I see, but I thought I'd like to try and remove the instability as I wonder
if it's one of the things preventing vectorisation of the @inbounds loop in
the `distance` function.
On Friday, September 16, 2016 at 7:54:33 AM UTC+1, Kristoffer Carlsson
wrote:
>
> It looks fine because for both the SSAValues with "problems" you later
> have:
>
> p::Array{Float64,1} = SSAValue(15)
>
> l::Array{Int64,1} = SSAValue(17)
>
> so they actually get correctly inferred.
>
> As long as your variables list and return value is ok then things are most
> likely ok.
>
> On Friday, September 16, 2016 at 4:37:09 AM UTC+2, Yichao Yu wrote:
>>
>> On Thu, Sep 15, 2016 at 10:08 AM, Ben Ward <axolotl...@gmail.com> wrote:
>> > Hi I have two functions and a function which calls them:
>> >
>> > @inline function expected_distance(::Type{JukesCantor69}, p::Float64)
>> > return -0.75 * log(1 - 4 * p / 3)
>> > end
>> >
>> > @inline function variance(::Type{JukesCantor69}, p::Float64, l::Int64)
>> > return p * (1 - p) / (((1 - 4 * p / 3) ^ 2) * l)
>> > end
>> >
>> > function distance{A<:NucleotideAlphabet}(::Type{JukesCantor69},
>> > seqs::Vector{BioSequence{A}})
>> > p, l = distance(Proportion{AnyMutation}, seqs)
>> > D = Vector{Float64}(length(p))
>> > V = Vector{Float64}(length(p))
>> > @inbounds for i in 1:length(p)
>> > D[i] = expected_distance(JukesCantor69, p[i])
>> > V[i] = variance(JukesCantor69, p[i], l[i])
>> > end
>> > return D, V
>> > end
>> >
>> > But I'm seeing type uncertainty:
>> >
>> > @code_warntype distance(JukesCantor69, dnas)
>> >
>> > Variables:
>> >
>> > #self#::Bio.Var.#distance
>> >
>> > #unused#::Type{Bio.Var.JukesCantor69}
>> >
>> > seqs::Array{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},1}
>> >
>> > p::Array{Float64,1}
>> >
>> > l::Array{Int64,1}
>> >
>> > #temp#@_6::Int64
>> >
>> > D::Array{Float64,1}
>> >
>> > V::Array{Float64,1}
>> >
>> > #temp#@_9::Int64
>> >
>> > i::Int64
>> >
>> >
>> > Body:
>> >
>> > begin
>> >
>> > SSAValue(0) = $(Expr(:invoke, LambdaInfo for
>> > distance(::Type{Bio.Var.Proportion{Bio.Var.AnyMutation}},
>> > ::Array{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},1}),
>> > :(Bio.Var.distance), Bio.Var.Proportion{Bio.Var.AnyMutation}, :(seqs)))
>> >
>> > #temp#@_6::Int64 = $(QuoteNode(1))
>> >
>> > SSAValue(15) =
>> > (Base.getfield)(SSAValue(0),1)::Union{Array{Float64,1},Array{Int64,1}}
>>
>> I guess we should probably print ssavalue types to make this easier to
>> analyse
>>
>> There's likely no type instability and the warning here is just spurious
>>
>> >
>> > SSAValue(16) = (Base.box)(Int64,(Base.add_int)(1,1))
>> >
>> > p::Array{Float64,1} = SSAValue(15)
>> >
>> > #temp#@_6::Int64 = SSAValue(16)
>> >
>> > SSAValue(17) =
>> > (Base.getfield)(SSAValue(0),2)::Union{Array{Float64,1},Array{Int64,1}}
>> >
>> > SSAValue(18) = (Base.box)(Int64,(Base.add_int)(2,1))
>> >
>> > l::Array{Int64,1} = SSAValue(17)
>> >
>> > #temp#@_6::Int64 = SSAValue(18) # line 314:
>> >
>> > SSAValue(7) = (Base.arraylen)(p::Array{Float64,1})::Int64
>> >
>> > D::Array{Float64,1} =
>> >
>> (Core.ccall)(:jl_alloc_array_1d,(Core.apply_type)(Core.Array,Float64,1)::Type{Array{Float64,1}},(Core.svec)(Core.Any,Core.Int)::SimpleVector,Array{Float64,1},0,SSAValue(7),0)::Array{Float64,1}
>>
>>
>> > # line 315:
>> >
>> > SSAValue(9) = (Base.arraylen)(p::Array{Float64,1})::Int64
>> >
>> > V::Array{Float64,1} =
>> >
>> (Core.ccall)(:jl_alloc_array_1d,(Core.apply_type)(Core.Array,Float64,1)::Type{Array{Float64,1}},(Core.svec)(Core.Any,Core.Int)::SimpleVector,Array{Float64,1},0,SSAValue(9),0)::Array{Float64,1}
>>
>>
>> > # line 316:
>> >
>> > $(Expr(:inbounds, true))
>> >
>> > SSAValue(11) = (Base.arraylen)(p::Array{Float64,1})::Int64
>> >
>> > SSAValue(19) =
>> >
>> (Base.select_value)((Base.sle_int)(1,SSAValue(11))::Bool,SSAValue(11),(Base.box)(Int64,(Base.sub_int)(1,1)))::Int64
>>
>>
>> >
>> > #temp#@_9::Int64 = 1
>> >
>> > 22:
>> >
>> > unless (Base.box)(Base.Bool,(Base.not_int)((#temp#@_9::Int64 ===
>> > (Base.box)(Int64,(Base.add_int)(SSAValue(19),1)))::Bool)) goto 43
>> >
>> > SSAValue(20) = #temp#@_9::Int64
>> >
>> > SSAValue(21) =
>> (Base.box)(Int64,(Base.add_int)(#temp#@_9::Int64,1))
>> >
>> > i::Int64 = SSAValue(20)
>> >
>> > #temp#@_9::Int64 = SSAValue(21) # line 317:
>> >
>> > SSAValue(12) =
>> (Base.arrayref)(p::Array{Float64,1},i::Int64)::Float64
>> >
>> > $(Expr(:inbounds, false))
>> >
>> > # meta: location
>> /Users/bward/.julia/v0.5/Bio/src/var/distances.jl
>> > expected_distance 69
>> >
>> > SSAValue(13) = $(Expr(:invoke, LambdaInfo for log(::Float64),
>> > :(Bio.Var.log),
>> >
>> :((Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),(Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)((Base.box)(Float64,(Base.sitofp)(Float64,4)),SSAValue(12))),(Base.box)(Float64,(Base.sitofp)(Float64,3)))))))))
>>
>>
>> >
>> > # meta: pop location
>> >
>> > $(Expr(:inbounds, :pop))
>> >
>> > SSAValue(5) =
>> > (Base.box)(Base.Float64,(Base.mul_float)(-0.75,SSAValue(13)))
>> >
>> >
>> >
>> (Base.arrayset)(D::Array{Float64,1},SSAValue(5),i::Int64)::Array{Float64,1}
>> > # line 318:
>> >
>> > SSAValue(14) =
>> (Base.arrayref)(p::Array{Float64,1},i::Int64)::Float64
>> >
>> > SSAValue(6) =
>> >
>> (Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)(SSAValue(14),(Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),SSAValue(14))))),(Base.box)(Base.Float64,(Base.mul_float)((Base.Math.box)(Base.Math.Float64,(Base.Math.powi_llvm)((Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),(Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)((Base.box)(Float64,(Base.sitofp)(Float64,4)),SSAValue(14))),(Base.box)(Float64,(Base.sitofp)(Float64,3)))))),(Base.box)(Int32,(Base.checked_trunc_sint)(Int32,2))))::Float64,(Base.box)(Float64,(Base.sitofp)(Float64,(Base.arrayref)(l::Array{Int64,1},i::Int64)::Int64))))))
>>
>>
>> >
>> >
>> >
>> (Base.arrayset)(V::Array{Float64,1},SSAValue(6),i::Int64)::Array{Float64,1}
>> >
>> > 41:
>> >
>> > goto 22
>> >
>> > 43:
>> >
>> > $(Expr(:inbounds, :pop)) # line 320:
>> >
>> > return
>> >
>> (Core.tuple)(D::Array{Float64,1},V::Array{Float64,1})::Tuple{Array{Float64,1},Array{Float64,1}}
>>
>>
>> >
>> > end::Tuple{Array{Float64,1},Array{Float64,1}}
>> >
>> >
>> > But I'm not sure which those lines correspond to in my code, as they're
>> > temporary values. I think at some point some code either results in an
>> > integer or a float. I wondered if it was inside the smaller function
>> called
>> > by the larger one.
>> >
>> > Thanks,
>> > Ben.
>>
>
