Initial commit w/MPI

.dev/Project.toml

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+[deps]
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"

.dev/clima_formatter_options.jl

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+clima_formatter_options = (
+    indent = 4,
+    margin = 80,
+    always_for_in = true,
+    whitespace_typedefs = true,
+    whitespace_ops_in_indices = true,
+    remove_extra_newlines = false,
+)

.dev/climaformat.jl

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+#!/usr/bin/env julia
+#
+# This is an adapted version of format.jl from JuliaFormatter with the
+# following license:
+#
+#    MIT License
+#    Copyright (c) 2019 Dominique Luna
+#
+#    Permission is hereby granted, free of charge, to any person obtaining a
+#    copy of this software and associated documentation files (the
+#    "Software"), to deal in the Software without restriction, including
+#    without limitation the rights to use, copy, modify, merge, publish,
+#    distribute, sublicense, and/or sell copies of the Software, and to permit
+#    persons to whom the Software is furnished to do so, subject to the
+#    following conditions:
+#
+#    The above copyright notice and this permission notice shall be included
+#    in all copies or substantial portions of the Software.
+#
+#    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+#    OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+#    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+#    NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+#    DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+#    OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+#    USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+using Pkg
+Pkg.activate(@__DIR__)
+Pkg.instantiate()
+
+using JuliaFormatter
+
+include("clima_formatter_options.jl")
+
+help = """
+Usage: climaformat.jl [flags] [FILE/PATH]...
+
+Formats the given julia files using the CLIMA formatting options.  If paths
+are given it will format the julia files in the paths. Otherwise, it will
+format all changed julia files.
+
+    -v, --verbose
+        Print the name of the files being formatted with relevant details.
+
+    -h, --help
+        Print this message.
+"""
+
+function parse_opts!(args::Vector{String})
+    i = 1
+    opts = Dict{Symbol, Union{Int, Bool}}()
+    while i ≤ length(args)
+        arg = args[i]
+        if arg[1] != '-'
+            i += 1
+            continue
+        end
+        if arg == "-v" || arg == "--verbose"
+            opt = :verbose
+        elseif arg == "-h" || arg == "--help"
+            opt = :help
+        else
+            error("invalid option $arg")
+        end
+        if opt in (:verbose, :help)
+            opts[opt] = true
+            deleteat!(args, i)
+        end
+    end
+    return opts
+end
+
+opts = parse_opts!(ARGS)
+if haskey(opts, :help)
+    write(stdout, help)
+    exit(0)
+end
+if isempty(ARGS)
+    filenames = readlines(`git ls-files "*.jl"`)
+else
+    filenames = ARGS
+end
+
+format(filenames; clima_formatter_options..., opts...)

.github/workflows/OS-Tests.yml

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+name: OS Tests
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  test-os:
+    timeout-minutes: 60
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
+    - name: Checkout
+      uses: actions/[email protected]
+
+    # Setup a filter and only run if src/ test/ folder content changes
+    # or project depedencies
+    - uses: dorny/paths-filter@v2
+      id: filter
+      with:
+        filters: |
+          run_test:
+            - '.github/workflows/OS-Tests.yml'
+            - 'src/**'
+            - 'test/**'
+            - 'Project.toml'
+
+    - name: Set up Julia
+      uses: julia-actions/setup-julia@latest
+      if: steps.filter.outputs.run_test == 'true'
+      with:
+        version: 1.6
+
+    - name: Cache artifacts
+      uses: actions/cache@v1
+      if: steps.filter.outputs.run_test == 'true'
+      env:
+        cache-name: cache-artifacts
+      with:
+        path: ~/.julia/artifacts 
+        key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+        restore-keys: |
+          ${{ runner.os }}-test-${{ env.cache-name }}-
+          ${{ runner.os }}-test-
+          ${{ runner.os }}-
+
+    - name: Install Project Packages
+      if: steps.filter.outputs.run_test == 'true'
+      run: |
+        julia --color=yes --project -e 'using Pkg; Pkg.instantiate()'
+        julia --color=yes --project -e 'using Pkg; Pkg.precompile(;strict=true)'
+        julia --color=yes --project -e 'using Pkg; Pkg.status()'
+
+    - name: Project Manifest
+      if: steps.filter.outputs.run_test == 'true'
+      run: |
+        julia --color=no --project -e 'using Pkg; Pkg.status(mode=Pkg.PKGMODE_MANIFEST)'
+
+    - name: Install Project Test Packages
+      if: steps.filter.outputs.run_test == 'true'
+      run: |
+        julia --color=yes --project=test -e 'using Pkg; Pkg.develop(path=pwd()); Pkg.instantiate()'
+        julia --color=yes --project=test -e 'using Pkg; Pkg.precompile(;strict=true)'
+        julia --color=yes --project=test -e 'using Pkg; Pkg.status()'
+
+    - name: Project Test Manifest
+      if: steps.filter.outputs.run_test == 'true'
+      run: |
+        julia --color=no --project=test -e 'using Pkg; Pkg.status(mode=Pkg.PKGMODE_MANIFEST)'
+
+    - name: Run Unit Tests
+      if: steps.filter.outputs.run_test == 'true'
+      run: |
+        julia --color=yes --project=test test/runtests.jl

.github/workflows/docs.yml

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+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+      - trying
+      - staging
+    tags: '*'
+  pull_request:
+
+jobs:
+  docbuild:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1.6.0
+      - name: Install dependencies
+        run: |
+          julia --project -e 'using Pkg; Pkg.instantiate()'
+          julia --project=docs/ -e 'using Pkg; Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GKSwstype: "100" # headless GR: https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988/2
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

Project.toml

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+name = "ClimaComms"
+uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
+authors = ["CliMA Contributors <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
+MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"

docs/Project.toml

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+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

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+if joinpath(@__DIR__, "..") ∉ LOAD_PATH
+    push!(LOAD_PATH, joinpath(@__DIR__, ".."))
+end
+using Documenter, ClimaComms
+
+format = Documenter.HTML(
+    prettyurls = !isempty(get(ENV, "CI", "")),
+    collapselevel = 1,
+)
+makedocs(
+    sitename = "ClimaComms.jl",
+    strict = false,
+    format = format,
+    checkdocs = :exports,
+    clean = true,
+    doctest = true,
+    modules = [ClimaComms],
+    pages = Any["Home" => "index.md", "API" => "api.md"],
+)
+
+#=
+deploydocs(
+    repo = "github.com/CliMA/ClimaComms.jl.git",
+    target = "build",
+    push_preview = true,
+    devbranch = "main",
+    forcepush = true,
+)
+=#

docs/src/api.md

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+# ClimaComms API
+
+```@meta
+CurrentModule = ClimaComms
+```
+
+```@docs
+ClimaComms
+```
+
+### Types
+```@docs
+ClimaComms.MPICommsType
+```
+
+### Interface
+```@docs
+ClimaComms.init
+ClimaComms.start
+ClimaComms.progress
+ClimaComms.finish
+```

docs/src/index.md

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+# ClimaComms.jl

src/ClimaComms.jl

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+"""
+    ClimaComms
+
+Abstracts the communications interface for the various CliMA components
+to enable use of MPI/SharedArrays/Gasp/etc.
+
+Call `init()` with the type of the communications infrastructure desired.
+Create a `RelayBuffer` to hold the data to be communicated; one each for
+every neighbor/direction. Call `get_stage()` for each send buffer and fill
+them. Call `start()` to initiate communication; `progress()` to drive the
+communication progress. To complete communication, call `finish()`. At
+this point, call `get_stage()` for each receive buffer and empty them.
+"""
+module ClimaComms
+
+abstract type AbstractCommsType end
+function init end
+function start end
+function progress end
+function finish end
+
+function init(::Type{CT}) where {CT <: AbstractCommsType}
+    error("No `init` method defined for $CT")
+end
+
+include("relay_buffers.jl")
+include("mpi_comms.jl")
+
+end # module