimaAnalysis.slice(var, time = t; kwargs...)
         if !all(isnan.(tmp.data))
             viz.heatmap2D!(fig, tmp)
-            CairoMakie.save(joinpath(root_path, "$(short_name)_$t.png"), fig)
+            CairoMakie.save(joinpath(tmpdir, "$(short_name)_$t.pdf"), fig)
         end
     end
 end
+figures = readdir(tmpdir)
+pdfunite() do unite
+    run(Cmd([unite, figures..., "figures.pdf"]))
+end

experiments/long_runs/soil.jl

@@ -44,6 +44,8 @@ using CairoMakie
 using Dates
 import NCDatasets
 
+using Poppler_jll: pdfunite
+
 const FT = Float64;
 time_interpolation_method = LinearInterpolation(PeriodicCalendar())
 regridder_type = :InterpolationsRegridder
@@ -365,6 +367,7 @@ setup_and_solve_problem(; greet = true);
 #### ClimaAnalysis ####
 simdir = ClimaAnalysis.SimDir(outdir)
 short_names = ["swc", "si", "sie"]
+tmpdir = mktempdir(root_path)
 for short_name in short_names
     var = get(simdir; short_name)
     times = ClimaAnalysis.times(var)
@@ -380,6 +383,10 @@ for short_name in short_names
                 :mask => ClimaAnalysis.Utils.kwargs(color = :white),
             ),
         )
-        CairoMakie.save(joinpath(root_path, "$(short_name)_$t.png"), fig)
+        CairoMakie.save(joinpath(tmpdir, "$(short_name)_$t.pdf"), fig)
     end
 end
+figures = readdir(tmpdir)
+pdfunite() do unite
+    run(Cmd([unite, figures..., "figures.pdf"]))
+end

test/Project.toml

@@ -23,6 +23,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"

test/diagnostics/diagnostics_tests.jl

@@ -1,14 +1,16 @@
 using Test
 using ClimaLand
 using ClimaLand.Diagnostics: @with_error
+import ClimaComms
+ClimaComms.@import_required_backends
+import ClimaParams
+import SciMLBase
+import ClimaTimeSteppers
+import ClimaDiagnostics
+using Dates
 
 @test isdefined(ClimaLand.Diagnostics, :compute_sw_albedo!)
 
-@test !hasmethod(
-    ClimaLand.Diagnostics.compute_sw_albedo!,
-    (Any, Any, Any, Any, Any),
-)
-
 # Define some diagnostics for a DummyModel
 
 @test ClimaLand.Diagnostics.ALL_DIAGNOSTICS isa Dict
@@ -30,17 +32,79 @@ ClimaLand.Diagnostics.add_diagnostic_variable!(
 
 @test length(ClimaLand.Diagnostics.ALL_DIAGNOSTICS) == 1
 
-ClimaLand.Diagnostics.define_diagnostics!(DummyModel())
+# First, run a simulation for 1 hour
+FT = Float32
+t0 = 0.0
+Δt = 100.0
+tf = 3Δt
+bucket_domain = ClimaLand.SphericalShell(;
+    radius = FT(100),
+    depth = FT(3.5),
+    nelements = (1, 10),
+    npolynomial = 1,
+)
+
+bucket_atmos, bucket_rad = ClimaLand.prescribed_analytic_forcing(FT)
+τc = FT(1.0)
+α_bareground_func = (coordinate_point) -> 0.2
+α_snow = FT(0.8)
+z_0m = FT(1e-2)
+z_0b = FT(1e-3)
+albedo = ClimaLand.Bucket.PrescribedBaregroundAlbedo{FT}(
+    α_snow,
+    α_bareground_func,
+    bucket_domain.space.surface,
+)
+bucket_parameters =
+    ClimaLand.Bucket.BucketModelParameters(FT; albedo, z_0m, z_0b, τc)
+
+model = ClimaLand.Bucket.BucketModel(
+    parameters = bucket_parameters,
+    domain = bucket_domain,
+    atmosphere = bucket_atmos,
+    radiation = bucket_rad,
+)
+
+Y, p, coords = ClimaLand.initialize(model)
+Y.bucket.T .= 280.0
+Y.bucket.W .= 0.0 # no moisture
+Y.bucket.Ws .= 0.0 # no runoff
+Y.bucket.σS .= 0.0
 
-# Just to trigger the error
-out = Y = p = t = land_model = nothing
+exp_tendency! = ClimaLand.make_exp_tendency(model)
+set_initial_cache! = ClimaLand.make_set_initial_cache(model)
+set_initial_cache!(p, Y, t0)
 
-@test_throws ErrorException("Cannot compute albedo with model = Nothing") ClimaLand.Diagnostics.compute_albedo!(
-    out,
+prob = SciMLBase.ODEProblem(
+    ClimaTimeSteppers.ClimaODEFunction((T_exp!) = exp_tendency!),
     Y,
+    (t0, tf),
     p,
-    t,
-    land_model,
 )
 
-@test_throws ErrorException ClimaLand.Diagnostics.get_diagnostic_variable("Foo")
+# ClimaDiagnostics
+
+ClimaLand.Diagnostics.define_diagnostics!(model)
+diags = ["rn", "lhf"]
+
+d_writer = ClimaDiagnostics.Writers.DictWriter()
+
+out = ClimaLand.Diagnostics.daily_averages(
+    FT,
+    diags...;
+    output_writer = d_writer,
+    reference_date = DateTime(2005),
+)
+
+diagnostic_handler = ClimaDiagnostics.DiagnosticsHandler(out, Y, p, t0; dt = Δt)
+
+diag_cb = ClimaDiagnostics.DiagnosticsCallback(diagnostic_handler)
+
+updateat = collect(t0:Δt:tf);
+drivers = ClimaLand.get_drivers(model)
+updatefunc = ClimaLand.make_update_drivers(drivers)
+driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
+cb = SciMLBase.CallbackSet(driver_cb)
+timestepper = ClimaTimeSteppers.RK4()
+ode_algo = ClimaTimeSteppers.ExplicitAlgorithm(timestepper)
+SciMLBase.solve(prob, ode_algo; dt = Δt, callback = cb)

test/runtests.jl

@@ -108,3 +108,8 @@ end
 @safetestset "Integrated soil and snow" begin
     include("integrated/soil_snow.jl")
 end
+
+# Diagnostics
+@safetestset "Diagnostics" begin
+    include("diagnostics/diagnostics_tests.jl")
+end