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.
