Fixes warnings during REPL startup while using custom SYSIMG's (#185)

* Fixes warnings during REPL startup while using custom SYSIMG's We encounter following warning during Julia REPL startup if we include DistributionsAD in the default SYSIMG, this commit fixes that issue ``` ┌ Warning: Error requiring `ForwardDiff` from `DistributionsAD` │ exception = │ LoadError: SystemError: opening file "/home/bmharsha/.julia/packages/DistributionsAD/pj8zf/src/reversediffx.jl": No such file or directory │ Stacktrace: │ [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) │ @ Base ./error.jl:168 │ [2] #systemerror#62 │ @ ./error.jl:167 [inlined] │ [3] systemerror │ @ ./error.jl:167 [inlined] │ [4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing) │ @ Base ./iostream.jl:293 │ [5] open │ @ ./iostream.jl:282 [inlined] │ [6] open(f::Base.var"#326#327"{String}, args::String; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) │ @ Base ./io.jl:328 │ [7] open │ @ ./io.jl:328 [inlined] │ [8] read │ @ ./io.jl:434 [inlined] │ [9] _include(mapexpr::Function, mod::Module, _path::String) │ @ Base ./loading.jl:1166 │ [10] include(mod::Module, _path::String) │ @ Base ./Base.jl:386 │ [11] include(x::String) │ @ DistributionsAD.ReverseDiffX ./reversediff.jl:1 │ [12] top-level scope │ @ reversediff.jl:55 │ [13] eval │ @ ./boot.jl:360 [inlined] │ [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) │ @ Base ./loading.jl:1116 │ [15] include_string(m::Module, txt::String, fname::String) │ @ Base ./loading.jl:1126 │ [16] macro expansion │ @ ~/.julia/packages/Requires/7Ncym/src/Requires.jl:42 [inlined] │ [17] top-level scope │ @ ~/.julia/packages/DistributionsAD/pj8zf/src/DistributionsAD.jl:74 │ [18] eval │ @ ./boot.jl:360 [inlined] │ [19] eval │ @ ~/.julia/packages/DistributionsAD/pj8zf/src/DistributionsAD.jl:1 [inlined] │ [20] (::DistributionsAD.var"#331#334")() │ @ DistributionsAD ~/.julia/packages/Requires/7Ncym/src/require.jl:99 │ [21] err(f::Any, listener::Module, modname::String) │ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:47 │ [22] (::DistributionsAD.var"#330#333")() │ @ DistributionsAD ~/.julia/packages/Requires/7Ncym/src/require.jl:98 │ [23] withpath(f::Any, path::String) │ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:37 │ [24] (::DistributionsAD.var"#329#332")() │ @ DistributionsAD ~/.julia/packages/Requires/7Ncym/src/require.jl:97 │ [25] listenpkg(f::Any, pkg::Base.PkgId) │ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:20 │ [26] macro expansion │ @ ~/.julia/packages/Requires/7Ncym/src/require.jl:95 [inlined] │ [27] top-level scope │ @ ~/.julia/packages/DistributionsAD/pj8zf/src/DistributionsAD.jl:73 │ [28] eval │ @ ./boot.jl:360 [inlined] │ [29] eval │ @ ~/.julia/packages/DistributionsAD/pj8zf/src/DistributionsAD.jl:1 [inlined] │ [30] (::DistributionsAD.var"#307#320")() │ @ DistributionsAD ~/.julia/packages/Requires/7Ncym/src/require.jl:99 │ [31] err(f::Any, listener::Module, modname::String) │ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:47 │ [32] (::DistributionsAD.var"#306#319")() │ @ DistributionsAD ~/.julia/packages/Requires/7Ncym/src/require.jl:98 │ [33] withpath(f::Any, path::String) │ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:37 │ [34] (::DistributionsAD.var"#305#318")() │ @ DistributionsAD ~/.julia/packages/Requires/7Ncym/src/require.jl:97 │ [35] listenpkg(f::Any, pkg::Base.PkgId) │ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:20 │ [36] macro expansion │ @ ~/.julia/packages/Requires/7Ncym/src/require.jl:95 [inlined] │ [37] macro expansion │ @ ~/.julia/packages/DistributionsAD/pj8zf/src/DistributionsAD.jl:70 [inlined] │ [38] (::DistributionsAD.var"#301#314")() │ @ DistributionsAD ~/.julia/packages/Requires/7Ncym/src/init.jl:11 │ [39] __init__() │ @ DistributionsAD ~/.julia/packages/Requires/7Ncym/src/init.jl:18 │ in expression starting at reversediff.jl:1 └ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:49 _ _ _ _(_)_ | Documentation: https://docs.julialang.org (_) | (_) (_) | _ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help. | | | | | | |/ _` | | | | |_| | | | (_| | | Version 1.6.2 (2021-07-14) _/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release |__/ | �[?2004h �[0Kjulia> �[7C �[7C �[?2004l ``` * Bumps the version number in Project.toml Preparing for a minor release * Reverts the usage of Requires.@include Macro
TuringLang · Aug 19, 2021 · 0ee831b · 0ee831b · yebai · Aug 19, 2021
1 parent c2a5918
commit 0ee831b
Show file tree

Hide file tree

Showing 3 changed files with 79 additions and 84 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,6 +1,6 @@
 name = "DistributionsAD"
 uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
-version = "0.6.28"
+version = "0.6.29"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

diff --git a/src/reversediff.jl b/src/reversediff.jl
@@ -52,7 +52,84 @@ using ..DistributionsAD: TuringPoissonBinomial,
                          VectorOfMultivariate,
                          FillVectorOfMultivariate
 
-include("reversediffx.jl")
+###############
+## logsumexp ##
+###############
+
+logsumexp(x::TrackedArray; dims=:) = track(logsumexp, x, dims = dims)
+@grad function logsumexp(x::AbstractArray; dims)
+    x_value = value(x)
+    lse = logsumexp(x_value; dims=dims)
+    return lse, Δ -> (Δ .* exp.(x_value .- lse),)
+end
+
+############
+## linalg ##
+############
+
+function LinearAlgebra.cholesky(A::Symmetric{<:Any, <:TrackedMatrix}; check=true)
+    uplo = A.uplo == 'U' ? (:U) : (:L)
+    factors, info = symm_turing_chol(parent(A), check, uplo)
+    return Cholesky{eltype(factors), typeof(factors)}(factors, 'U', info)
+end
+function LinearAlgebra.cholesky(A::TrackedMatrix; check=true)
+    factors, info = turing_chol(A, check)
+    return Cholesky{eltype(factors), typeof(factors)}(factors, 'U', info)
+end
+
+function symm_turing_chol(x::TrackedArray{V,D}, check, uplo) where {V,D}
+    tp = tape(x)
+    x_value = value(x)
+    (factors,info), back = DistributionsAD.symm_turing_chol_back(x_value, check, uplo)
+    C = Cholesky{eltype(factors), typeof(factors)}(factors, 'U', info)
+    out = track(C.factors, D, tp)
+    record!(tp, SpecialInstruction, symm_turing_chol, (x, check, uplo), out, (back, issuccess(C)))
+    return out, C.info
+end
+function turing_chol(x::TrackedArray{V,D}, check) where {V,D}
+    tp = tape(x)
+    x_value = value(x)
+    (factors,info), back = DistributionsAD.turing_chol_back(x_value, check)
+    C = Cholesky{eltype(factors), typeof(factors)}(factors, 'U', info)
+    out = track(C.factors, D, tp)
+    record!(tp, SpecialInstruction, turing_chol, (x, check), out, (back, issuccess(C)))
+    return out, C.info
+end
+
+for f in (:turing_chol, :symm_turing_chol)
+    @eval begin
+        @noinline function ReverseDiff.special_reverse_exec!(
+            instruction::SpecialInstruction{typeof($f)},
+        )
+            output = instruction.output
+            instruction.cache[2] || throw(PosDefException(C.info))
+            input = instruction.input
+            input_deriv = deriv(input[1])
+            P = instruction.cache[1]
+            input_deriv .+= P((factors = deriv(output),))[1]
+            unseed!(output)
+            return nothing
+        end
+    end
+end
+
+@noinline function ReverseDiff.special_forward_exec!(
+    instruction::SpecialInstruction{typeof(turing_chol)},
+)
+    output, input = instruction.output, instruction.input
+    factors = turing_chol(value.(input)...)[1]
+    value!(output, factors)
+    return nothing
+end
+
+@noinline function ReverseDiff.special_forward_exec!(
+    instruction::SpecialInstruction{typeof(symm_turing_chol)},
+)
+    output, input = instruction.output, instruction.input
+    factors = symm_turing_chol(value.(input)...)[1]
+    value!(output, factors)
+    return nothing
+end
 
 adapt_randn(rng::Random.AbstractRNG, x::TrackedArray, dims...) = adapt_randn(rng, value(x), dims...)
 

diff --git a/src/reversediffx.jl b/src/reversediffx.jl