sparsity patterns for kernels of BilinearOperator now also done by SparseConnectivityTracer, could removed Symbolics as a main dependence now, version bump + changelog

Author: chmerdon

CHANGELOG.md

@@ -1,5 +1,13 @@
 # CHANGES
 
+## v1.5.0
+
+### Added
+  - new parameter `autodiff_backend` for NonlinearOperator to change differentiation backend
+
+### Changed
+  - sparsity patterns of local jacobians are now resolved by SparseConnectivityTracer
+  - local jacobians are now prepared by DifferentiationInterface 
 
 ## v1.4.0
 

Project.toml

@@ -1,7 +1,7 @@
 name = "ExtendableFEM"
 uuid = "a722555e-65e0-4074-a036-ca7ce79a4aed"
 authors = ["Christian Merdon <[email protected]>", "Patrick Jaap <[email protected]>"]
-version = "1.3.0"
+version = "1.5.0"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
@@ -21,7 +21,6 @@ SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
 SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35"
-Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 
@@ -70,9 +69,10 @@ OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
 OrdinaryDiffEqSDIRK = "2d112036-d095-4a1e-ab9a-08536f3ecdbf"
 SimplexGridFactory = "57bfcd06-606e-45d6-baf4-4ba06da0efd5"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TetGen = "c5d3f3f7-f850-59f6-8a2e-ffc6dc1317ea"
 Triangulate = "f7e6ffb2-c36d-4f8f-a77e-16e897189344"
 
 [targets]
-test = ["Aqua", "ExampleJuggler", "ExplicitImports", "IncompleteLU", "Metis", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "SimplexGridFactory", "StaticArrays", "Test", "TetGen", "Triangulate"]
+test = ["Aqua", "ExampleJuggler", "ExplicitImports", "IncompleteLU", "Metis", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "SimplexGridFactory", "StaticArrays", "Symbolics", "Test", "TetGen", "Triangulate"]

src/ExtendableFEM.jl

@@ -66,16 +66,15 @@ using LinearAlgebra: LinearAlgebra, copyto!, isposdef, mul!, norm
 using LinearSolve: LinearSolve, LinearProblem, UMFPACKFactorization, deleteat!,
     init, solve
 using Printf: Printf, @printf, @sprintf
-using SparseArrays: SparseArrays, AbstractSparseArray, SparseMatrixCSC, findnz, nnz,
+using SparseArrays: SparseArrays, AbstractSparseArray, findnz, nnz,
     nzrange, rowvals, sparse
 using ADTypes: ADTypes, KnownJacobianSparsityDetector
-using SparseConnectivityTracer: SparseConnectivityTracer, TracerSparsityDetector
+using SparseConnectivityTracer: SparseConnectivityTracer, TracerSparsityDetector, jacobian_sparsity
 using DifferentiationInterface: DifferentiationInterface,
     AutoSparse,
     AutoForwardDiff,
     prepare_jacobian
 using SparseMatrixColorings: GreedyColoringAlgorithm, sparsity_pattern
-using Symbolics: Symbolics
 using SciMLBase: SciMLBase
 using TimerOutputs: TimerOutput, print_timer, @timeit
 using UnicodePlots: UnicodePlots

src/common_operators/bilinear_operator.jl

@@ -410,7 +410,8 @@ function build_assembler!(A::AbstractMatrix, O::BilinearOperator{Tv}, FE_test, F
         coupling_matrix::Matrix{Bool} = ones(Bool, nansatz, ntest)
         if use_sparsity_pattern
             kernel_params = (result, input) -> (O.kernel(result, input, O.QP_infos[1]))
-            sparsity_pattern = SparseMatrixCSC{Float64, Int}(Symbolics.jacobian_sparsity(kernel_params, zeros(Tv, op_offsets_test[end]), zeros(Tv, op_offsets_ansatz[end])))
+            detector = TracerSparsityDetector()
+            sparsity_pattern = jacobian_sparsity(kernel_params, zeros(Tv, op_offsets_test[end]), zeros(Tv, op_offsets_ansatz[end]), detector)
 
             ## find out which test and ansatz functions couple
             for id in 1:nansatz
@@ -779,7 +780,8 @@ function build_assembler!(A, O::BilinearOperator{Tv}, FE_test, FE_ansatz; time =
         coupling_matrix::Matrix{Bool} = ones(Bool, nansatz, ntest)
         if use_sparsity_pattern
             kernel_params = (result, input) -> (O.kernel(result, input, O.QP_infos[1]))
-            sparsity_pattern = SparseMatrixCSC{Float64, Int}(Symbolics.jacobian_sparsity(kernel_params, zeros(Tv, op_offsets_test[end]), zeros(Tv, op_offsets_ansatz[end])))
+            detector = TracerSparsityDetector()
+            sparsity_pattern = jacobian_sparsity(kernel_params, zeros(Tv, op_offsets_test[end]), zeros(Tv, op_offsets_ansatz[end]), detector)
 
             ## find out which test and ansatz functions couple
             for id in 1:nansatz

src/common_operators/bilinear_operator_dg.jl

@@ -367,7 +367,8 @@ function build_assembler!(A, O::BilinearOperatorDG{Tv}, FE_test, FE_ansatz, FE_a
         coupling_matrix::Matrix{Bool} = ones(Bool, nansatz, ntest)
         if use_sparsity_pattern
             kernel_params = (result, input) -> (O.kernel(result, input, O.QP_infos[1]))
-            sparsity_pattern = SparseMatrixCSC{Float64, Int}(Symbolics.jacobian_sparsity(kernel_params, zeros(Tv, op_offsets_test[end]), zeros(Tv, op_offsets_ansatz[end])))
+            detector = TracerSparsityDetector()
+            sparsity_pattern = jacobian_sparsity(kernel_params, zeros(Tv, op_offsets_test[end]), zeros(Tv, op_offsets_ansatz[end]), detector)
 
             ## find out which test and ansatz functions couple
             for id in 1:nansatz
@@ -782,7 +783,8 @@ function build_assembler!(A, O::BilinearOperatorDG{Tv}, FE_test, FE_ansatz; time
         coupling_matrix::Matrix{Bool} = ones(Bool, nansatz, ntest)
         if use_sparsity_pattern
             kernel_params = (result, input) -> (O.kernel(result, input, O.QP_infos[1]))
-            sparsity_pattern = SparseMatrixCSC{Float64, Int}(Symbolics.jacobian_sparsity(kernel_params, zeros(Tv, op_offsets_test[end]), zeros(Tv, op_offsets_ansatz[end])))
+            detector = TracerSparsityDetector()
+            sparsity_pattern = jacobian_sparsity(kernel_params, zeros(Tv, op_offsets_test[end]), zeros(Tv, op_offsets_ansatz[end]), detector)
 
             ## find out which test and ansatz functions couple
             for id in 1:nansatz

test/runtests.jl

@@ -8,6 +8,7 @@ using Metis
 using Aqua
 using Triangulate
 using SimplexGridFactory
+using Symbolics
 
 
 include("test_dgblf.jl")