Merge pull request #590 from CliMA/ar/distributed-model

.buildkite/pipeline.yml

@@ -47,6 +47,9 @@ steps:
       - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.precompile()'"
       - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.status()'"
       - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.test()'"
+
+      # Set up the mpiexecjl command
+      - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using MPI; MPI.install_mpiexecjl()'"
     agents:
       queue: Oceananigans
       architecture: CPU
@@ -163,7 +166,7 @@ steps:
 ##### HydrostaticFreeSurfaceModel
 #####
 
-  - label: "💧 gpu hydrostatic free surface model tests"
+  - label: "🐡 gpu hydrostatic free surface model tests"
     env:
       JULIA_DEPOT_PATH: "$SVERDRUP_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
       TEST_GROUP: "hydrostatic_free_surface"
@@ -174,7 +177,7 @@ steps:
       architecture: GPU
     depends_on: "init_gpu"
 
-  - label: "💦 cpu hydrostatic free surface model tests"
+  - label: "🐠 cpu hydrostatic free surface model tests"
     env:
       JULIA_DEPOT_PATH: "$TARTARUS_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
       TEST_GROUP: "hydrostatic_free_surface"
@@ -190,7 +193,7 @@ steps:
 ##### ShallowWaterModel
 #####
 
-  - label: "💧 gpu shallow water model tests"
+  - label: "🦑 gpu shallow water model tests"
     env:
       JULIA_DEPOT_PATH: "$SVERDRUP_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
       TEST_GROUP: "shallow_water"
@@ -201,7 +204,7 @@ steps:
       architecture: GPU
     depends_on: "init_gpu"
 
-  - label: "💦 cpu shallow water model tests"
+  - label: "🦐 cpu shallow water model tests"
     env:
       JULIA_DEPOT_PATH: "$TARTARUS_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
       TEST_GROUP: "shallow_water"
@@ -240,6 +243,23 @@ steps:
       architecture: CPU
     depends_on: "init_cpu"
 
+#####
+##### Distributed/MPI
+#####
+
+  - label: "🐉 cpu distributed tests"
+    env:
+      JULIA_DEPOT_PATH: "$TARTARUS_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
+      TEST_GROUP: "distributed"
+      CUDA_VISIBLE_DEVICES: "-1"
+    commands:
+      - "PATH=$PATH:$TARTARUS_HOME/julia-$JULIA_VERSION/bin"  # Need julia binary in $PATH for mpiexecjl to work.
+      - "$TARTARUS_HOME/.julia-$BUILDKITE_BUILD_NUMBER/bin/mpiexecjl -np 4 $TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.test()'"
+    agents:
+      queue: Oceananigans
+      architecture: CPU
+    depends_on: "init_cpu"
+
 #####
 ##### Regression
 #####
@@ -317,7 +337,7 @@ steps:
 ##### Clean up
 #####
 
-  - label: "🧻 clean up gpu environment"
+  - label: "🧽 clean up gpu environment"
     command: "rm -rf $SVERDRUP_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
     agents:
       queue: Oceananigans

Manifest.toml

@@ -2,16 +2,22 @@
 
 [[AbstractFFTs]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "051c95d6836228d120f5f4b984dd5aba1624f716"
+git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "0.5.0"
+version = "1.0.1"
 
 [[Adapt]]
 deps = ["LinearAlgebra"]
 git-tree-sha1 = "ffcfa2d345aaee0ef3d8346a073d5dd03c983ebe"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 version = "3.2.0"
 
+[[ArrayInterface]]
+deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"]
+git-tree-sha1 = "e7edcc1ac140cce87b7442ff0fa88b5f19fb71fa"
+uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
+version = "3.1.3"
+
 [[Artifacts]]
 deps = ["Pkg"]
 git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
@@ -106,16 +112,22 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
+[[DocStringExtensions]]
+deps = ["LibGit2", "Markdown", "Pkg", "Test"]
+git-tree-sha1 = "50ddf44c53698f5e784bbebb3f4b21c5807401b1"
+uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+version = "0.8.3"
+
 [[ExprTools]]
 git-tree-sha1 = "10407a39b87f29d47ebaca8edbc75d7c302ff93e"
 uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
 version = "0.1.3"
 
 [[FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"]
-git-tree-sha1 = "8fda0934cb99db617171f7296dc361f4d6fa5424"
+git-tree-sha1 = "1b48dbde42f307e48685fa9213d8b9f8c0d87594"
 uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-version = "1.3.0"
+version = "1.3.2"
 
 [[FFTW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -146,6 +158,11 @@ git-tree-sha1 = "fd83fa0bde42e01952757f01149dd968c06c4dba"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
 version = "1.12.0+1"
 
+[[IfElse]]
+git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef"
+uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
+version = "0.1.0"
+
 [[IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "d979e54b71da82f3a65b62553da4fc3d18c9004c"
@@ -163,15 +180,21 @@ version = "1.0.0"
 
 [[JLD2]]
 deps = ["CodecZlib", "DataStructures", "MacroTools", "Mmap", "Pkg", "Printf", "Requires", "UUIDs"]
-git-tree-sha1 = "bb9a457481adf060ab5898823a49d4f854ff4ddd"
+git-tree-sha1 = "b8343a7f96591404ade118b3a7014e1a52062465"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.0"
+version = "0.4.2"
 
 [[JLLWrappers]]
 git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
 version = "1.2.0"
 
+[[JSON3]]
+deps = ["Dates", "Mmap", "Parsers", "StructTypes", "UUIDs"]
+git-tree-sha1 = "62d4063c67d7c84d5788107878bb925ceaadd252"
+uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+version = "1.7.1"
+
 [[KernelAbstractions]]
 deps = ["Adapt", "CUDA", "Cassette", "InteractiveUtils", "MacroTools", "SpecialFunctions", "StaticArrays", "UUIDs"]
 git-tree-sha1 = "ee7f03c23d874c8353813a44315daf82a1e82046"
@@ -184,6 +207,12 @@ git-tree-sha1 = "b616937c31337576360cb9fb872ec7633af7b194"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
 version = "3.6.0"
 
+[[LazyArtifacts]]
+deps = ["Pkg"]
+git-tree-sha1 = "4bb5499a1fc437342ea9ab7e319ede5a457c0968"
+uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
+version = "1.3.0"
+
 [[LibCURL_jll]]
 deps = ["LibSSH2_jll", "Libdl", "MbedTLS_jll", "Pkg", "Zlib_jll", "nghttp2_jll"]
 git-tree-sha1 = "897d962c20031e6012bba7b3dcb7a667170dad17"
@@ -211,10 +240,22 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[MKL_jll]]
-deps = ["IntelOpenMP_jll", "Libdl", "Pkg"]
-git-tree-sha1 = "eb540ede3aabb8284cb482aa41d00d6ca850b1f8"
+deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
+git-tree-sha1 = "c253236b0ed414624b083e6b72bfe891fbd2c7af"
 uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
-version = "2020.2.254+0"
+version = "2021.1.1+1"
+
+[[MPI]]
+deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "Pkg", "Random", "Requires", "Serialization", "Sockets"]
+git-tree-sha1 = "d3aae0fd4d9e1a09c3e2fc728fbe2522ec6d54bc"
+uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195"
+version = "0.16.1"
+
+[[MPICH_jll]]
+deps = ["CompilerSupportLibraries_jll", "Libdl", "Pkg"]
+git-tree-sha1 = "4d37f1e07b4e2a74462eebf9ee48c626d15ffdac"
+uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
+version = "3.3.2+10"
 
 [[MacroTools]]
 deps = ["Markdown", "Random"]
@@ -232,6 +273,12 @@ git-tree-sha1 = "0eef589dd1c26a3ac9d753fe1a8bcad63f956fa6"
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 version = "2.16.8+1"
 
+[[MicrosoftMPI_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "e5c90234b3967684c9c6f87b4a54549b4ce21836"
+uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf"
+version = "10.1.3+0"
+
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
@@ -255,9 +302,15 @@ version = "400.701.400+0"
 
 [[OffsetArrays]]
 deps = ["Adapt"]
-git-tree-sha1 = "76622f08645764e040b4d7e86d0ff471fd126ae4"
+git-tree-sha1 = "b3dfef5f2be7d7eb0e782ba9146a5271ee426e90"
 uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-version = "1.5.3"
+version = "1.6.2"
+
+[[OpenMPI_jll]]
+deps = ["Libdl", "Pkg"]
+git-tree-sha1 = "41b983e26a7ab8c9bf05f7d70c274b817d541b46"
+uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
+version = "4.0.2+2"
 
 [[OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -272,9 +325,27 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.3+4"
 
 [[OrderedCollections]]
-git-tree-sha1 = "d45739abcfc03b51f6a42712894a593f74c80a23"
+git-tree-sha1 = "4fa2ba51070ec13fcc7517db714445b4ab986bdf"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.3.3"
+version = "1.4.0"
+
+[[Parsers]]
+deps = ["Dates"]
+git-tree-sha1 = "223a825cccef2228f3fdbf2ecc7ca93363059073"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "1.0.16"
+
+[[PencilArrays]]
+deps = ["ArrayInterface", "JSON3", "Libdl", "LinearAlgebra", "MPI", "OffsetArrays", "Reexport", "Requires", "StaticArrays", "StaticPermutations", "TimerOutputs"]
+git-tree-sha1 = "6921d07316f41e2be5befd8b815eee28d3fab9f8"
+uuid = "0e08944d-e94e-41b1-9406-dcf66b6a9d2e"
+version = "0.9.0"
+
+[[PencilFFTs]]
+deps = ["AbstractFFTs", "FFTW", "LinearAlgebra", "MPI", "PencilArrays", "Reexport", "TimerOutputs"]
+git-tree-sha1 = "a7665838a566accd7d9cf308bbb497126dc5edf4"
+uuid = "4a48f351-57a6-4416-9ec4-c37015456aae"
+version = "0.12.1"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -340,16 +411,27 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
 deps = ["ChainRulesCore", "OpenSpecFun_jll"]
-git-tree-sha1 = "75394dbe2bd346beeed750fb02baa6445487b862"
+git-tree-sha1 = "5919936c0e92cff40e57d0ddf0ceb667d42e5902"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "1.2.1"
+version = "1.3.0"
+
+[[Static]]
+deps = ["IfElse"]
+git-tree-sha1 = "98ace568bf638e89eac33c99337f3c8c6e2227b8"
+uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
+version = "0.2.0"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
 git-tree-sha1 = "9da72ed50e94dbff92036da395275ed114e04d49"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
 version = "1.0.1"
 
+[[StaticPermutations]]
+git-tree-sha1 = "193c3daa18ff3e55c1dae66acb6a762c4a3bdb0b"
+uuid = "15972242-4b8f-49a0-b8a1-9ac0e7a1a45d"
+version = "0.3.0"
+
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -360,6 +442,12 @@ git-tree-sha1 = "26ea43b4be7e919a2390c3c0f824e7eb4fc19a0a"
 uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
 version = "0.5.0"
 
+[[StructTypes]]
+deps = ["Dates", "UUIDs"]
+git-tree-sha1 = "d7f4287dbc1e590265f50ceda1b40ed2bb31bbbb"
+uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
+version = "1.4.0"
+
 [[TableTraits]]
 deps = ["IteratorInterfaceExtensions"]
 git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e"
@@ -378,9 +466,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[TimerOutputs]]
 deps = ["Printf"]
-git-tree-sha1 = "3318281dd4121ecf9713ce1383b9ace7d7476fdd"
+git-tree-sha1 = "32cdbe6cd2d214c25a0b88f985c9e0092877c236"
 uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
-version = "0.5.7"
+version = "0.5.8"
 
 [[TranscodingStreams]]
 deps = ["Random", "Test"]

Project.toml

@@ -1,6 +1,6 @@
 name = "Oceananigans"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.52.1"
+version = "0.53.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -14,9 +14,11 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+PencilFFTs = "4a48f351-57a6-4416-9ec4-c37015456aae"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -33,9 +35,11 @@ FFTW = "^1"
 Glob = "1.3"
 JLD2 = "^0.2, ^0.3, 0.4"
 KernelAbstractions = "^0.3, 0.4, 0.5"
+MPI = "0.16"
 NCDatasets = "^0.10, ^0.11"
 OffsetArrays = "^1.4"
 OrderedCollections = "^1.1"
+PencilFFTs = "0.12"
 SafeTestsets = "0.0.1"
 SeawaterPolynomials = "^0.2"
 StructArrays = "0.4, 0.5"