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WIP HYPRE extension #1081

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WIP HYPRE extension #1081

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5 changes: 3 additions & 2 deletions .github/workflows/Check.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,19 +32,20 @@ jobs:
PackageSpec(name = "ExplicitImports", version = "1.6"),
PackageSpec(name = "Metis"),
PackageSpec(name = "BlockArrays"),
PackageSpec(name = "HYPRE"),
])
- name: ExplicitImports.jl code checks
shell: julia --project {0}
run: |
using Ferrite, ExplicitImports, Metis, BlockArrays
using Ferrite, ExplicitImports, Metis, BlockArrays, HYPRE
# Check Ferrite
allow_unanalyzable = (ColoringAlgorithm,) # baremodules
check_no_implicit_imports(Ferrite; allow_unanalyzable)
check_no_stale_explicit_imports(Ferrite; allow_unanalyzable)
check_all_qualified_accesses_via_owners(Ferrite)
check_no_self_qualified_accesses(Ferrite)
# Check extension modules
for ext in (:FerriteBlockArrays, :FerriteMetis)
for ext in (:FerriteBlockArrays, :FerriteHYPRE, :FerriteMetis)
extmod = Base.get_extension(Ferrite, ext)
if extmod !== nothing
check_no_implicit_imports(extmod)
Expand Down
8 changes: 7 additions & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,20 @@ WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"

[weakdeps]
BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771"
MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
Metis = "2679e427-3c69-5b7f-982b-ece356f1e94b"

[extensions]
FerriteBlockArrays = "BlockArrays"
FerriteHYPRE = ["HYPRE", "MPI"]
FerriteMetis = "Metis"

[compat]
BlockArrays = "0.16, 1"
EnumX = "1"
HYPRE = "1.3"
MPI = "0.20"
Metis = "1.3"
NearestNeighbors = "0.4"
OrderedCollections = "1"
Expand All @@ -37,6 +42,7 @@ julia = "1.9"

[extras]
BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771"
Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
FerriteGmsh = "4f95f4f8-b27c-4ae5-9a39-ea55e634e36b"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
Expand All @@ -55,4 +61,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"

[targets]
test = ["BlockArrays", "Downloads", "FerriteGmsh", "ForwardDiff", "Gmsh", "IterativeSolvers", "Metis", "Pkg", "NBInclude", "OhMyThreads", "ProgressMeter", "Random", "SHA", "TaskLocalValues", "Test", "TimerOutputs", "Logging"]
test = ["BlockArrays", "Downloads", "FerriteGmsh", "ForwardDiff", "Gmsh", "HYPRE", "IterativeSolvers", "Metis", "Pkg", "NBInclude", "OhMyThreads", "ProgressMeter", "Random", "SHA", "TaskLocalValues", "Test", "TimerOutputs", "Logging"]
82 changes: 69 additions & 13 deletions docs/Manifest.toml
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Expand Up @@ -2,7 +2,7 @@

julia_version = "1.10.5"
manifest_format = "2.0"
project_hash = "4e52f4aa4cee9f66ec4f633f0ae538fbd227ac5e"
project_hash = "de8ffdfec9d1f3a15bebd18bcb5ace52305c3d9c"

[[deps.ADTypes]]
git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081"
Expand Down Expand Up @@ -183,6 +183,11 @@ git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd"
uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
version = "1.0.8+1"

[[deps.CEnum]]
git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc"
uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
version = "0.5.0"

[[deps.CPUSummary]]
deps = ["CpuId", "IfElse", "PrecompileTools", "Static"]
git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec"
Expand Down Expand Up @@ -366,9 +371,9 @@ version = "1.9.1"

[[deps.DiffEqBase]]
deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"]
git-tree-sha1 = "6b1af0db32958b200b7b1745796432e75821bf48"
git-tree-sha1 = "ada2a9faba0e365dca3cc456b5eca94cf3887ac3"
uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
version = "6.155.2"
version = "6.156.1"

[deps.DiffEqBase.extensions]
DiffEqBaseCUDAExt = "CUDA"
Expand Down Expand Up @@ -494,9 +499,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
version = "1.0.4"

[[deps.EnzymeCore]]
git-tree-sha1 = "ee11500b17d87b22bc638e9ed8c71a7478c53d61"
git-tree-sha1 = "9c3a42611e525352e9ad5e4134ddca5c692ff209"
uuid = "f151be2c-9106-41f4-ab19-57ee4f262869"
version = "0.8.3"
version = "0.8.4"
weakdeps = ["Adapt"]

[deps.EnzymeCore.extensions]
Expand Down Expand Up @@ -580,10 +585,13 @@ version = "1.0.0"

[deps.Ferrite.extensions]
FerriteBlockArrays = "BlockArrays"
FerriteHYPRE = ["HYPRE", "MPI"]
FerriteMetis = "Metis"

[deps.Ferrite.weakdeps]
BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771"
MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
Metis = "2679e427-3c69-5b7f-982b-ece356f1e94b"

[[deps.FerriteGmsh]]
Expand Down Expand Up @@ -772,9 +780,9 @@ version = "1.3.14+0"

[[deps.Graphs]]
deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9"
git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780"
uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
version = "1.11.2"
version = "1.12.0"

[[deps.Grisu]]
git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
Expand All @@ -793,6 +801,28 @@ git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed"
uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
version = "1.10.8"

[[deps.HYPRE]]
deps = ["CEnum", "HYPRE_jll", "Libdl", "MPI"]
git-tree-sha1 = "1594ec3b54b5736531e0f0c36b036c9140ce4141"
uuid = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771"
version = "1.6.0"

[deps.HYPRE.extensions]
HYPREPartitionedArrays = ["PartitionedArrays", "SparseArrays", "SparseMatricesCSR"]
HYPRESparseArrays = "SparseArrays"
HYPRESparseMatricesCSR = ["SparseArrays", "SparseMatricesCSR"]

[deps.HYPRE.weakdeps]
PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"

[[deps.HYPRE_jll]]
deps = ["Artifacts", "JLLWrappers", "LAPACK_jll", "LazyArtifacts", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenBLAS_jll", "OpenMPI_jll", "Pkg", "TOML"]
git-tree-sha1 = "b77d3eca75f8442e034ccf415c87405a49e77985"
uuid = "0a602bbd-b08b-5d75-8d32-0de6eef44785"
version = "2.23.1+1"

[[deps.HarfBuzz_jll]]
deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"]
git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f"
Expand All @@ -807,9 +837,9 @@ version = "0.1.17"

[[deps.Hwloc_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "378267a829b1e17423d32ce6d905f37a12c1fd84"
git-tree-sha1 = "dd3b49277ec2bb2c6b94eb1604d4d0616016f7a6"
uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
version = "2.11.1+1"
version = "2.11.2+0"

[[deps.IOCapture]]
deps = ["Logging", "Random"]
Expand Down Expand Up @@ -928,6 +958,12 @@ git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd"
uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d"
version = "3.100.2+0"

[[deps.LAPACK_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "libblastrampoline_jll"]
git-tree-sha1 = "1b25c30fa49db281be615793e0f85282a8f22822"
uuid = "51474c39-65e3-53ba-86ba-03b1b862ec14"
version = "3.12.0+2"

[[deps.LERC_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434"
Expand Down Expand Up @@ -1209,6 +1245,20 @@ git-tree-sha1 = "70a59df96945782bb0d43b56d0fbfdf1ce2e4729"
uuid = "86086c02-e288-5929-a127-40944b0018b7"
version = "5.6.0+0"

[[deps.MPI]]
deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "PkgVersion", "PrecompileTools", "Requires", "Serialization", "Sockets"]
git-tree-sha1 = "892676019c58f34e38743bc989b0eca5bce5edc5"
uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195"
version = "0.20.22"

[deps.MPI.extensions]
AMDGPUExt = "AMDGPU"
CUDAExt = "CUDA"

[deps.MPI.weakdeps]
AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e"
CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"

[[deps.MPICH_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
git-tree-sha1 = "19d4bd098928a3263693991500d05d74dbdc2004"
Expand Down Expand Up @@ -1671,6 +1721,12 @@ deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.10.0"

[[deps.PkgVersion]]
deps = ["Pkg"]
git-tree-sha1 = "f9501cc0430a26bc3d156ae1b5b0c1b47af4d6da"
uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688"
version = "0.3.3"

[[deps.PlotThemes]]
deps = ["PlotUtils", "Statistics"]
git-tree-sha1 = "6e55c6841ce3411ccb3457ee52fc48cb698d6fb0"
Expand Down Expand Up @@ -1889,9 +1945,9 @@ version = "0.6.43"

[[deps.SciMLBase]]
deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
git-tree-sha1 = "71857d6bab17e7ac6802d86ffcc75423b8c1d812"
git-tree-sha1 = "ce6fb9b0d756446d902e4495f2447fa2ebfbb1f4"
uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
version = "2.54.0"
version = "2.54.2"

[deps.SciMLBase.extensions]
SciMLBaseChainRulesCoreExt = "ChainRulesCore"
Expand Down Expand Up @@ -2543,9 +2599,9 @@ version = "1.18.0+0"

[[deps.libpng_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4"
git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280"
uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
version = "1.6.43+1"
version = "1.6.44+0"

[[deps.libvorbis_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"]
Expand Down
2 changes: 2 additions & 0 deletions docs/Project.toml
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Expand Up @@ -8,11 +8,13 @@ FerriteGmsh = "4f95f4f8-b27c-4ae5-9a39-ea55e634e36b"
FerriteMeshParser = "0f8c756f-80dd-4a75-85c6-b0a5ab9d4620"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
Gmsh = "705231aa-382f-11e9-3f0c-b7cb4346fdeb"
HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771"
IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
OhMyThreads = "67456a42-1dca-4109-a031-0a68de7e3ad5"
Optim = "429524aa-4258-5aef-a3af-852621145aeb"
OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
Expand Down
93 changes: 93 additions & 0 deletions ext/FerriteHYPRE.jl
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@@ -0,0 +1,93 @@
module FerriteHYPRE

using Ferrite: Ferrite, ConstraintHandler, SparsityPattern
using HYPRE.LibHYPRE: @check, HYPRE_BigInt, HYPRE_Complex, HYPRE_IJMatrixAddToValues,
HYPRE_IJMatrixSetValues, HYPRE_IJVectorAddToValues, HYPRE_Int
using HYPRE: HYPRE, HYPREMatrix, HYPREVector
using MPI: MPI

###################################
## Creating the sparsity pattern ##
###################################

function Ferrite.allocate_matrix(::Type{<:HYPREMatrix}, sp::SparsityPattern)

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# Create a new matrix
ilower = HYPRE_BigInt(1)
iupper = HYPRE_BigInt(Ferrite.getnrows(sp))
@assert Ferrite.getnrows(sp) == Ferrite.getncols(sp)
A = HYPREMatrix(MPI.COMM_SELF, ilower, iupper)

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# Add the rows, one at a time
nrows = HYPRE_Int(1)
ncols = HYPRE_Int[0]
rows = HYPRE_BigInt[0]
cols = HYPRE_BigInt[]
values = HYPRE_Complex[]
for (rowidx, colidxs) in zip(1:Ferrite.getnrows(sp), Ferrite.eachrow(sp))
rows[1] = rowidx
n = length(colidxs)
ncols[1] = n
resize!(cols, n)
copyto!(cols, colidxs)
resize!(values, n)
fill!(values, 0)
@check HYPRE_IJMatrixSetValues(A, nrows, ncols, rows, cols, values)
end
HYPRE.Internals.assemble_matrix(A)
return A

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end

############################################
### HYPREAssembler and associated methods ##
############################################

struct HYPREAssembler <: Ferrite.AbstractAssembler
A::HYPRE.HYPREAssembler
end

Ferrite.matrix_handle(a::HYPREAssembler) = a.A.A.A # :)
Ferrite.vector_handle(a::HYPREAssembler) = a.A.b.b # :)

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function Ferrite.start_assemble(K::HYPREMatrix, f::HYPREVector)
return HYPREAssembler(HYPRE.start_assemble!(K, f))

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end

function Ferrite.assemble!(a::HYPREAssembler, dofs::AbstractVector{<:Integer}, ke::AbstractMatrix, fe::AbstractVector)
HYPRE.assemble!(a.A, dofs, ke, fe)
return

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end

function Ferrite.finish_assemble(assembler::HYPREAssembler)
HYPRE.finish_assemble!(assembler.A)
return

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end

function Ferrite.apply!(

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::HYPREMatrix, ::Union{HYPREVector, AbstractVector}, ::ConstraintHandler
)
msg = "Condensation of constraints with `apply!` after assembling not supported " *

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"for HYPREMatrix, use local condensation with `apply_assemble!` instead."
error(msg)

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end


### Methods for arrayutils.jl ##

function Ferrite.addindex!(A::HYPREMatrix, v, i::Int, j::Int)
nrows = HYPRE_Int(1)
ncols = Ref{HYPRE_Int}(1)
rows = Ref{HYPRE_BigInt}(i)
cols = Ref{HYPRE_BigInt}(j)
values = Ref{HYPRE_Complex}(v)
@check HYPRE_IJMatrixAddToValues(A.ijmatrix, nrows, ncols, rows, cols, values)
return A

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end

function Ferrite.addindex!(b::HYPREVector, v, i::Int)
nvalues = HYPRE_Int(1)
indices = Ref{HYPRE_BigInt}(i)
values = Ref{HYPRE_Complex}(v)
@check HYPRE_IJVectorAddToValues(b.ijvector, nvalues, indices, values)
return b

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end

end # module FerriteHYPRE
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