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Specialize Base.similar for VectorOfArray with multidimensional parent #359

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merged 10 commits into from
Feb 22, 2024
Merged

Specialize Base.similar for VectorOfArray with multidimensional parent #359

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8b58d81
add `parent` and specialize `Base.similar`
jlchan Feb 21, 2024
6cf6d8f
add test
jlchan Feb 21, 2024
959d80e
formatting
jlchan Feb 21, 2024
859793e
Update src/vector_of_array.jl
jlchan Feb 21, 2024
a07264c
Update src/vector_of_array.jl
ChrisRackauckas Feb 21, 2024
1352de9
Update and rename test/upstream.jl to test/downstream/odesolve.jl
ChrisRackauckas Feb 21, 2024
44de083
Update runtests.jl
ChrisRackauckas Feb 21, 2024
17ce92a
Update Project.toml
ChrisRackauckas Feb 21, 2024
2dac21d
Update Project.toml
ChrisRackauckas Feb 21, 2024
43072c8
Update odesolve.jl
ChrisRackauckas Feb 21, 2024
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17 changes: 16 additions & 1 deletion src/vector_of_array.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -156,13 +156,16 @@
VectorOfArray{T, N + 1, typeof(vec)}(vec)
end

# allow multi-dimensional arrays as long as they're linearly indexed
# allow multi-dimensional arrays as long as they're linearly indexed.
# currently restricted to arrays whose elements are all the same type
function VectorOfArray(array::AbstractArray{AT}) where {T, N, AT <: AbstractArray{T, N}}
@assert IndexStyle(typeof(array)) isa IndexLinear

return VectorOfArray{T, N + 1, typeof(array)}(array)
end

Base.parent(vec::VectorOfArray) = vec.u

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function DiffEqArray(vec::AbstractVector{T},
ts::AbstractVector,
::NTuple{N, Int},
Expand Down Expand Up @@ -721,6 +724,18 @@
VectorOfArray([similar(VA[:, i], T) for i in eachindex(VA.u)])
end

# for VectorOfArray with multi-dimensional parent arrays of arrays where all elements are the same type
function Base.similar(vec::VectorOfArray{

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T, N, AT}) where {T, N, AT <: AbstractArray{<:AbstractArray{T}}}
return VectorOfArray(similar(Base.parent(vec)))

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end

# special-case when the multi-dimensional parent array is just an AbstractVector (call the old method)
function Base.similar(vec::VectorOfArray{

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T, N, AT}) where {T, N, AT <: AbstractVector{<:AbstractArray{T}}}
return Base.similar(vec, eltype(vec))

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end

# fill!
# For DiffEqArray it ignores ts and fills only u
function Base.fill!(VA::AbstractVectorOfArray, x)
Expand Down
4 changes: 4 additions & 0 deletions test/basic_indexing.jl
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Expand Up @@ -250,6 +250,10 @@ foo!(u_matrix)
foo!(u_vector)
@test u_matrix ≈ u_vector

# test that, for VectorOfArray with multi-dimensional parent arrays,
# `similar` preserves the structure of the parent array
@test typeof(parent(similar(u_matrix))) == typeof(parent(u_matrix))

# test efficiency
num_allocs = @allocations foo!(u_matrix)
@test num_allocs == 0
4 changes: 3 additions & 1 deletion test/downstream/Project.toml
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Expand Up @@ -2,6 +2,7 @@
ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"

Expand All @@ -10,4 +11,5 @@ ModelingToolkit = "8.33"
MonteCarloMeasurements = "1.1"
OrdinaryDiffEq = "6.31"
Unitful = "1.17"
Tracker = "0.2"
Tracker = "0.2"
StaticArrays = "1"
13 changes: 12 additions & 1 deletion test/upstream.jl → test/downstream/odesolve.jl
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@@ -1,4 +1,4 @@
using OrdinaryDiffEq, NLsolve, RecursiveArrayTools, Test, ArrayInterface
using OrdinaryDiffEq, NLsolve, RecursiveArrayTools, Test, ArrayInterface, StaticArrays
function lorenz(du, u, p, t)
du[1] = 10.0 * (u[2] - u[1])
du[2] = u[1] * (28.0 - u[3]) - u[2]
Expand Down Expand Up @@ -49,3 +49,14 @@ end
ArrayPartition(zeros(1), [0.75])),
(0.0, 1.0)),
Rodas5()).retcode == ReturnCode.Success

function rhs!(duu::VectorOfArray, uu::VectorOfArray, p, t)
du = parent(duu)
u = parent(uu)
du .= u
end

u = fill(SVector{2}(ones(2)), 2, 3)
ode = ODEProblem(rhs!, VectorOfArray(u), (0.0, 1.0))
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sol = solve(ode, Tsit5())
@test SciMLBase.successful_retcode(sol)
72 changes: 18 additions & 54 deletions test/runtests.jl
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Expand Up @@ -19,67 +19,31 @@ end

@time begin
if GROUP == "Core" || GROUP == "All"
@time @safetestset "Quality Assurance" begin
include("qa.jl")
end
@time @safetestset "Utils Tests" begin
include("utils_test.jl")
end
@time @safetestset "NamedArrayPartition Tests" begin
include("named_array_partition_tests.jl")
end
@time @safetestset "Partitions Tests" begin
include("partitions_test.jl")
end
@time @safetestset "VecOfArr Indexing Tests" begin
include("basic_indexing.jl")
end
@time @safetestset "SymbolicIndexingInterface API test" begin
include("symbolic_indexing_interface_test.jl")
end
@time @safetestset "VecOfArr Interface Tests" begin
include("interface_tests.jl")
end
@time @safetestset "Table traits" begin
include("tabletraits.jl")
end
@time @safetestset "StaticArrays Tests" begin
include("copy_static_array_test.jl")
end
@time @safetestset "Linear Algebra Tests" begin
include("linalg.jl")
end
@time @safetestset "Upstream Tests" begin
include("upstream.jl")
end
@time @safetestset "Adjoint Tests" begin
include("adjoints.jl")
end
@time @safetestset "Measurement Tests" begin
include("measurements.jl")
end
@time @safetestset "Quality Assurance" include("qa.jl")
@time @safetestset "Utils Tests" include("utils_test.jl")
@time @safetestset "NamedArrayPartition Tests" include("named_array_partition_tests.jl")
@time @safetestset "Partitions Tests" include("partitions_test.jl")
@time @safetestset "VecOfArr Indexing Tests" include("basic_indexing.jl")
@time @safetestset "SymbolicIndexingInterface API test" include("symbolic_indexing_interface_test.jl")
@time @safetestset "VecOfArr Interface Tests" include("interface_tests.jl")
@time @safetestset "Table traits" include("tabletraits.jl")
@time @safetestset "StaticArrays Tests" include("copy_static_array_test.jl")
@time @safetestset "Linear Algebra Tests" include("linalg.jl")
@time @safetestset "Adjoint Tests" include("adjoints.jl")
@time @safetestset "Measurement Tests" include("measurements.jl")
end

if GROUP == "Downstream"
activate_downstream_env()
@time @safetestset "DiffEqArray Indexing Tests" begin
include("downstream/symbol_indexing.jl")
end
@time @safetestset "Event Tests with ArrayPartition" begin
include("downstream/downstream_events.jl")
end
@time @safetestset "Measurements and Units" begin
include("downstream/measurements_and_units.jl")
end
@time @safetestset "TrackerExt" begin
include("downstream/TrackerExt.jl")
end
@time @safetestset "DiffEqArray Indexing Tests" include("downstream/symbol_indexing.jl")
@time @safetestset "ODE Solve Tests" include("downstream/odesolve.jl")
@time @safetestset "Event Tests with ArrayPartition" include("downstream/downstream_events.jl")
@time @safetestset "Measurements and Units" include("downstream/measurements_and_units.jl")
@time @safetestset "TrackerExt" include("downstream/TrackerExt.jl")
end

if GROUP == "GPU"
activate_gpu_env()
@time @safetestset "VectorOfArray GPU" begin
include("gpu/vectorofarray_gpu.jl")
end
@time @safetestset "VectorOfArray GPU" include("gpu/vectorofarray_gpu.jl")
end
end
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