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Merge pull request #141 from JuliaGeodynamics/bk-chmy
Integration with Chmy.jl
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| ```@meta | ||
| EditURL = "../../../tutorials/Tutorial_Chmy_MPI.jl" | ||
| ``` | ||
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| # Create an initial model setup for Chmy and run it in parallel | ||
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| ## Aim | ||
| In this tutorial, your will learn how to use [Chmy](https://github.com/PTsolvers/Chmy.jl) to perform a 2D diffusion simulation | ||
| on one or multiple CPU's or GPU's. | ||
| `Chmy` is a package that allows you to specify grids and fields and create finite difference simulations | ||
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| ## 1. Load Chmy and required packages | ||
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| ```julia | ||
| using Chmy, Chmy.Architectures, Chmy.Grids, Chmy.Fields, Chmy.BoundaryConditions, Chmy.GridOperators, Chmy.KernelLaunch | ||
| using KernelAbstractions | ||
| using Printf | ||
| using CairoMakie | ||
| using GeophysicalModelGenerator | ||
| ``` | ||
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| In case you want to use GPU's, you need to sort out whether you have AMD or NVIDIA GPU's | ||
| and load the package accordingly: | ||
| using AMDGPU | ||
| AMDGPU.allowscalar(false) | ||
| using CUDA | ||
| CUDA.allowscalar(false) | ||
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| To run this in parallel you need to load this: | ||
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| ```julia | ||
| using Chmy.Distributed | ||
| using MPI | ||
| MPI.Init() | ||
| ``` | ||
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| ## 2. Define computational routines | ||
| You need to specify compute kernel for the gradients: | ||
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| ```julia | ||
| @kernel inbounds = true function compute_q!(q, C, χ, g::StructuredGrid, O) | ||
| I = @index(Global, NTuple) | ||
| I = I + O | ||
| q.x[I...] = -χ * ∂x(C, g, I...) | ||
| q.y[I...] = -χ * ∂y(C, g, I...) | ||
| end | ||
| ``` | ||
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| You need to specify compute kernel to update the concentration | ||
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| ```julia | ||
| @kernel inbounds = true function update_C!(C, q, Δt, g::StructuredGrid, O) | ||
| I = @index(Global, NTuple) | ||
| I = I + O | ||
| C[I...] -= Δt * divg(q, g, I...) | ||
| end | ||
| ``` | ||
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| And a main function is required: | ||
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| ```julia | ||
| @views function main(backend=CPU(); nxy_l=(126, 126)) | ||
| arch = Arch(backend, MPI.COMM_WORLD, (0, 0)) | ||
| topo = topology(arch) | ||
| me = global_rank(topo) | ||
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| # geometry | ||
| dims_l = nxy_l | ||
| dims_g = dims_l .* dims(topo) | ||
| grid = UniformGrid(arch; origin=(-2, -2), extent=(4, 4), dims=dims_g) | ||
| launch = Launcher(arch, grid, outer_width=(16, 8)) | ||
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| ##@info "mpi" me grid | ||
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| nx, ny = dims_g | ||
| # physics | ||
| χ = 1.0 | ||
| # numerics | ||
| Δt = minimum(spacing(grid))^2 / χ / ndims(grid) / 2.1 | ||
| # allocate fields | ||
| C = Field(backend, grid, Center()) | ||
| P = Field(backend, grid, Center(), Int32) # phases | ||
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| q = VectorField(backend, grid) | ||
| C_v = (me==0) ? KernelAbstractions.zeros(CPU(), Float64, size(interior(C)) .* dims(topo)) : nothing | ||
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| # Use the `GeophysicalModelGenerator` to set the initial conditions. Note that | ||
| # you have to call this for a `Phases` and a `Temp` grid, which we call `C` here. | ||
| add_box!(P,C,grid, xlim=(-1.0,1.0), zlim=(-1.0,1.0), phase=ConstantPhase(4), T=ConstantTemp(400)) | ||
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| # set BC's and updates the halo: | ||
| bc!(arch, grid, C => Neumann(); exchange=C) | ||
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| # visualisation | ||
| fig = Figure(; size=(400, 320)) | ||
| ax = Axis(fig[1, 1]; aspect=DataAspect(), xlabel="x", ylabel="y", title="it = 0") | ||
| plt = heatmap!(ax, centers(grid)..., interior(C) |> Array; colormap=:turbo) | ||
| Colorbar(fig[1, 2], plt) | ||
| # action | ||
| nt = 100 | ||
| for it in 1:nt | ||
| (me==0) && @printf("it = %d/%d \n", it, nt) | ||
| launch(arch, grid, compute_q! => (q, C, χ, grid)) | ||
| launch(arch, grid, update_C! => (C, q, Δt, grid); bc=batch(grid, C => Neumann(); exchange=C)) | ||
| end | ||
| KernelAbstractions.synchronize(backend) | ||
| gather!(arch, C_v, C) | ||
| if me == 0 | ||
| fig = Figure(; size=(400, 320)) | ||
| ax = Axis(fig[1, 1]; aspect=DataAspect(), xlabel="x", ylabel="y", title="it = 0") | ||
| plt = heatmap!(ax, C_v; colormap=:turbo) # how to get the global grid for axes? | ||
| Colorbar(fig[1, 2], plt) | ||
| save("out_gather_$nx.png", fig) | ||
| end | ||
| return | ||
| end | ||
| ``` | ||
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| In the code above, the part that calls `GMG` is: | ||
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| ```julia | ||
| add_box!(P,C,grid, xlim=(-1.0,1.0), zlim=(-1.0,1.0), phase=ConstantPhase(4), T=ConstantTemp(400)) | ||
| ``` | ||
| which works just like any of the other GMG function. | ||
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| ## 3. Run the simulation on one CPU machine or GPU card: | ||
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| Running the code on the CPU is done with this: | ||
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| ```julia | ||
| n = 128 | ||
| main(; nxy_l=(n, n) .- 2) | ||
| ``` | ||
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| If you instead want to run this on AMD or NVIDIA GPU's do this: | ||
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| ```julia | ||
| # main(ROCBackend(); nxy_l=(n, n) .- 2) | ||
| # main(CUDABackend(); nxy_l=(n, n) .- 2) | ||
| ``` | ||
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| And we need to finalize the simulation with | ||
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| ```julia | ||
| MPI.Finalize() | ||
| ``` | ||
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| ## 4. Run the simulation on an MPI-parallel machine | ||
| If you want to run this on multiple cores, you will need to setup the [MPI.jl]() package, | ||
| such that `mpiexecjl` is created on the command line. | ||
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| You can than run it with: | ||
| mpiexecjl -n 4 --project=. julia Tutorial_Chmy_MPI.jl | ||
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| The full file can be downloaded [here](../../../tutorials/Tutorial_Chmy_MPI.jl) | ||
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| --- | ||
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| *This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).* | ||
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| #helper functions to make GMG work with Chmy grids and fields | ||
| module Chmy_utils | ||
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| using Chmy, Chmy.Grids, Chmy.Fields | ||
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| import GeophysicalModelGenerator: create_CartGrid, CartGrid, CartData | ||
| import GeophysicalModelGenerator: add_box!, add_sphere!, add_ellipsoid!, add_cylinder! | ||
| import GeophysicalModelGenerator: add_layer!, add_polygon!, add_slab!, add_stripes!, add_volcano! | ||
| import GeophysicalModelGenerator: above_surface, below_surface | ||
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| println("Loading Chmy-GMG tools") | ||
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| """ | ||
| CartGrid = create_CartGrid(grid::StructuredGrid; ylevel=0.0) | ||
| Creates a GMG `CartGrid` data structure from a `Chmy` grid object | ||
| """ | ||
| function create_CartGrid(grid::StructuredGrid; ylevel=0.0) | ||
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| coord1D = Vector.(coords(grid, Vertex())) | ||
| coord1D_cen = Vector.(coords(grid, Center())) | ||
| N = length.(coord1D) | ||
| L = extent(grid, Vertex()) | ||
| X₁ = origin(grid, Vertex()) | ||
| Δ = spacing(grid) | ||
| ConstantΔ = false; | ||
| if isa(grid, UniformGrid) | ||
| ConstantΔ = true | ||
| end | ||
| if ndims(grid)==2 | ||
| # we need a special treatment of this, as all GMG routines work with 3D coordinates | ||
| X₁ = (X₁[1], ylevel, X₁[2]) | ||
| L = (L[1], 0.0, L[2]) | ||
| Δ = (Δ[1], 0.0, Δ[2]) | ||
| N = (N[1],1,N[2]) | ||
| coord1D = (coord1D[1], [0.0], coord1D[2]) | ||
| coord1D_cen = (coord1D_cen[1], [0.0], coord1D_cen[2]) | ||
| end | ||
| Xₙ = X₁ .+ L | ||
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| return CartGrid(ConstantΔ,N,Δ,L,X₁,Xₙ,coord1D, coord1D_cen) | ||
| end | ||
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| # all functions to be ported | ||
| function_names = (:add_box!, :add_sphere!, :add_ellipsoid!, :add_cylinder!, :add_layer!, :add_polygon!, :add_slab!, :add_stripes!, :add_volcano!) | ||
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| for fn in function_names | ||
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| @eval begin | ||
| """ | ||
| $($fn)( Phase::Field, | ||
| Temp::Field, | ||
| Grid::StructuredGrid; # required input | ||
| kwargs...) | ||
| Sets `$($fn)` function for `Chmy` fields and grids. | ||
| """ | ||
| function $fn( Phase::Field, | ||
| Temp::Field, | ||
| Grid::StructuredGrid; # required input | ||
| kwargs...) | ||
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| CartGrid = create_CartGrid(Grid) | ||
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| cell = false | ||
| if all(location(Phase).==Center()) | ||
| cell = true | ||
| end | ||
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| return ($fn)(Phase, Temp, CartGrid; cell=cell, kwargs...) | ||
| end | ||
| end | ||
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| end | ||
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| # all functions to be ported | ||
| function_names = (:above_surface, :below_surface) | ||
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| for fn in function_names | ||
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| @eval begin | ||
| """ | ||
| $($fn)( Grid::StructuredGrid, field::Field, DataSurface_Cart::CartData; kwargs...) | ||
| Sets `$($fn)` function for `Chmy` grids and the field `field` which can be either on vertices or centers | ||
| """ | ||
| function $fn( Grid::StructuredGrid, | ||
| field::Field, | ||
| DataSurface_Cart::CartData; | ||
| kwargs...) | ||
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| CartGrid = create_CartGrid(Grid) | ||
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| cell = false | ||
| if all(location(field).==Center()) | ||
| cell = true | ||
| end | ||
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| return ($fn)(CartGrid, DataSurface_Cart; cell=cell, kwargs...) | ||
| end | ||
| end | ||
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| end | ||
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| end # end of module |
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Registration pull request created: JuliaRegistries/General/116914
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