Distributed regridding of bathymetry

src/Bathymetry.jl

@@ -7,7 +7,7 @@ using ..DataWrangling: download_progress
 
 using Oceananigans
 using Oceananigans.Architectures: architecture, on_architecture
-using Oceananigans.DistributedComputations: child_architecture
+using Oceananigans.DistributedComputations: DistributedGrid, reconstruct_global_grid, barrier!, all_reduce
 using Oceananigans.Grids: halo_size, λnodes, φnodes
 using Oceananigans.Grids: x_domain, y_domain
 using Oceananigans.Grids: topology
@@ -95,11 +95,12 @@ function regrid_bathymetry(target_grid;
     filepath = joinpath(dir, filename)
     fileurl  = url * "/" * filename # joinpath on windows creates the wrong url
 
-    @root if !isfile(filepath) # perform all this only on rank 0, aka the "root" rank
+    # No need for @root here, because only rank 0 accesses this function
+    if !isfile(filepath)
         Downloads.download(fileurl, filepath; progress=download_progress)
     end
-    
-    dataset = Dataset(filepath)
+
+    dataset = Dataset(filepath, "r")
 
     FT = eltype(target_grid)
 
@@ -115,7 +116,7 @@ function regrid_bathymetry(target_grid;
     close(dataset)
 
     # Diagnose target grid information
-    arch = child_architecture(architecture(target_grid))
+    arch = architecture(target_grid)
     φ₁, φ₂ = y_domain(target_grid)
     λ₁, λ₂ = x_domain(target_grid)
 
@@ -247,6 +248,39 @@ function interpolate_bathymetry_in_passes(native_z, target_grid;
     return target_z
 end
 
+# Regridding bathymetry for distributed grids, we handle the whole process
+# on just one rank, and share the results with the other processors.
+function regrid_bathymetry(target_grid::DistributedGrid; kw...)
+    global_grid = reconstruct_global_grid(target_grid)
+    global_grid = on_architecture(CPU(), global_grid)
+    arch = architecture(target_grid)
+    Nx, Ny, _ = size(global_grid)
+
+    # If all ranks open a gigantic bathymetry and the memory is 
+    # shared, we could easily have OOM errors. 
+    # We perform the reconstruction only on rank 0 and share the result.
+    bottom_height = if arch.local_rank == 0
+        bottom_field = regrid_bathymetry(global_grid; kw...)
+        bottom_field.data[1:Nx, 1:Ny, 1]
+    else
+        zeros(Nx, Ny)
+    end
+
+    # Synchronize
+    ClimaOcean.global_barrier(arch.communicator)
+
+    # Share the result (can we share SubArrays?)
+    bottom_height = all_reduce(+, bottom_height, arch)
+
+    # Partition the result
+    local_bottom_height = Field{Center, Center, Nothing}(target_grid)
+    set!(local_bottom_height, bottom_height)
+    fill_halo_regions!(local_bottom_height)
+
+    return local_bottom_height
+end
+
+
 """
     remove_minor_basins!(z_data, keep_major_basins)
 

test/test_distributed_utils.jl

@@ -3,7 +3,9 @@ include("runtests_setup.jl")
 using MPI
 MPI.Init()
 
+using NCDatasets
 using ClimaOcean.ECCO: download_dataset, metadata_path
+using Oceananigans.DistributedComputations: reconstruct_global_grid
 using CFTime
 using Dates
 
@@ -74,3 +76,72 @@ end
         @test isfile(metadata_path(metadatum))
     end
 end
+
+@testset "Distributed Bathymetry interpolation" begin
+    # We start by building a fake bathyemtry on rank 0 and save it to file
+    @root begin
+        λ = -180:0.1:180
+        φ = 0:0.1:50
+
+        Nλ = length(λ)
+        Nφ = length(φ)
+
+        ds = NCDataset("./trivial_bathymetry.nc", "c")
+
+        # Define the dimension "lon" and "lat" with the size 361 and 51 resp.
+        defDim(ds, "lon", Nλ)
+        defDim(ds, "lat", Nφ)
+        defVar(ds, "lat", Float32, ("lat", ))
+        defVar(ds, "lon", Float32, ("lon", ))
+
+        # Define the variables z
+        z = defVar(ds, "z", Float32, ("lon","lat"))
+
+        # Generate some example data
+        data = [Float32(-i) for i = 1:Nλ, j = 1:Nφ]
+
+        # write a the complete data set
+        ds["lon"][:] = λ
+        ds["lat"][:] = φ
+        z[:,:] = data
+
+        close(ds)
+    end
+
+    global_grid = LatitudeLongitudeGrid(CPU();
+                                        size = (40, 40, 1),
+                                        longitude = (0, 100),
+                                        latitude = (0, 20),
+                                        z = (0, 1))
+
+    global_height = regrid_bathymetry(global_grid; 
+                                    dir = "./",
+                                    filename = "trivial_bathymetry.nc",
+                                    interpolation_passes=10)
+
+    arch_x  = Distributed(CPU(), partition=Partition(4, 1))
+    arch_y  = Distributed(CPU(), partition=Partition(1, 4))
+    arch_xy = Distributed(CPU(), partition=Partition(2, 2))
+
+    for arch in (arch_x, arch_y, arch_xy)
+        local_grid = LatitudeLongitudeGrid(arch;
+                                           size = (40, 40, 1),
+                                           longitude = (0, 100),
+                                           latitude = (0, 20),
+                                            z = (0, 1))
+
+        local_height = regrid_bathymetry(local_grid; 
+                                         dir = "./",
+                                         filename = "trivial_bathymetry.nc",
+                                         interpolation_passes=10)
+
+        Nx, Ny, _ = size(local_grid)
+        rx, ry, _ = arch.local_index
+        irange    = (rx - 1) * Nx + 1 : rx * Nx
+        jrange    = (ry - 1) * Ny + 1 : ry * Ny
+
+        @handshake begin
+            @test interior(global_height, irange, jrange, 1) == interior(local_height, :, :, 1)
+        end
+    end
+end