diff --git a/Project.toml b/Project.toml index 79b73556..77563c83 100644 --- a/Project.toml +++ b/Project.toml @@ -5,8 +5,11 @@ version = "0.3.9" [deps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" +Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" +Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196" +GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" diff --git a/examples/gpu-usage/Manifest.toml b/examples/gpu-usage/Manifest.toml new file mode 100644 index 00000000..77120059 --- /dev/null +++ b/examples/gpu-usage/Manifest.toml @@ -0,0 +1,1088 @@ +# This file is machine-generated - editing it directly is not advised + +[[AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.0.1" + +[[AbstractGPs]] +deps = ["ChainRulesCore", "Distances", "Distributions", "FillArrays", "Functors", "GPUArrays", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] +path = "../.." +uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" +version = "0.3.8" + +[[Adapt]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "3.3.1" + +[[ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" + +[[ArrayInterface]] +deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] +git-tree-sha1 = "cdb00a6fb50762255021e5571cf95df3e1797a51" +uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" +version = "3.1.23" + +[[Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + +[[BFloat16s]] +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "4af69e205efc343068dc8722b8dfec1ade89254a" +uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" +version = "0.1.0" + +[[Base64]] +uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" + +[[Bzip2_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e" +uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" +version = "1.0.6+5" + +[[CEnum]] +git-tree-sha1 = "215a9aa4a1f23fbd05b92769fdd62559488d70e9" +uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" +version = "0.4.1" + +[[CUDA]] +deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "DataStructures", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"] +git-tree-sha1 = "889889f1c13467406a126cd2789b4844487ddfc1" +uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" +version = "3.3.5" + +[[Cairo_jll]] 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"ece2350174195bb31de1a63bea3a41ae1aa593b6" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "0.9.1+5" diff --git a/examples/gpu-usage/Project.toml b/examples/gpu-usage/Project.toml new file mode 100644 index 00000000..91ec0ee7 --- /dev/null +++ b/examples/gpu-usage/Project.toml @@ -0,0 +1,16 @@ +[deps] +AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918" +CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" +Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196" +Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +Optim = "429524aa-4258-5aef-a3af-852621145aeb" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" + +[compat] +AbstractGPs = "0.3" +CUDA = "3" +Functors = "0.2" +Literate = "2.5" +Optim = "1" +Plots = "1" diff --git a/examples/gpu-usage/script.jl b/examples/gpu-usage/script.jl new file mode 100644 index 00000000..43a89e46 --- /dev/null +++ b/examples/gpu-usage/script.jl @@ -0,0 +1,83 @@ +# # A Minimal Working Example of AbstractGPs on CUDA +# +# ## Setup + +using AbstractGPs +using CUDA +using Optim +using Functors +using LogExpFunctions + +using Plots +default(; legend=:outertopright, size=(700, 400)) + +using Random +Random.seed!(4321) +#md nothing #hide + +# First, a function to create the kernel. +# N.B. we can't use a ScaledKernel because of the hardcoded Vector - +# https://github.com/JuliaGaussianProcesses/KernelFunctions.jl/issues/299 + +make_kernel(ℓ_inv) = Matern52Kernel() ∘ ScaleTransform(ℓ_inv) +#md nothing #hide + +# Next, sample some data from a GP + +lik_noise = 0.01 +f = GP(make_kernel(1.0)) +x = rand(20) +fx = f(x, lik_noise) +y = rand(fx) +#md nothing #hide + +# Move everything to the GPU and compute the covariance + +gpu(f) = fmap(cu, f) + +x, y = gpu(x), gpu(y) +fx = f(x) +cov(fx) isa CuArray + +# Create an objective function and optimise the kernel parameters and inducing +# points + +jitter = 1e-4 +function objective_function(x, y) + function negative_elbo(params) + kernel = make_kernel(params[1]) + f = GP(kernel) + fx = f(x, lik_noise) + z = logistic.(params[2:end]) + fz = f(z, jitter) # "observing" the latent process with some (small) amount of jitter improves numerical stability + return -elbo(fx, y, fz) + end + return negative_elbo +end + +x0 = cu(rand(6) * 2) +# TODO: this doesn't work with CUDA.allowscalar(false) because of Optim +opt = optimize(objective_function(x, y), x0, LBFGS()) +#md nothing #hide + +# Construct the approximate posterior using the optimised parameters + +opt_kernel = make_kernel(opt.minimizer[1]) +opt_f = GP(opt_kernel) +opt_fx = opt_f(x, lik_noise) +ap = approx_posterior(VFE(), opt_fx, y, opt_f(logistic.(opt.minimizer[2:end]), jitter)) + +# Plot the optimised posterior (requires some casting to and from CuArrays) + +scatter( + Array(x), + Array(y); + xlim=(0, 1), + xlabel="x", + ylabel="y", + title="posterior (VI with sparse grid)", + label="Train Data", +) +x_plot = cu(collect(0:0.001:1)) +plot!(x_plot, Array(mean(ap(x_plot))); label=false) +vline!(logistic.(opt.minimizer[3:end]); label="Pseudo-points") diff --git a/src/AbstractGPs.jl b/src/AbstractGPs.jl index e2aa4c96..e0a0e206 100644 --- a/src/AbstractGPs.jl +++ b/src/AbstractGPs.jl @@ -10,6 +10,9 @@ using Random using Statistics using StatsBase using RecipesBase +using Functors +using Distances +using GPUArrays using KernelFunctions: ColVecs, RowVecs @@ -62,6 +65,9 @@ include(joinpath("util", "plotting.jl")) # Testing utilities. include(joinpath("util", "test_util.jl")) +# GPU compatibility +include(joinpath("util", "gpu.jl")) + # Deprecations. include("deprecations.jl") diff --git a/src/finite_gp_projection.jl b/src/finite_gp_projection.jl index 0c1c6bef..d595a876 100644 --- a/src/finite_gp_projection.jl +++ b/src/finite_gp_projection.jl @@ -10,6 +10,8 @@ struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ} <: AbstractMvNormal Σy::TΣ end +@functor FiniteGP + function FiniteGP(f::AbstractGP, x::AbstractVector, σ²::AbstractVector{<:Real}) return FiniteGP(f, x, Diagonal(σ²)) end @@ -17,7 +19,7 @@ end const default_σ² = 1e-18 function FiniteGP(f::AbstractGP, x::AbstractVector, σ²::Real=default_σ²) - return FiniteGP(f, x, Fill(σ², length(x))) + return FiniteGP(f, x, _fill_like(x, σ²)) end function FiniteGP( diff --git a/src/mean_function.jl b/src/mean_function.jl index 3b16d72f..6eacec36 100644 --- a/src/mean_function.jl +++ b/src/mean_function.jl @@ -10,7 +10,7 @@ struct ZeroMean{T<:Real} <: MeanFunction end """ This is an AbstractGPs-internal workaround for AD issues; ideally we would just extend Base.map """ -_map_meanfunction(::ZeroMean{T}, x::AbstractVector) where {T} = zeros(T, length(x)) +_map_meanfunction(::ZeroMean{T}, x::AbstractVector) where {T} = Zeros{T}(length(x)) function ChainRulesCore.rrule(::typeof(_map_meanfunction), m::ZeroMean, x::AbstractVector) map_ZeroMean_pullback(Δ) = (NoTangent(), NoTangent(), ZeroTangent()) @@ -28,7 +28,7 @@ struct ConstMean{T<:Real} <: MeanFunction c::T end -_map_meanfunction(m::ConstMean, x::AbstractVector) = fill(m.c, length(x)) +_map_meanfunction(m::ConstMean, x::AbstractVector) = Fill(m.c, length(x)) """ CustomMean{Tf} <: MeanFunction diff --git a/src/util/gpu.jl b/src/util/gpu.jl new file mode 100644 index 00000000..836497d2 --- /dev/null +++ b/src/util/gpu.jl @@ -0,0 +1,60 @@ +# TODO: these should be in KernelFunctions +function KernelFunctions.pairwise( + ::SqEuclidean, x::AbstractGPUArray{<:Real,2}, y::AbstractGPUArray{<:Real,2}, kwargs... +) + return sum(abs2, x; dims=1)' .+ sum(abs2, y; dims=1) .- 2x'y +end + +function KernelFunctions.pairwise(d::SqEuclidean, x::AbstractGPUArray{<:Real,2}, kwargs...) + return KernelFunctions.pairwise(d, x, x) +end + +function KernelFunctions.pairwise( + ::Euclidean, x::AbstractGPUArray{<:Real,2}, y::AbstractGPUArray{<:Real,2}; kwargs... +) + return .√KernelFunctions.pairwise(SqEuclidean(), x, y) +end +function KernelFunctions.pairwise(d::Euclidean, x::AbstractGPUArray{<:Real,2}; kwargs...) + return KernelFunctions.pairwise(d, x, x) +end + +function KernelFunctions.pairwise( + ::Euclidean, x::AbstractGPUArray, y::AbstractGPUArray; kwargs... +) + return .√KernelFunctions.pairwise(SqEuclidean(), reshape(x, 1, :), reshape(y, 1, :)) +end +function KernelFunctions.pairwise(d::Euclidean, x::AbstractGPUArray; kwargs...) + return KernelFunctions.pairwise(d, x, x) +end + +#TODO: overload colwise for var(fx) + +# Temporarily needed until var(fx) is working +function tr_Cf_invΣy(f::FiniteGP, Σy::Diagonal{<:Any,<:AbstractGPUArray}, chol_Σy::Cholesky) + return sum(diag(cov(f.f, f.x)) ./ diag(Σy)) +end + +# Fixes a bug with cholesky of Diagonal CuArrays +function _cholesky(X::Diagonal{<:Real,T}) where {T<:AbstractGPUArray} + # Bit of a hack - should maybe specialise to CuArray? + return cholesky(T.name.wrapper(X)) +end + +_fill_like(x::AbstractVector, σ²) = similar(x) .= σ² +_fill_like(x::Union{ColVecs,RowVecs}, σ²) = similar(x[1], length(x)) .= σ² + +# # If we want to use FillArrays for fx.Σy, something like the following is needed in cov(fx): + +# _add_broadcasted(A, B) = A .+ B + +# # TODO: this is potentially much harder for var(fx) +# function _add_broadcasted(A::AbstractGPUArray, B::Diagonal{T, <:FillArrays.AbstractFill}) where T +# return Base.materialize(Base.broadcasted(Base.BroadcastStyle(typeof(A)), +, A, B)) +# end +# _add_broadcasted(B::Diagonal{T, <:FillArrays.AbstractFill}, A::AbstractGPUArray) where T = _add_broadcasted(A, B) + +# # A more general approach? +# const WrappedFillArray{T,N} = Adapt.WrappedArray{T, N, FillArrays.AbstractFill,FillArrays.AbstractFill{T,N}} +# function _add_broadcasted(A::AbstractGPUArray, B::WrappedFillArray) where T +# Base.materialize(Base.broadcasted(Base.BroadcastStyle(typeof(A)), +, A, B)) +# end