Merge pull request #116 from ErikQQY/qqy/sct

Add extension for SparseConnectivityTracer

.github/workflows/Downgrade.yml

@@ -21,7 +21,7 @@ jobs:
         group:
           - Core
         version:
-          - '1'
+          - '1.10'
         os:
           - ubuntu-latest
           - macos-latest

Project.toml

@@ -1,7 +1,7 @@
 name = "PreallocationTools"
 uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
 authors = ["Chris Rackauckas <[email protected]>"]
-version = "0.4.24"
+version = "0.4.25"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -10,31 +10,36 @@ ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 
 [weakdeps]
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
 
 [extensions]
 PreallocationToolsReverseDiffExt = "ReverseDiff"
+PreallocationToolsSparseConnectivityTracerExt = "SparseConnectivityTracer"
 
 [compat]
-Adapt = "3.4, 4"
-Aqua = "0.8"
-ArrayInterface = "7.7"
-ForwardDiff = "0.10.19"
-LabelledArrays = "1.15"
-LinearAlgebra = "1"
-Optimization = "3.19"
-OptimizationOptimJL = "0.1.5"
-OrdinaryDiffEq = "6.65"
-Pkg = "1"
-Random = "1"
-RecursiveArrayTools = "3.2"
-ReverseDiff = "1"
+Adapt = "4.1.1"
+ADTypes = "1.13"
+Aqua = "0.8.11"
+ArrayInterface = "7.18.0"
+ForwardDiff = "0.10.38"
+LabelledArrays = "1.16.0"
+LinearAlgebra = "1.10"
+Optimization = "4.1.1"
+OptimizationOptimJL = "0.4.1"
+OrdinaryDiffEq = "6.91.0"
+Pkg = "1.10"
+Random = "1.10.8"
+RecursiveArrayTools = "3.29.0"
+ReverseDiff = "1.15.3"
 SafeTestsets = "0.1"
-SparseArrays = "1"
-Symbolics = "5.12"
-Test = "1"
+SparseArrays = "1.10"
+SparseConnectivityTracer = "0.6.12"
+Symbolics = "6.29.0"
+Test = "1.10"
 julia = "1.10"
 
 [extras]
+ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -47,8 +52,9 @@ RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Aqua", "Random", "LabelledArrays", "LinearAlgebra", "OrdinaryDiffEq", "Test", "RecursiveArrayTools", "Pkg", "SafeTestsets", "Optimization", "OptimizationOptimJL", "SparseArrays", "Symbolics"]
+test = ["Aqua", "ADTypes", "Random", "LabelledArrays", "LinearAlgebra", "OrdinaryDiffEq", "Test", "RecursiveArrayTools", "Pkg", "SafeTestsets", "Optimization", "OptimizationOptimJL", "SparseArrays", "Symbolics", "SparseConnectivityTracer"]

ext/PreallocationToolsSparseConnectivityTracerExt.jl

@@ -0,0 +1,46 @@
+module PreallocationToolsSparseConnectivityTracerExt
+
+using PreallocationTools
+isdefined(Base, :get_extension) ? (import SparseConnectivityTracer) :
+(import ..SparseConnectivityTracer)
+
+function PreallocationTools.get_tmp(
+        dc::DiffCache, u::T) where {T <: SparseConnectivityTracer.Dual}
+    if isbitstype(T)
+        nelem = div(sizeof(T), sizeof(eltype(dc.dual_du))) * length(dc.du)
+        if nelem > length(dc.dual_du)
+            PreallocationTools.enlargediffcache!(dc, nelem)
+        end
+        PreallocationTools._restructure(dc.du, reinterpret(T, view(dc.dual_du, 1:nelem)))
+    else
+        PreallocationTools._restructure(dc.du, zeros(T, size(dc.du)))
+    end
+end
+
+function PreallocationTools.get_tmp(
+        dc::DiffCache, ::Type{T}) where {T <: SparseConnectivityTracer.Dual}
+    if isbitstype(T)
+        nelem = div(sizeof(T), sizeof(eltype(dc.dual_du))) * length(dc.du)
+        if nelem > length(dc.dual_du)
+            PreallocationTools.enlargediffcache!(dc, nelem)
+        end
+        PreallocationTools._restructure(dc.du, reinterpret(T, view(dc.dual_du, 1:nelem)))
+    else
+        PreallocationTools._restructure(dc.du, zeros(T, size(dc.du)))
+    end
+end
+
+function PreallocationTools.get_tmp(
+        dc::DiffCache, u::AbstractArray{T}) where {T <: SparseConnectivityTracer.Dual}
+    if isbitstype(T)
+        nelem = div(sizeof(T), sizeof(eltype(dc.dual_du))) * length(dc.du)
+        if nelem > length(dc.dual_du)
+            PreallocationTools.enlargediffcache!(dc, nelem)
+        end
+        PreallocationTools._restructure(dc.du, reinterpret(T, view(dc.dual_du, 1:nelem)))
+    else
+        PreallocationTools._restructure(dc.du, zeros(T, size(dc.du)))
+    end
+end
+
+end

test/core_nesteddual.jl

@@ -90,11 +90,13 @@ newtonsol = solve(optprob, Newton())
 cache = DiffCache(zeros(ps, ps), [4, 4, 2])
 prob = ODEProblem{true, SciMLBase.FullSpecialize}(foo, ones(ps, ps), (0.0, 1.0),
     (coeffs, cache))
-realsol = solve(prob, TRBDF2(chunk_size = 2), saveat = 0.0:0.1:10.0, reltol = 1e-8)
+realsol = solve(prob, TRBDF2(autodiff = AutoForwardDiff(chunksize = 2)),
+    saveat = 0.0:0.1:10.0, reltol = 1e-8)
 
 function objfun(x, prob, realsol, cache)
     prob = remake(prob, u0 = eltype(x).(prob.u0), p = (x, cache))
-    sol = solve(prob, TRBDF2(chunk_size = 2), saveat = 0.0:0.1:10.0, reltol = 1e-8)
+    sol = solve(prob, TRBDF2(autodiff = AutoForwardDiff(chunksize = 2)),
+        saveat = 0.0:0.1:10.0, reltol = 1e-8)
 
     ofv = 0.0
     if any((s.retcode != ReturnCode.Success for s in sol))

test/core_odes.jl

@@ -1,6 +1,6 @@
 using LinearAlgebra,
       OrdinaryDiffEq, Test, PreallocationTools, LabelledArrays,
-      RecursiveArrayTools
+      RecursiveArrayTools, ADTypes
 
 #Base array
 function foo(du, u, (A, tmp), t)
@@ -10,17 +10,17 @@ function foo(du, u, (A, tmp), t)
     nothing
 end
 #with defined chunk_size
-chunk_size = 5
+chunk_size = 9
 u0 = ones(5, 5)
 A = ones(5, 5)
 cache = DiffCache(zeros(5, 5), chunk_size)
 prob = ODEProblem{true, SciMLBase.FullSpecialize}(foo, u0, (0.0, 1.0), (A, cache))
-sol = solve(prob, Rodas5P(chunk_size = chunk_size))
+sol = solve(prob, Rodas5P(autodiff = AutoForwardDiff(chunksize = chunk_size)))
 @test sol.retcode == ReturnCode.Success
 
 cache = FixedSizeDiffCache(zeros(5, 5), chunk_size)
 prob = ODEProblem{true, SciMLBase.FullSpecialize}(foo, u0, (0.0, 1.0), (A, cache))
-sol = solve(prob, Rodas5P(chunk_size = chunk_size))
+sol = solve(prob, Rodas5P(autodiff = AutoForwardDiff(chunksize = chunk_size)))
 @test sol.retcode == ReturnCode.Success
 
 #with auto-detected chunk_size
@@ -60,7 +60,7 @@ end
 chunk_size = 4
 prob = ODEProblem{true, SciMLBase.FullSpecialize}(foo, u0, (0.0, 1.0),
     (A, DiffCache(c, chunk_size)))
-sol = solve(prob, Rodas5P(chunk_size = chunk_size))
+sol = solve(prob, Rodas5P(autodiff = AutoForwardDiff(chunksize = chunk_size)))
 @test sol.retcode == ReturnCode.Success
 #with auto-detected chunk_size
 prob = ODEProblem{true, SciMLBase.FullSpecialize}(foo, u0, (0.0, 1.0), (A, DiffCache(c)))

test/gpu_all.jl

@@ -1,5 +1,5 @@
 using LinearAlgebra,
-      OrdinaryDiffEq, Test, PreallocationTools, CUDA, ForwardDiff
+      OrdinaryDiffEq, Test, PreallocationTools, CUDA, ForwardDiff, ADTypes
 
 # upstream
 OrdinaryDiffEq.DiffEqBase.anyeltypedual(x::FixedSizeDiffCache, counter = 0) = Any
@@ -56,17 +56,17 @@ function foo(du, u, (A, tmp), t)
     nothing
 end
 #with specified chunk_size
-chunk_size = 10
+chunk_size = 9
 u0 = cu(rand(10, 10)) #example kept small for test purposes.
 A = cu(-randn(10, 10))
 cache = DiffCache(cu(zeros(10, 10)), chunk_size)
 prob = ODEProblem{true, SciMLBase.FullSpecialize}(foo, u0, (0.0f0, 1.0f0), (A, cache))
-sol = solve(prob, TRBDF2(chunk_size = chunk_size))
+sol = solve(prob, TRBDF2(autodiff = AutoForwardDiff(chunksize = chunk_size)))
 @test sol.retcode == ReturnCode.Success
 
 cache = FixedSizeDiffCache(cu(zeros(10, 10)), chunk_size)
 prob = ODEProblem{true, SciMLBase.FullSpecialize}(foo, u0, (0.0f0, 1.0f0), (A, cache))
-sol = solve(prob, TRBDF2(chunk_size = chunk_size))
+sol = solve(prob, TRBDF2(autodiff = AutoForwardDiff(chunksize = chunk_size)))
 @test sol.retcode == ReturnCode.Success
 
 #with auto-detected chunk_size