Merge pull request #35 from j-fu/jf-parallel2

Restructuring for parallelization
j-fu · Jul 16, 2024 · 91aa015 · 91aa015 · j-fu · Jul 16, 2024
2 parents d0cacb0 + 24f73ab
commit 91aa015
Show file tree

Hide file tree

Showing 31 changed files with 5,463 additions and 462 deletions.
diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
@@ -1,4 +1,7 @@
-style = "sciml"
+style = "yas"
 always_for_in = false
-separate_kwargs_with_semicolon = true
 format_markdown = true
+import_to_using = false
+pipe_to_function_call = false
+short_to_long_function_def = false
+always_use_return = false
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -15,15 +15,26 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
+          - '1.9' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
           - '1'   # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia.
           - 'nightly'
         os:
           - ubuntu-latest
-          - macos-latest
           - windows-latest
+          - macos-latest # arm
+          - macOS-13 # intel
         arch:
           - x64
+          - aarch64
+        exclude:
+          - os: ubuntu-latest
+            arch: aarch64
+          - os: windows-latest
+            arch: aarch64
+          - os: macOS-13 
+            arch: aarch64
+          - os: macos-latest
+            arch: x64
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
@@ -42,6 +53,8 @@ jobs:
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        env:
+          JULIA_NUM_THREADS: 4
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v3
   docs:

diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,7 @@
 QUARRY
 docs/build
 *~
-Manifest.toml
+Manifest*.toml
 .repl_history
 quarry
 
diff --git a/Project.toml b/Project.toml
@@ -1,13 +1,15 @@
 name = "ExtendableSparse"
 uuid = "95c220a8-a1cf-11e9-0c77-dbfce5f500b3"
 authors = ["Juergen Fuhrmann <juergen.fuhrmann@wias-berlin.de>"]
-version = "1.4.1"
+version = "1.5.0"
 
 [deps]
 AMGCLWrap = "4f76b812-4ba5-496d-b042-d70715554288"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 ILUZero = "88f59080-6952-5380-9ea5-54057fb9a43f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Metis = "2679e427-3c69-5b7f-982b-ece356f1e94b"
+OhMyThreads = "67456a42-1dca-4109-a031-0a68de7e3ad5"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -29,7 +31,7 @@ ExtendableSparseIncompleteLUExt = "IncompleteLU"
 ExtendableSparsePardisoExt = "Pardiso"
 
 [compat]
-AMGCLWrap = "0.3.1,0.4"
+AMGCLWrap = "0.4"
 AlgebraicMultigrid = "0.4,0.5,0.6"
 DocStringExtensions = "0.8, 0.9"
 ILUZero = "0.2"
@@ -38,7 +40,7 @@ Pardiso = "0.5.1"
 Requires = "1.1.3"
 Sparspak = "0.3.6"
 StaticArrays = "1.5.24"
-julia = "1.6"
+julia = "1.9"
 
 [extras]
 AMGCLWrap = "4f76b812-4ba5-496d-b042-d70715554288"

diff --git a/docs/make.jl b/docs/make.jl
@@ -5,6 +5,7 @@ function mkdocs()
     makedocs(; sitename = "ExtendableSparse.jl",
              modules = [ExtendableSparse],
              doctest = false,
+             warnonly = true,
              clean = false,
              authors = "J. Fuhrmann",
              repo = "https://github.com/j-fu/ExtendableSparse.jl",

diff --git a/docs/src/internal.md b/docs/src/internal.md
@@ -13,6 +13,17 @@ Pages = ["sparsematrixlnk.jl"]
 Modules = [ExtendableSparse]
 Pages = ["sparsematrixcsc.jl"]
 ```
+## New API 
+Under development - aimed at multithreading
+```@autodocs
+Modules = [ExtendableSparse]
+Pages = ["abstractsparsematrixextension.jl",
+    "abstractextendablesparsematrixcsc.jl",
+    "sparsematrixdilnkc.jl",
+    "genericextendablesparsematrixcsc.jl",
+    "genericmtextendablesparsematrixcsc.jl"]
+```
+
 
 ## Misc methods
 

diff --git a/src/ExtendableSparse.jl b/src/ExtendableSparse.jl
@@ -1,12 +1,17 @@
 module ExtendableSparse
-using SparseArrays,StaticArrays
-using LinearAlgebra
-using Sparspak
-using ILUZero
 
-if  !isdefined(Base, :get_extension)
-    using Requires
-end
+using DocStringExtensions: DocStringExtensions, SIGNATURES, TYPEDEF,TYPEDFIELDS
+using ILUZero: ILUZero, ldiv!, nnz
+using OhMyThreads: @tasks
+using LinearAlgebra: LinearAlgebra, Diagonal, Hermitian, Symmetric, Tridiagonal,
+    cholesky, cholesky!, convert, lu!, mul!, norm, transpose
+using SparseArrays: SparseArrays, AbstractSparseMatrix, SparseMatrixCSC,
+    dropzeros!, findnz, nzrange, sparse, spzeros
+using Sparspak: Sparspak, sparspaklu, sparspaklu!
+using StaticArrays: StaticArrays, SMatrix, SVector
+using SuiteSparse: SuiteSparse
+import SparseArrays: AbstractSparseMatrixCSC, rowvals, getcolptr, nonzeros
+
 
 # Define our own constant here in order to be able to
 # test things at least a little bit..
@@ -17,58 +22,57 @@ if USE_GPL_LIBS
 end
 
 
-using DocStringExtensions
-
-import SparseArrays: AbstractSparseMatrixCSC, rowvals, getcolptr, nonzeros
 
 include("matrix/sparsematrixcsc.jl")
+include("matrix/abstractsparsematrixextension.jl")
 include("matrix/sparsematrixlnk.jl")
+include("matrix/sparsematrixdilnkc.jl")
+include("matrix/abstractextendablesparsematrixcsc.jl")
 include("matrix/extendable.jl")
+include("matrix/genericmtextendablesparsematrixcsc.jl")
+include("matrix/genericextendablesparsematrixcsc.jl")
+
+const ExtendableSparseMatrix=ExtendableSparseMatrixCSC
+const MTExtendableSparseMatrixCSC{Tv,Ti}=GenericMTExtendableSparseMatrixCSC{SparseMatrixDILNKC{Tv,Ti},Tv,Ti}
+MTExtendableSparseMatrixCSC(m,n,args...)=MTExtendableSparseMatrixCSC{Float64,Int64}(m,n,args...)
+
+const STExtendableSparseMatrixCSC{Tv,Ti}=GenericExtendableSparseMatrixCSC{SparseMatrixDILNKC{Tv,Ti},Tv,Ti}
+STExtendableSparseMatrixCSC(m,n,args...)=STExtendableSparseMatrixCSC{Float64,Int64}(m,n,args...)
 
-export SparseMatrixLNK,
-       ExtendableSparseMatrix, flush!, nnz, updateindex!, rawupdateindex!, colptrs, sparse
+
+export ExtendableSparseMatrixCSC, MTExtendableSparseMatrixCSC, STExtendableSparseMatrixCSC, GenericMTExtendableSparseMatrixCSC
+export SparseMatrixLNK, ExtendableSparseMatrix,flush!, nnz, updateindex!, rawupdateindex!, colptrs, sparse, reset!, nnznew
+export partitioning!
 
 export eliminate_dirichlet, eliminate_dirichlet!, mark_dirichlet
 
 include("factorizations/factorizations.jl")
 
+include("experimental/Experimental.jl")
+
+include("factorizations/simple_iteration.jl")
+export simple, simple!
+
+include("matrix/sprand.jl")
+export sprand!, sprand_sdd!, fdrand, fdrand!, fdrand_coo, solverbenchmark
+
+export rawupdateindex!, updateindex!
+
+
+
+
 export JacobiPreconditioner,
     ILU0Preconditioner,
     ILUZeroPreconditioner,
     PointBlockILUZeroPreconditioner,
     ParallelJacobiPreconditioner,
     ParallelILU0Preconditioner,
-    BlockPreconditioner,allow_views,
-    reorderlinsys
+    BlockPreconditioner,allow_views
 
 export AbstractFactorization, LUFactorization, CholeskyFactorization, SparspakLU
 export issolver
 export factorize!, update!
 
-include("factorizations/simple_iteration.jl")
-export simple, simple!
-
-include("matrix/sprand.jl")
-export sprand!, sprand_sdd!, fdrand, fdrand!, fdrand_coo, solverbenchmark
-
-
-@static if  !isdefined(Base, :get_extension)
-    function __init__()
-        @require Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2"  begin
-            include("../ext/ExtendableSparsePardisoExt.jl")
-        end
-        @require IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"  begin
-            include("../ext/ExtendableSparseIncompleteLUExt.jl")
-        end
-        @require AlgebraicMultigrid = "2169fc97-5a83-5252-b627-83903c6c433c" begin
-            include("../ext/ExtendableSparseAlgebraicMultigridExt.jl")
-        end
-        @require AMGCLWrap = "4f76b812-4ba5-496d-b042-d70715554288" begin
-            include("../ext/ExtendableSparseAMGCLWrapExt.jl")
-        end
-    end
-end
-
 """
 ```
 ILUTPreconditioner(;droptol=1.0e-3)

diff --git a/src/experimental/Experimental.jl b/src/experimental/Experimental.jl
@@ -0,0 +1,44 @@
+module Experimental
+using ExtendableSparse, SparseArrays
+using LinearAlgebra
+using SparseArrays: AbstractSparseMatrixCSC
+import SparseArrays: nonzeros, getcolptr,nzrange
+import ExtendableSparse: flush!, reset!, rawupdateindex!, findindex
+using ExtendableSparse: ColEntry, AbstractPreconditioner, @makefrommatrix, phash
+using ExtendableSparse:  AbstractExtendableSparseMatrixCSC, AbstractSparseMatrixExtension
+using DocStringExtensions
+using Metis
+using Base.Threads
+using OhMyThreads: @tasks
+import ExtendableSparse: factorize!, update!, partitioning!
+
+include(joinpath(@__DIR__, "ExtendableSparseMatrixParallel", "ExtendableSparseParallel.jl"))
+
+include(joinpath(@__DIR__, "ExtendableSparseMatrixParallel", "ilu_Al-Kurdi_Mittal.jl"))
+#using .ILUAM
+include(joinpath(@__DIR__, "ExtendableSparseMatrixParallel", "pilu_Al-Kurdi_Mittal.jl"))
+#using .PILUAM
+
+include(joinpath(@__DIR__, "ExtendableSparseMatrixParallel" ,"iluam.jl"))
+include(joinpath(@__DIR__, "ExtendableSparseMatrixParallel", "piluam.jl"))
+
+@eval begin
+    @makefrommatrix ILUAMPreconditioner
+    @makefrommatrix PILUAMPreconditioner
+end
+
+function factorize!(p::PILUAMPreconditioner, A::ExtendableSparseMatrixParallel)
+    p.A = A
+    update!(p)
+    p
+end
+
+export ExtendableSparseMatrixParallel, SuperSparseMatrixLNK
+export addtoentry!, reset!, dummy_assembly!, preparatory_multi_ps_less_reverse, fr, addtoentry!,  compare_matrices_light
+export     ILUAMPreconditioner,    PILUAMPreconditioner
+export     reorderlinsys, nnz_noflush
+
+
+
+end
+