Yes, if you change the first line to
@inbounds for site in 1:nsites
Then that will declare everything inside that outer loop as being in
bounds. If you'd like to make a more restricted declaration, than you
should put it on specific lines inside the loop.
On Friday, August 26, 2016 at 1:43:08 PM UTC-4, Ben Ward wrote:
>
> Hi, Just wondering, I have the following doube loop:
>
> for site in 1:nsites
> votes[1] = votes[2] = votes[3] = votes[4] = votes[5] = 0
> for seq in 1:neqs
> nuc = mat[seq, site]
> votes[1] += iscompatible(nuc, DNA_A)
> votes[2] += iscompatible(nuc, DNA_C)
> votes[3] += iscompatible(nuc, DNA_G)
> votes[4] += iscompatible(nuc, DNA_T)
> votes[5] += iscompatible(nuc, DNA_Gap)
> end
> end
>
> Say I add an @inbounds macro to the outer loop to eliminate bounds checks,
> will it's effects extend to setmatrix statements in the inner loop.
> Inspecting the expanded macro I believe it is the case, as an @inbounds is
> set to true, and then after the inner loop is popped. But I'm not 100% sure
> if I am correct that is indeed how it works:
>
> *quote # REPL[63], line 2:*
>
> * begin *
>
> * $(Expr(:inbounds, true))*
>
> * for site = 1:nsites # REPL[63], line 3:*
>
> * votes[1] = (votes[2] = (votes[3] = (votes[4] = (votes[5] =
> 0)))) # REPL[63], line 4:*
>
> * for seq = 1:neqs # REPL[63], line 5:*
>
> * nuc = mat[seq,site] # REPL[63], line 6:*
>
> * votes[1] += iscompatible(nuc,DNA_A) # REPL[63], line 7:*
>
> * votes[2] += iscompatible(nuc,DNA_C) # REPL[63], line 8:*
>
> * votes[3] += iscompatible(nuc,DNA_G) # REPL[63], line 9:*
>
> * votes[4] += iscompatible(nuc,DNA_T) # REPL[63], line 10:*
>
> * votes[5] += iscompatible(nuc,DNA_Gap)*
>
> * end*
>
> * end*
>
> * $(Expr(:inbounds, :pop))*
>
> * end*
>
> *end*
>
> I'd also like someone's opinion. Will I benefit from @simd on the inner
> loop?
>
> The function `iscompatible` is annotated with @inline, and has no
> branching:
>
> @inline function iscompatible{T<:Nucleotide}(x::T, y::T)
> return compatbits(x) & compatbits(y) != 0
> end
>
> # Return the compatibility bits of `nt`.
> @inline function compatbits(nt::Nucleotide)
> return reinterpret(UInt8, nt)
> end
>
> As per the assumptions of an simd loop I read in the docs, each iteration
> is independent, order does not matter.
> I'd just like some advice as if I'm right this will be the first time I
> use a simd loop to speed up my loops.
>
> Thanks,
> Ben.
>
