What if you add @simd after @inbounds?
On Friday, September 16, 2016 at 5:48:00 PM UTC+2, Ben Ward wrote:
>
> The code for that function not shown is rather similar to the version that
> is shown:
>
> function
> distance{T<:MutationType,A<:NucleotideAlphabet}(::Type{Proportion{T}},
> seqs::Vector{BioSequence{A}})
> d, l = distance(Count{T}, seqs)
> D = Vector{Float64}(length(d))
> @inbounds for i in 1:length(D)
> D[i] = d[i] / l[i]
> end
> return D, l
> end
>
> Which has a @code_warntype which seems ok:
>
> *julia> **@code_warntype distance(Proportion{AnyMutation}, dnas2)*
>
> Variables:
>
> #self#::Bio.Var.#distance
>
> #unused#::Type{Bio.Var.Proportion{Bio.Var.AnyMutation}}
>
> seqs@_3::Array{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},1}
>
> d::Array{Int64,1}
>
> l::Array{Int64,1}
>
> #temp#@_6::Int64
>
> D::Array{Float64,1}
>
> #temp#@_8::Int64
>
> i::Int64
>
> seqs@_10::Array{Bio.Seq.DNANucleotide,2}
>
>
> Body:
>
> begin
>
> $(Expr(:inbounds, false))
>
> # meta: location /Users/bward/.julia/v0.5/Bio/src/var/distances.jl
> distance 133
>
> # meta: location
> /Users/bward/.julia/v0.5/Bio/src/var/mutation_counting.jl count_mutations
> 263
>
> seqs@_10::Array{Bio.Seq.DNANucleotide,2} = $(Expr(:invoke,
> LambdaInfo for
> seqmatrix(::Array{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},1},
> ::Symbol), :(Bio.Var.seqmatrix), :(seqs@_3), :(:seq)))
>
> # meta: pop location
>
> # meta: pop location
>
> $(Expr(:inbounds, :pop))
>
> SSAValue(0) = $(Expr(:invoke, LambdaInfo for
> count_mutations(::Type{Bio.Var.AnyMutation},
> ::Array{Bio.Seq.DNANucleotide,2}), :(Bio.Var.count_mutations),
> Bio.Var.AnyMutation, :(seqs@_10)))
>
> #temp#@_6::Int64 = $(QuoteNode(1))
>
> SSAValue(9) = (Base.getfield)(SSAValue(0),1)::Array{Int64,1}
>
> SSAValue(10) = (Base.box)(Int64,(Base.add_int)(1,1))
>
> d::Array{Int64,1} = SSAValue(9)
>
> #temp#@_6::Int64 = SSAValue(10)
>
> SSAValue(11) = (Base.getfield)(SSAValue(0),2)::Array{Int64,1}
>
> SSAValue(12) = (Base.box)(Int64,(Base.add_int)(2,1))
>
> l::Array{Int64,1} = SSAValue(11)
>
> #temp#@_6::Int64 = SSAValue(12) # line 256:
>
> SSAValue(6) = (Base.arraylen)(d::Array{Int64,1})::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(6),0)::Array{Float64,1}
>
> # line 257:
>
> $(Expr(:inbounds, true))
>
> SSAValue(8) = (Base.arraylen)(D::Array{Float64,1})::Int64
>
> SSAValue(13) =
> (Base.select_value)((Base.sle_int)(1,SSAValue(8))::Bool,SSAValue(8),(Base.box)(Int64,(Base.sub_int)(1,1)))::Int64
>
> #temp#@_8::Int64 = 1
>
> 26:
>
> unless (Base.box)(Base.Bool,(Base.not_int)((#temp#@_8::Int64 ===
> (Base.box)(Int64,(Base.add_int)(SSAValue(13),1)))::Bool)) goto 37
>
> SSAValue(14) = #temp#@_8::Int64
>
> SSAValue(15) = (Base.box)(Int64,(Base.add_int)(#temp#@_8::Int64,1))
>
> i::Int64 = SSAValue(14)
>
> #temp#@_8::Int64 = SSAValue(15) # line 258:
>
> SSAValue(5) =
> (Base.box)(Base.Float64,(Base.div_float)((Base.box)(Float64,(Base.sitofp)(Float64,(Base.arrayref)(d::Array{Int64,1},i::Int64)::Int64)),(Base.box)(Float64,(Base.sitofp)(Float64,(Base.arrayref)(l::Array{Int64,1},i::Int64)::Int64))))
>
>
> (Base.arrayset)(D::Array{Float64,1},SSAValue(5),i::Int64)::Array{Float64,1}
>
> 35:
>
> goto 26
>
> 37:
>
> $(Expr(:inbounds, :pop)) # line 260:
>
> return
> (Core.tuple)(D::Array{Float64,1},l::Array{Int64,1})::Tuple{Array{Float64,1},Array{Int64,1}}
>
> end::Tuple{Array{Float64,1},Array{Int64,1}}
>
> But then again the loop in this function is also not vectorised which I
> struggle to see why... unless division can't be.
>
> On Friday, September 16, 2016 at 3:27:47 AM UTC+1, Ralph Smith wrote:
>>
>> SSAValue(15) = (Base.getfield)(SSAValue(0),1)
>> *::Union{Array{Float64,1},Array{Int64,1}}*
>>
>>
>> indicates that the first element of SSAValue(0) is ambiguous. Earlier it
>> shows that this means p from
>>
>> p, l = distance(Proportion{AnyMutation}, seqs)
>>
>> which we can't analyze from what you show here.
>>
>> On Thursday, September 15, 2016 at 10:08:16 AM UTC-4, Ben Ward 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}}*
>>>
>>> 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.
>>>
>>
