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HYPRE.jl
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Upgrade PartitionedArrays from 0.3.x to 0.5.x. (#18) 

This patch upgrades the PartitionedArrays dependency from the 0.3.x
release series to 0.5.x (closes #17). Also updates documentation build
dependencies.
pull/23/head
Fredrik Ekre 1 year ago committed by GitHub
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9d35b752d5
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5 changed files with 232 additions and 117 deletions
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  1. 4
      Project.toml
  2. 154
      docs/Manifest.toml
  3. 5
      docs/src/api.md
  4. 165
      src/HYPRE.jl
  5. 15
      test/runtests.jl

4
Project.toml
Unescape View File

@ -12,9 +12,9 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" @@ -12,9 +12,9 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
[compat]
CEnum = "0.4"
CEnum = "0.4, 0.5"
MPI = "0.19, 0.20"
PartitionedArrays = "0.3"
PartitionedArrays = "0.5"
SparseMatricesCSR = "0.6"
julia = "1.6"

154
docs/Manifest.toml
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@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
# This file is machine-generated - editing it directly is not advised
julia_version = "1.9.0"
julia_version = "1.10.5"
manifest_format = "2.0"
project_hash = "7c98a97551e318432a6ba3bc3fd4758623a247ac"
@ -19,23 +19,33 @@ deps = ["LinearAlgebra", "Requires"] @@ -19,23 +19,33 @@ deps = ["LinearAlgebra", "Requires"]
git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24"
uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
version = "3.6.2"
weakdeps = ["StaticArrays"]
[deps.Adapt.extensions]
AdaptStaticArraysExt = "StaticArrays"
[deps.Adapt.weakdeps]
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
version = "1.1.1"
[[deps.ArrayLayouts]]
deps = ["FillArrays", "LinearAlgebra", "SparseArrays"]
git-tree-sha1 = "1d9e98721e71dcf4db5a7d34f55d8aa07c43468f"
uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
version = "1.0.6"
[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
[[deps.BlockArrays]]
deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"]
git-tree-sha1 = "bed8cfec0c348753a79d915cc82999c395299297"
uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
version = "0.16.33"
[[deps.CEnum]]
git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90"
uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
@ -47,10 +57,16 @@ git-tree-sha1 = "61bc114e595167090b4cbcb7305ddeacd4274f16" @@ -47,10 +57,16 @@ git-tree-sha1 = "61bc114e595167090b4cbcb7305ddeacd4274f16"
uuid = "7a955b69-7140-5f4e-a0ed-f168c5e2e749"
version = "1.3.2"
[[deps.CodecZlib]]
deps = ["TranscodingStreams", "Zlib_jll"]
git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759"
uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
version = "0.7.6"
[[deps.CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "1.0.2+0"
version = "1.1.1+0"
[[deps.Dates]]
deps = ["Printf"]
@ -73,18 +89,22 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" @@ -73,18 +89,22 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
version = "0.9.3"
[[deps.Documenter]]
deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "REPL", "SnoopPrecompile", "Test", "Unicode"]
git-tree-sha1 = "2afe1f1706b90fd4a8593d70b5324d04ddefed69"
repo-rev = "master"
repo-url = "https://github.com/JuliaDocs/Documenter.jl.git"
deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "CodecZlib", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "TOML", "Test", "Unicode"]
git-tree-sha1 = "5a1ee886566f2fa9318df1273d8b778b9d42712d"
uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
version = "0.28.0-DEV"
version = "1.7.0"
[[deps.Downloads]]
deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
version = "1.6.0"
[[deps.Expat_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7"
uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
version = "2.6.2+0"
[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
@ -94,6 +114,18 @@ git-tree-sha1 = "ed569cb9e7e3590d5ba884da7edc50216aac5811" @@ -94,6 +114,18 @@ git-tree-sha1 = "ed569cb9e7e3590d5ba884da7edc50216aac5811"
uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
version = "1.1.0"
[[deps.Git]]
deps = ["Git_jll"]
git-tree-sha1 = "04eff47b1354d702c3a85e8ab23d539bb7d5957e"
uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2"
version = "1.3.1"
[[deps.Git_jll]]
deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"]
git-tree-sha1 = "ea372033d09e4552a04fd38361cd019f9003f4f4"
uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb"
version = "2.46.2+0"
[[deps.HYPRE]]
deps = ["CEnum", "HYPRE_jll", "Libdl", "MPI", "PartitionedArrays", "SparseArrays", "SparseMatricesCSR"]
path = ".."
@ -140,6 +172,11 @@ git-tree-sha1 = "cc6ca91b2ca8d3600478d40097d30a6f046d0759" @@ -140,6 +172,11 @@ git-tree-sha1 = "cc6ca91b2ca8d3600478d40097d30a6f046d0759"
uuid = "51474c39-65e3-53ba-86ba-03b1b862ec14"
version = "3.11.0+0"
[[deps.LazilyInitializedFields]]
git-tree-sha1 = "8f7f3cabab0fd1800699663533b6d5cb3fc0e612"
uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf"
version = "1.2.2"
[[deps.LazyArtifacts]]
deps = ["Artifacts", "Pkg"]
uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
@ -147,25 +184,36 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -147,25 +184,36 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
[[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
version = "0.6.3"
version = "0.6.4"
[[deps.LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
version = "7.84.0+0"
version = "8.4.0+0"
[[deps.LibGit2]]
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
[[deps.LibGit2_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
version = "1.6.4+0"
[[deps.LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
version = "1.10.2+0"
version = "1.11.0+1"
[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
[[deps.Libiconv_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175"
uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
version = "1.17.0+0"
[[deps.LinearAlgebra]]
deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@ -218,7 +266,7 @@ version = "0.1.1" @@ -218,7 +266,7 @@ version = "0.1.1"
[[deps.MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.28.2+0"
version = "2.28.2+1"
[[deps.MicrosoftMPI_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@ -231,7 +279,7 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -231,7 +279,7 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"
[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
version = "2022.10.11"
version = "2023.1.10"
[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
@ -246,7 +294,7 @@ version = "1.12.9" @@ -246,7 +294,7 @@ version = "1.12.9"
[[deps.OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
version = "0.3.21+4"
version = "0.3.23+4"
[[deps.OpenMPI_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
@ -254,6 +302,17 @@ git-tree-sha1 = "f3080f4212a8ba2ceb10a34b938601b862094314" @@ -254,6 +302,17 @@ git-tree-sha1 = "f3080f4212a8ba2ceb10a34b938601b862094314"
uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
version = "4.1.5+0"
[[deps.OpenSSL_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10"
uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
version = "3.0.15+1"
[[deps.PCRE2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15"
version = "10.42.0+1"
[[deps.Parsers]]
deps = ["Dates", "PrecompileTools", "UUIDs"]
git-tree-sha1 = "a5aef8d4a6e8d81f171b2bd4be5265b01384c74c"
@ -261,15 +320,15 @@ uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" @@ -261,15 +320,15 @@ uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "2.5.10"
[[deps.PartitionedArrays]]
deps = ["CircularArrays", "Distances", "FillArrays", "IterativeSolvers", "LinearAlgebra", "MPI", "Printf", "Random", "SparseArrays", "SparseMatricesCSR"]
git-tree-sha1 = "efdde29f1a7def5f81d1ed0265b3c7bc1c3ee00f"
deps = ["BlockArrays", "CircularArrays", "Distances", "FillArrays", "IterativeSolvers", "LinearAlgebra", "MPI", "Printf", "Random", "SparseArrays", "SparseMatricesCSR", "StaticArrays"]
git-tree-sha1 = "912e48995e001f7b24d425fb1eebbb97e8c3cb09"
uuid = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
version = "0.3.2"
version = "0.5.4"
[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.9.0"
version = "1.10.0"
[[deps.PrecompileTools]]
deps = ["Preferences"]
@ -292,7 +351,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -292,7 +351,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
[[deps.Random]]
deps = ["SHA", "Serialization"]
deps = ["SHA"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
[[deps.RecipesBase]]
@ -301,6 +360,12 @@ git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" @@ -301,6 +360,12 @@ git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff"
uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
version = "1.3.4"
[[deps.RegistryInstances]]
deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"]
git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51"
uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3"
version = "0.1.0"
[[deps.Requires]]
deps = ["UUIDs"]
git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7"
@ -314,18 +379,13 @@ version = "0.7.0" @@ -314,18 +379,13 @@ version = "0.7.0"
[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
[[deps.SnoopPrecompile]]
deps = ["Preferences"]
git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c"
uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c"
version = "1.0.3"
[[deps.Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
[[deps.SparseArrays]]
deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
version = "1.10.0"
[[deps.SparseMatricesCSR]]
deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
@ -333,10 +393,29 @@ git-tree-sha1 = "38677ca58e80b5cad2382e5a1848f93b054ad28d" @@ -333,10 +393,29 @@ git-tree-sha1 = "38677ca58e80b5cad2382e5a1848f93b054ad28d"
uuid = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
version = "0.6.7"
[[deps.StaticArrays]]
deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.9.7"
[deps.StaticArrays.extensions]
StaticArraysChainRulesCoreExt = "ChainRulesCore"
StaticArraysStatisticsExt = "Statistics"
[deps.StaticArrays.weakdeps]
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
[[deps.StaticArraysCore]]
git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682"
uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
version = "1.4.3"
[[deps.Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
version = "1.9.0"
version = "1.10.0"
[[deps.StatsAPI]]
deps = ["LinearAlgebra"]
@ -349,9 +428,9 @@ deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -349,9 +428,9 @@ deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
[[deps.SuiteSparse_jll]]
deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"]
deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
version = "5.10.1+6"
version = "7.2.1+1"
[[deps.TOML]]
deps = ["Dates"]
@ -367,6 +446,11 @@ version = "1.10.0" @@ -367,6 +446,11 @@ version = "1.10.0"
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
[[deps.TranscodingStreams]]
git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.11.2"
[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
@ -377,19 +461,19 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" @@ -377,19 +461,19 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.13+0"
version = "1.2.13+1"
[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.7.0+0"
version = "5.11.0+0"
[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.48.0+0"
version = "1.52.0+1"
[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+0"
version = "17.4.0+2"

5
docs/src/api.md
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@ -32,3 +32,8 @@ HYPRE.ILU @@ -32,3 +32,8 @@ HYPRE.ILU
HYPRE.PCG
HYPRE.ParaSails
```
```@docs
HYPRE.GetNumIterations
HYPRE.GetFinalRelativeResidualNorm
```

165
src/HYPRE.jl
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@ -3,10 +3,9 @@ @@ -3,10 +3,9 @@
module HYPRE
using MPI: MPI
using PartitionedArrays: own_length, tuple_of_arrays, own_to_global, global_length,
own_to_local, local_to_global, global_to_own, global_to_local,
MPIArray, PSparseMatrix, PVector, PartitionedArrays, AbstractLocalIndices,
local_values, own_values, partition
using PartitionedArrays: PartitionedArrays, AbstractLocalIndices, MPIArray, PSparseMatrix,
PVector, SplitMatrix, ghost_to_global, local_values, own_to_global, own_values,
partition
using SparseArrays: SparseArrays, SparseMatrixCSC, nnz, nonzeros, nzrange, rowvals
using SparseMatricesCSR: SparseMatrixCSR, colvals, getrowptr
@ -344,36 +343,48 @@ function subarray_unsafe_supported() @@ -344,36 +343,48 @@ function subarray_unsafe_supported()
return VERSION >= v"1.9.0"
end
# TODO: This has some duplicated code with to_hypre_data(::SparseMatrixCSC, ilower, iupper)
function Internals.to_hypre_data(A::SparseMatrixCSC, r::AbstractLocalIndices, c::AbstractLocalIndices)
g_to_l_rows = global_to_local(r) # Not sure about this assert
l_to_g_rows = local_to_global(r)
@assert g_to_l_rows.own_to_local isa UnitRange && g_to_l_rows.own_to_local.start == 1
n_local_rows = own_length(r)
n_local_cols = own_length(c)
ilower = l_to_g_rows[1]
iupper = l_to_g_rows[own_length(r)]
a_rows = rowvals(A)
a_vals = nonzeros(A)
function Internals.to_hypre_data(
A::SplitMatrix{<:SparseMatrixCSC}, r::AbstractLocalIndices, c::AbstractLocalIndices
)
# Own/ghost to global index mappings
own_to_global_row = own_to_global(r)
own_to_global_col = own_to_global(c)
ghost_to_global_col = ghost_to_global(c)
# HYPRE requires contiguous row indices
ilower = own_to_global_row[1]
iupper = own_to_global_row[end]
@assert iupper - ilower + 1 == length(own_to_global_row)
# Extract sparse matrices from the SplitMatrix. We are only interested in the owned
# rows, so only consider own-own and own-ghost blocks.
Aoo = A.blocks.own_own::SparseMatrixCSC
Aoo_rows = rowvals(Aoo)
Aoo_vals = nonzeros(Aoo)
Aog = A.blocks.own_ghost::SparseMatrixCSC
Aog_rows = rowvals(Aog)
Aog_vals = nonzeros(Aog)
@assert size(Aoo, 1) == size(Aog, 1) == length(own_to_global_row)
# Initialize the data buffers HYPRE wants
nrows = HYPRE_Int(iupper - ilower + 1) # Total number of rows
nrows = HYPRE_Int(length(own_to_global_row)) # Total number of rows
ncols = zeros(HYPRE_Int, nrows) # Number of colums for each row
rows = collect(HYPRE_BigInt, ilower:iupper) # The row indices
# cols = Vector{HYPRE_BigInt}(undef, nnz) # The column indices
# values = Vector{HYPRE_Complex}(undef, nnz) # The values
# First pass to count nnz per row (note that the fact that columns are permuted
# doesn't matter for this pass)
a_rows = rowvals(A)
a_vals = nonzeros(A)
@inbounds for j in 1:size(A, 2)
for i in nzrange(A, j)
row = a_rows[i]
row > n_local_rows && continue # Skip ghost rows
# grow = r.lid_to_gid[lrow]
ncols[row] += 1
# First pass to count nnz per row (note that global column indices and column
# permutation doesn't matter for this pass)
@inbounds for own_col in 1:size(Aoo, 2)
for k in nzrange(Aoo, own_col)
own_row = Aoo_rows[k]
ncols[own_row] += 1
end
end
@inbounds for ghost_col in 1:size(Aog, 2)
for k in nzrange(Aog, ghost_col)
own_row = Aog_rows[k]
ncols[own_row] += 1
end
end
@ -386,61 +397,83 @@ function Internals.to_hypre_data(A::SparseMatrixCSC, r::AbstractLocalIndices, c: @@ -386,61 +397,83 @@ function Internals.to_hypre_data(A::SparseMatrixCSC, r::AbstractLocalIndices, c:
lastinds = zeros(Int, nrows)
cumsum!((@view lastinds[2:end]), (@view ncols[1:end-1]))
# Second pass to populate the output -- here we need to take care of the permutation
# of columns. TODO: Problem that they are not sorted?
l_to_g_cols = local_to_global(c)
@inbounds for j in 1:size(A, 2)
for i in nzrange(A, j)
row = a_rows[i]
row > n_local_cols && continue # Skip ghost rows
k = lastinds[row] += 1
val = a_vals[i]
cols[k] = l_to_g_cols[j]
values[k] = val
# Second pass to populate the output. Here we need to map column
# indices from own/ghost to global
@inbounds for own_col in 1:size(Aoo, 2)
for k in nzrange(Aoo, own_col)
own_row = Aoo_rows[k]
i = lastinds[own_row] += 1
values[i] = Aoo_vals[k]
cols[i] = own_to_global_col[own_col]
end
end
@inbounds for ghost_col in 1:size(Aog, 2)
for k in nzrange(Aog, ghost_col)
own_row = Aog_rows[k]
i = lastinds[own_row] += 1
values[i] = Aog_vals[k]
cols[i] = ghost_to_global_col[ghost_col]
end
end
# Sanity checks and return
@assert nrows == length(ncols) == length(rows)
return nrows, ncols, rows, cols, values
end
# TODO: Possibly this can be optimized if it is possible to pass overlong vectors to HYPRE.
# At least values should be possible to directly share, but cols needs to translated
# to global ids.
function Internals.to_hypre_data(A::SparseMatrixCSR, r::AbstractLocalIndices, c::AbstractLocalIndices)
g_to_l_rows = global_to_local(r)
l_to_g_rows = local_to_global(r)
@assert g_to_l_rows.own_to_local isa UnitRange && g_to_l_rows.own_to_local.start == 1
n_local_rows = own_length(r)
ilower = l_to_g_rows[1]
iupper = l_to_g_rows[n_local_rows]
a_cols = colvals(A)
a_vals = nonzeros(A)
nnz = getrowptr(A)[n_local_rows + 1] - 1
function Internals.to_hypre_data(
A::SplitMatrix{<:SparseMatrixCSR}, r::AbstractLocalIndices, c::AbstractLocalIndices
)
# Own/ghost to global index mappings
own_to_global_row = own_to_global(r)
own_to_global_col = own_to_global(c)
ghost_to_global_col = ghost_to_global(c)
# HYPRE requires contiguous row indices
ilower = own_to_global_row[1]
iupper = own_to_global_row[end]
@assert iupper - ilower + 1 == length(own_to_global_row)
# Extract sparse matrices from the SplitMatrix. We are only interested in the owned
# rows, so only consider own-own and own-ghost blocks.
Aoo = A.blocks.own_own::SparseMatrixCSR
Aoo_cols = colvals(Aoo)
Aoo_vals = nonzeros(Aoo)
Aog = A.blocks.own_ghost::SparseMatrixCSR
Aog_cols = colvals(Aog)
Aog_vals = nonzeros(Aog)
@assert size(Aoo, 1) == size(Aog, 1) == length(own_to_global_row)
# Initialize the data buffers HYPRE wants
nnz = SparseArrays.nnz(Aoo) + SparseArrays.nnz(Aog)
nrows = HYPRE_Int(iupper - ilower + 1) # Total number of rows
ncols = zeros(HYPRE_Int, nrows) # Number of columns for each row
rows = collect(HYPRE_BigInt, ilower:iupper) # The row indices
cols = Vector{HYPRE_BigInt}(undef, nnz) # The column indices
values = Vector{HYPRE_Complex}(undef, nnz) # The values
# Loop over the (owned) rows and collect all values
l_to_g_cols = local_to_global(c)
k = 0
@inbounds for i in own_to_local(r)
nzr = nzrange(A, i)
ncols[i] = length(nzr)
for j in nzr
k += 1
col = a_cols[j]
val = a_vals[j]
cols[k] = l_to_g_cols[col]
values[k] = val
# For CSR we only need a single pass to over the owned rows to collect everything
i = 0
for own_row in 1:size(Aoo, 1)
nzro = nzrange(Aoo, own_row)
nzrg = nzrange(Aog, own_row)
ncols[own_row] = length(nzro) + length(nzrg)
for k in nzro
i += 1
own_col = Aoo_cols[k]
cols[i] = own_to_global_col[own_col]
values[i] = Aoo_vals[k]
end
for k in nzrg
i += 1
ghost_col = Aog_cols[k]
cols[i] = ghost_to_global_col[ghost_col]
values[i] = Aog_vals[k]
end
@assert nnz == k
end
# Sanity checks and return
@assert nnz == i
@assert nrows == length(ncols) == length(rows)
return nrows, ncols, rows, cols, values
end

15
test/runtests.jl
Unescape View File

@ -91,13 +91,6 @@ end @@ -91,13 +91,6 @@ end
@test H.iupper == H.jupper == 10
end
function default_local_values_csr(I,J,V,row_indices,col_indices)
# Adapted from p_sparse_matrix.jl line 487
m = local_length(row_indices)
n = local_length(col_indices)
sparsecsr(I,J,V,m,n)
end
function distribute_as_parray(parts, backend)
if backend == :debug
parts = DebugArray(parts)
@ -151,8 +144,8 @@ end @@ -151,8 +144,8 @@ end
parts = 1:2
end
parts = distribute_as_parray(parts, backend)
CSC = psparse!(diag_data(parts)...) |> fetch
CSR = psparse!(default_local_values_csr, diag_data(parts)...) |> fetch
CSC = psparse(diag_data(parts)...) |> fetch
CSR = psparse(sparsecsr, diag_data(parts)...) |> fetch
for A in [CSC, CSR]
map(local_values(A), A.row_partition, A.col_partition, parts) do values, rows, cols, p
@ -276,7 +269,7 @@ end @@ -276,7 +269,7 @@ end
return collect(row_indices), values
end
I, V = tuple_of_arrays(IV)
pb = pvector!(I, V, rows) |> fetch
pb = pvector(I, V, rows) |> fetch
H = HYPREVector(pb)
# Check for valid vector
@test H.ijvector != HYPRE_IJVector(C_NULL)
@ -694,7 +687,7 @@ function topartitioned(x::Vector, A::SparseMatrixCSC, b::Vector, backend) @@ -694,7 +687,7 @@ function topartitioned(x::Vector, A::SparseMatrixCSC, b::Vector, backend)
return findnz(A)..., b, x
end
II, JJ, VV, bb, xx = tuple_of_arrays(tmp)
A_p = psparse!(II, JJ, VV, rows, cols) |> fetch
A_p = psparse(II, JJ, VV, rows, cols) |> fetch
b_p = PVector(bb, rows)
x_p = PVector(xx, cols)
return x_p, A_p, b_p

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