Le mardi 29 mars 2016 à 09:43 -0700, 博陈 a écrit :
> I tried the built-in profiler, and find that the problem lies in
> lines I end with ******, the result is shown below:
> that proved my guess, how can I pre-allocate these arrays? If I don't
> want to divide this code into several parts that calculate these
> arrays separately.
Can you show us which lines the numbers correspond to? There's no line
211 in the script you posted.
Regards
> | lines | backtrace |
> | 169 | 9011 | ***********
> | 173 | 1552 |
> | 175 | 2604 |
> | 179 | 2906 |
> | 181 | 1541 |
> | 192 | 4458 |
> | 211 | 13332 ************|
> | 214 | 8431 |************
> | 218 | 15871 |***********
> | 221 | 2538 |
>
> > Have you tried:
> >
> > (a) calling @code_typewarn on your function
> > (b) using the built-in profiler?
> >
> >
> > On Tue, Mar 29, 2016 at 9:23 AM, 博陈 <chenph...@gmail.com> wrote:
> > > First of all, have a look at the result.
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > My code calculates the evolution of 1-d 2-electron system in the electric
> > > field, some variables are calculated during the evolution.
> > > According to the result of @time evolution, my code must have a
> > > pre-allocation problem. Before you see the long code, i suggest that the
> > > hotspot might be around the Arrays prop_e, \phio, pp. I have learnt that
> > > I can use m = Array(Float64, 1) outside a "for" loop and empty!(m) and
> > > push!(m, new_m) inside the loop to pre-allocate the variable m, but in my
> > > situations, I don't know how to pre-allocate these arrays.
> > >
> > > Below is the script (precisely, the main function) itself.
> > >
> > > function evolution(ϕ::Array{Complex{Float64}, 2},
> > > ele::Array{Float64, 1}, dx::Float64, dt::Float64,
> > > flags::Tuple{Int64, Int64, Int64, Int64})
> > > ϕg = copy(ϕ)
> > > FFTW.set_num_threads(8)
> > > ns = length( ϕ[:, 1] )
> > > x = get_x(ns, dx)
> > > p = get_p(ns, dx)
> > > if flags[4] == 1
> > > pp = similar(p)
> > > A = -cumsum(ele) * dt
> > > A² = A.*A
> > > ##### splitting
> > > r_sp = 150.0
> > > δ_sp = 5.0
> > > splitter = Array(Float64, ns, ns)
> > > end
> > > nt = length( ele )
> > >
> > > # ##### Pre-allocate result and temporary arrays
> > > #if flags[1] == 1
> > > σ = zeros(Complex128, nt)
> > > #end
> > > #if flags[2] == 1
> > > a = zeros(Float64, nt)
> > > #end
> > > #if flags[3] == 1
> > > r_ionization = 20.0
> > > n1 = round(Int, ns/2 - r_ionization/dx)
> > > n2 = round(Int, ns/2 + r_ionization/dx)
> > > ip = zeros(Float64, nt)
> > > #end
> > >
> > > ##### FFT plan
> > > p_fft! = plan_fft!( similar(ϕ), flags=FFTW.MEASURE )
> > >
> > > prop_x = similar( ϕ )
> > > prop_p = similar( prop_x )
> > > prop_e = similar( prop_x )
> > > # this two versions just cost the same time
> > > xplusy = Array(Float64, ns, ns)
> > > #xplusy = Array( Float64, ns^2)
> > >
> > > ##### absorb boundary
> > > r_a = ns * dx /2 - 50.0
> > > δ = 10.0
> > > absorb = Array(Float64, ns, ns)
> > >
> > > k0 = 2π / (ns * dx)
> > >
> > > @inbounds for j in 1:ns
> > > @inbounds for i in 1:ns
> > > prop_x[i, j] = exp( -im * get_potential(x[i], x[j]) * dt / 2 )
> > > prop_p[i, j] = exp( -im * (p[i]^2 + p[j]^2)/2 * dt )
> > >
> > > xplusy[i, j] = x[i] + x[j]
> > >
> > > absorb[i, j] = (1.0 - get_out(x[i], r_a, δ ))* (1.0 -
> > > get_out(x[j],
> > > r_a, δ))
> > > end
> > > end
> > >
> > > if flags[2] == 1
> > > pvpx = Array(Float64, ns, ns)
> > > @inbounds for j in 1:ns
> > > @inbounds for i in 1:ns
> > > pvpx[i, j] = get_pvpx(x[i], x[j])
> > > end
> > > end
> > > end
> > >
> > > if flags[4] == 1
> > > ϕo = zeros(Complex128, ns, ns)
> > > ϕp = zeros(Complex128, ns, ns)
> > > @inbounds for j in 1:ns
> > > @inbounds for i in 1:ns
> > > splitter[i, j] = get_out(x[i], r_sp, δ_sp) *
> > > get_out(x[j], r_sp, δ_sp)
> > > end
> > > end
> > > end
> > >
> > > for i in 1:nt
> > > for j in eachindex(ϕ)
> > > prop_e[j] = exp( -im * ele[i] * xplusy[j] * dt/2.0)
> > > ************************************169
> > > end
> > >
> > > for j in eachindex(ϕ)
> > > ϕ[j] *= prop_x[j] * prop_e[j]
> > > end
> > > p_fft! * ϕ
> > > for j in eachindex(ϕ)
> > > ϕ[j] *= prop_p[j]
> > > end
> > > p_fft! \ ϕ
> > > for j in eachindex(ϕ)
> > > ϕ[j] *= prop_x[j] * prop_e[j]
> > > end
> > > ########## autocorrelation function σ(t)
> > > if flags[1] == 1
> > > for j in eachindex(ϕ)
> > > σ[i] += conj(ϕg[j]) * ϕ[j]
> > > end
> > > end
> > > ########## dipole acceleration a(t)
> > > if flags[2] == 1
> > > for j in eachindex(ϕ)
> > > a[i] += abs(ϕ[j])^2 * (pvpx[j] + 2ele[i])
> > > end
> > > end
> > > ########## ionization probability ip(t)
> > > if flags[3] == 1
> > > for j1 in n1:n2
> > > for j2 in 1:ns
> > > ip[i] += abs( ϕ[j2+ns*(j1-1)] )^2
> > > end
> > > end
> > > for j1 in [1:n1-1; n2+1:ns]
> > > for j2 in n1:n2
> > > ip[i] += abs( ϕ[j2+ns*(j1-1)] )^2
> > > end
> > > end
> > > end
> > > ########## get momentum
> > > if flags[4] == 1
> > > for j in eachindex(ϕo)
> > > ϕo[j] = ϕ[j] * splitter[j] * exp( -im * A[i]*xplusy[j] )
> > > **********************************211
> > > end
> > > for j in eachindex(p)
> > > pp[j] = p[j]^2 /2 * (nt-i) - p[j] *sum( A[i:nt] ) + sum(
> > > A²[1:nt] ) /2 ******************214
> > > end
> > > for j2 in 1:ns
> > > for j1 in 1:ns
> > > ϕo[j1, j2] = ϕo[j1, j2] * exp( -im * (pp[j1] +
> > > pp[j2]) * dt)************************218
> > > end
> > > end
> > > p_fft! * ϕo
> > > for j in eachindex(ϕp)
> > > ϕp[j] += ϕo[j]
> > > end
> > > end
> > >
> > > ########## absorb boundary
> > > if mod(i, 300) == 0
> > > for j in eachindex(ϕ)
> > > ϕ[j] *= absorb[j]
> > > end
> > > end
> > >
> > > if (mod(i, 500) == 0)
> > > println("i = $i")
> > > flush(STDOUT)
> > > end
> > > end
> > > σ *= dx^2
> > > a *= dx^2
> > > ip *= dx^2
> > >
> > > save("data/fs.jld", "ϕ", ϕ)
> > > if flags[1] == 1
> > > save("data/sigma.jld", "σ", σ)
> > > end
> > > if flags[2] == 1
> > > save("data/a.jld", "a", a)
> > > end
> > > if flags[3] == 1
> > > save("data/ip.jld", "ip", ip)
> > > end
> > > if flags[4] == 1
> > > save("data/pf.jld", "ϕp", ϕp)
> > > end
> > >
> > > #return σ, a, ip, ϕ
> > > nothing
> > > end
> > >
> > >
> >
