Messages from Usenet group comp.lang.idl-pvwave, compiled by Paulo Penteado
On Nov 6, 1:31 am, tarequea...@gmail.com wrote: > Hello all, > > help me! I am running a code 'infested' with for loops.And as u can > guess, its painfully slow. The part of my code with loop looks like > the following: > > jump1: > > ;Setting up the Green functions array which will have the same number > of elements as of amp_vec > > G=fltarr(n_elements(amp_vec),n_elements(amp_vec)) > G_phi=fltarr(n_elements(amp_vec)) > G_rp=fltarr(n_elements(amp_vec)) > G_r=fltarr(n_elements(amp_vec)) > G_in=fltarr(n_elements(amp_vec)) > G_out=fltarr(n_elements(amp_vec)) > G_p=fltarr(n_elements(amp_vec)) > G_h=fltarr(n_elements(amp_vec)) > gp=fltarr(n_elements(amp_vec)) > gh=fltarr(n_elements(amp_vec)) > G_in_msum = fltarr(n_elements(amp_vec)) > G_out_msum = fltarr(n_elements(amp_vec)) > G_in_phisum = fltarr(n_elements(amp_vec)) > G_out_phisum = fltarr(n_elements(amp_vec)) > > if ignore_realdata eq 1. then begin > amp_vec= abs(randomn(0.5,n_radial_points,/double)) > a=1. > ;print,' amp_vec is',amp_vec > endif > > do_u_like_to_start_with_rp_loop = 0 ; Set 1 if YES,0 if NO > > if do_u_like_to_start_with_rp_loop eq 1. then BEGIN > PRINT,' WE ARE USING rp PREFERED LOOP' > goto,jump2 > > ENDIF > > PRINT,' WE ARE USING r PREFERED LOOP' > for i_r= 0,n_radial_points-1 do begin > > loop_time = systime(1) > > if ignore_realdata eq 1. then begin > > r_scld=( i_r*2.)/(n_radial_points -1) ;---------> We took off > trap radius from here for scaling purpose,see note > > ;---------> Also note the use of factor 2. This is because, we > want to get values outside > ;----------> the cylinder. But this is just for demonstration purpose!!!! > > endif else begin > > r_scld=( i_r)/(n_radial_points -1) ; took off the factor 2 > > endelse > ;r_scld = 2. > > ;print,'r_scld value is ',r_scld > > for i_rp= 0,n_radial_points-1 do begin > > if ignore_realdata eq 1. then begin > > rp_mat = randomn(1,n_radial_points,/double) > ;print,'rp_mat is',rp_mat > > rp_scld = rp_mat(i_rp) > > endif else begin > > ;rp_scld=( i_rp/((n_radial_points-1))) * float(amp_vec(i_rp)) > rp_scld= float(amp_vec(i_rp)) > ;print,' amp_vec is',amp_vec > > endelse > > ; rp_scld=( i_rp/((n_radial_points-1))) * float(amp_vec(i_rp)) > > ;rp_mat = randomn(1,n_radial_points,/double) > ; print,'rp_mat is',rp_mat > > ;rp_scld = rp_mat(i_rp) > > ;rp_scld = 0.5 > > ;;print,'rp_scld for i_rp= ',i_rp,' is, ',rp_scld > > if (r_scld gt rp_scld) then begin > r_plus = r_scld > r_minus = rp_scld > endif else begin > r_minus = r_scld > r_plus = rp_scld > endelse > > ;print,'r_plus value is ',r_plus > ;print,'r_minus value is ',r_minus > > for i_m=1,20 do begin ;n_radial_points do begin > > ;;print,'starting i_m value is ',i_m > > ;if (n_radial_points le 5) then i_phi_max = 20 else i_phi_max = > n_radial_points > ;print,'i phi max is = ',i_phi_max > i_phi_max = 20. > > for i_phi=0,i_phi_max - 1 do begin > ; print,'starting i_phi value is',i_phi > > count= i_phi + 1. > ;print,'count is ',count > phi=(count*2*!PI)/(i_phi_max) > > ; print,'phi value is= ',phi > ; phi= 0.785398163 ; <----- In radian > > a= 1. ; -----> Scaled trap radius > > gp(i_phi) = 2.0*(1./i_m)*(r_minus/r_plus)^i_m * > cos(i_m*(phi)) > gh(i_phi) = 2.0*(1./i_m)*(r_minus * r_plus/a^2)^i_m * > cos(i_m*(phi)) > > ;print,'cos(i_m*phi) is',cos(i_m*phi) > > ;if (i_r eq 0.) && (i_rp eq 0.) && (i_m eq 1.) then begin > > ;print,' the 1st gp is ',gp(i_phi) > ;print,' the 1st gh is ',gh(i_phi) > ;endif > > ;if (i_r eq n_radial_points - 1.) && (i_rp eq > n_radial_points -1.) && (i_m eq n_radial_points -1.) then begin > > ;print,' the Last gp is ',gp(i_phi) > ;print,' the Last gh is ',gh(i_phi) > > ;endif > > endfor ; end of phi loop > > G_in_phisum [i_m -1] = total(gp) ; Add up the phi elements > for a specific m > G_out_phisum [i_m -1] = total(gh) > > endfor ; end of m-loop > > G_in_msum(i_rp) = total(G_in_phisum) ; Add up all m values for > a specific rp value > G_out_msum(i_rp) = total(G_out_phisum) > > G_in(i_rp) = -alog((r_plus)^2.) + G_in_msum[i_rp] > G_out(i_rp) = -alog((a^2./rp_scld)^2.) + G_out_msum[i_rp] > > ;print,'G_in is',G_in > ;print,'G_out is',G_out > > G(i_r,i_rp)= G_in(i_rp) - G_out(i_rp) - alog((a/rp_scld)^2.) > > index=where(finite(G,/NaN) ,count) > ;print,' index is ',index > if (count ne 0) then G[index] = 0. > ; non_zero = where(G,count) > ; print,'non zero value is',non_zero > ; > ; if count ne 0. then G = G[non_zero] > > ;print,' last log part',alog((a/rp_scld)^2.) > ;print,' G_in - G_out is ',G_in - G_out > ;print,'G inside rp loop is ',G(i_r,i_rp),' for i_r =',i_r,' > and i_rp =',i_rp > > endfor ;end of rp loop > > ;G_p= G_in > ;G_h= G_out > ;print,'G_p is',G_p,'and G_h is',G_h > ;G(i_r,i_rp)= G_p(i_rp) - G_h(i_rp) - alog((a/rp_scld)^2.) > > ;print,'rp_scld is ',rp_scld > > ; print,' G inside the r loop is',G > > ; if i_r eq (n_radial_points-1) then print,'Last r_scld value is=', > r_scld > > ;if i_r eq ( (n_radial_points-1)/10.) then print,'First 1/10th > r_scld value is=', r_scld > ;if i_r eq ( (n_radial_points-1)/2.) then print,'First 1/2th > r_scld value is=', r_scld > ;if i_r eq ( (n_radial_points-1)*3./4.) then print,'3/4 th r_scld > value is=', r_scld > ;if i_r eq (n_radial_points-1) then print,'Last r_scld value is=', > r_scld > > if i_r eq (n_radial_points - 1.) then begin > > print,'The time it took to finish ',i_r,'th loop is', systime(1) - > loop_time,'seconds' > > endif > > endfor ; end of r loop > > ;print,'here is the PROFILER report for r prefered loop' > > ;print,'G is ',G ;[n_radial_points - 1] > > if ignore_realdata eq 1 then begin > > r_vec=(findgen(n_radial_points)/(n_radial_points)) > potential=fltarr(n_radial_points) > prod = fltarr(n_radial_points) > > endif else begin > > r_vec=(findgen(n_theta_points)/(n_theta_points)) > potential=fltarr(n_theta_points) > prod = fltarr(n_theta_points) > endelse > > if ignore_realdata eq 1 then p= n_radial_points else p= n_theta_points > > for k = 0,100 do begin ;p -1 do begin > ;rp_mat = randomn(1,n_radial_points,/double) > ;print,' amp_vec is',amp_vec > ;print,'amp_vec is',amp_vec[k] > ;print,'G[*,k] is',G[*,k] > prod =amp_vec[k] * G(*,k) > prod_invfft = abs( fft(prod,/inverse)) > potential[k] = int_tabulated(r_vec,prod_invfft) > ;print,'potential is',potential > > ===== > So as u can see there are 4 for loops running. the m loop with > running index i_m should be 200. But setting it to 200 slows down the > program. > > My supervisor said that, this should be a very fast way of calculating > green function than the traditional way(which my group-mate is doing). > > what I am doing wrong? > Any help will be HIGHLY appreciated! > > Best, > > Tareque Well, the first thing you are doing wrong is posting a gigantic chunk of code for people to go over! I'd love to help, but I really don't have time to re-write the whole thing for you. Can you break it down into a couple smaller sections? If you can summarize what each chunk of code is actually trying to do, isolated from the rest of the code as a whole, that will be extremely helpful. For a first suggestion for now (I have class to teach in a couple minutes) I'd point out that your array declarations can be sped up, even though those aren't in a for loop. Look: G=fltarr(n_elements(amp_vec),n_elements(amp_vec)) G_phi=fltarr(n_elements(amp_vec)) G_rp=fltarr(n_elements(amp_vec)) G_r=fltarr(n_elements(amp_vec)) should be: namp_vec = n_elements(amp_vec) g = fltarr(namp_vec,namp_vec) g_phi = fltarr(namp_vec) g_rp = fltarr(namp_vec) g_r = fltarr(namp_vec) or even: namp_vec = n_elements(amp_vec) g = fltarr(namp_vec,namp_vec) g_phi = fltarr(namp_vec) g_rp = g_phi & g_r = g_phi In the long run this won't make a big difference for the speed of your code, but it does help highlight a very important lesson when you are trying to optimize your code for speed - avoid all unnecessary computation. Something like that in a for loop that iterates many times can make a difference. Anyway, please, try to extract a few sections of your code and explain what they are doing indpendent of the rest of your code. I really doubt anyone will have the time to look through the whole thing for you.
On Nov 6, 1:31 am, tarequea...@gmail.com wrote: > Hello all, > > help me! I am running a code 'infested' with for loops.And as u can > guess, its painfully slow. The part of my code with loop looks like > the following: > > jump1: > > ;Setting up the Green functions array which will have the same number > of elements as of amp_vec > > G=fltarr(n_elements(amp_vec),n_elements(amp_vec)) > G_phi=fltarr(n_elements(amp_vec)) > G_rp=fltarr(n_elements(amp_vec)) > G_r=fltarr(n_elements(amp_vec)) > G_in=fltarr(n_elements(amp_vec)) > G_out=fltarr(n_elements(amp_vec)) > G_p=fltarr(n_elements(amp_vec)) > G_h=fltarr(n_elements(amp_vec)) > gp=fltarr(n_elements(amp_vec)) > gh=fltarr(n_elements(amp_vec)) > G_in_msum = fltarr(n_elements(amp_vec)) > G_out_msum = fltarr(n_elements(amp_vec)) > G_in_phisum = fltarr(n_elements(amp_vec)) > G_out_phisum = fltarr(n_elements(amp_vec)) > > if ignore_realdata eq 1. then begin > amp_vec= abs(randomn(0.5,n_radial_points,/double)) > a=1. > ;print,' amp_vec is',amp_vec > endif > > do_u_like_to_start_with_rp_loop = 0 ; Set 1 if YES,0 if NO > > if do_u_like_to_start_with_rp_loop eq 1. then BEGIN > PRINT,' WE ARE USING rp PREFERED LOOP' > goto,jump2 > > ENDIF > > PRINT,' WE ARE USING r PREFERED LOOP' > for i_r= 0,n_radial_points-1 do begin > > loop_time = systime(1) > > if ignore_realdata eq 1. then begin > > r_scld=( i_r*2.)/(n_radial_points -1) ;---------> We took off > trap radius from here for scaling purpose,see note > > ;---------> Also note the use of factor 2. This is because, we > want to get values outside > ;----------> the cylinder. But this is just for demonstration purpose!!!! > > endif else begin > > r_scld=( i_r)/(n_radial_points -1) ; took off the factor 2 > > endelse > ;r_scld = 2. > > ;print,'r_scld value is ',r_scld > > for i_rp= 0,n_radial_points-1 do begin > > if ignore_realdata eq 1. then begin > > rp_mat = randomn(1,n_radial_points,/double) > ;print,'rp_mat is',rp_mat > > rp_scld = rp_mat(i_rp) > > endif else begin > > ;rp_scld=( i_rp/((n_radial_points-1))) * float(amp_vec(i_rp)) > rp_scld= float(amp_vec(i_rp)) > ;print,' amp_vec is',amp_vec > > endelse > > ; rp_scld=( i_rp/((n_radial_points-1))) * float(amp_vec(i_rp)) > > ;rp_mat = randomn(1,n_radial_points,/double) > ; print,'rp_mat is',rp_mat > > ;rp_scld = rp_mat(i_rp) > > ;rp_scld = 0.5 > > ;;print,'rp_scld for i_rp= ',i_rp,' is, ',rp_scld > > if (r_scld gt rp_scld) then begin > r_plus = r_scld > r_minus = rp_scld > endif else begin > r_minus = r_scld > r_plus = rp_scld > endelse > > ;print,'r_plus value is ',r_plus > ;print,'r_minus value is ',r_minus > > for i_m=1,20 do begin ;n_radial_points do begin > > ;;print,'starting i_m value is ',i_m > > ;if (n_radial_points le 5) then i_phi_max = 20 else i_phi_max = > n_radial_points > ;print,'i phi max is = ',i_phi_max > i_phi_max = 20. > > for i_phi=0,i_phi_max - 1 do begin > ; print,'starting i_phi value is',i_phi > > count= i_phi + 1. > ;print,'count is ',count > phi=(count*2*!PI)/(i_phi_max) > > ; print,'phi value is= ',phi > ; phi= 0.785398163 ; <----- In radian > > a= 1. ; -----> Scaled trap radius > > gp(i_phi) = 2.0*(1./i_m)*(r_minus/r_plus)^i_m * > cos(i_m*(phi)) > gh(i_phi) = 2.0*(1./i_m)*(r_minus * r_plus/a^2)^i_m * > cos(i_m*(phi)) > > ;print,'cos(i_m*phi) is',cos(i_m*phi) > > ;if (i_r eq 0.) && (i_rp eq 0.) && (i_m eq 1.) then begin > > ;print,' the 1st gp is ',gp(i_phi) > ;print,' the 1st gh is ',gh(i_phi) > ;endif > > ;if (i_r eq n_radial_points - 1.) && (i_rp eq > n_radial_points -1.) && (i_m eq n_radial_points -1.) then begin > > ;print,' the Last gp is ',gp(i_phi) > ;print,' the Last gh is ',gh(i_phi) > > ;endif > > endfor ; end of phi loop > > G_in_phisum [i_m -1] = total(gp) ; Add up the phi elements > for a specific m > G_out_phisum [i_m -1] = total(gh) > > endfor ; end of m-loop > > G_in_msum(i_rp) = total(G_in_phisum) ; Add up all m values for > a specific rp value > G_out_msum(i_rp) = total(G_out_phisum) > > G_in(i_rp) = -alog((r_plus)^2.) + G_in_msum[i_rp] > G_out(i_rp) = -alog((a^2./rp_scld)^2.) + G_out_msum[i_rp] > > ;print,'G_in is',G_in > ;print,'G_out is',G_out > > G(i_r,i_rp)= G_in(i_rp) - G_out(i_rp) - alog((a/rp_scld)^2.) > > index=where(finite(G,/NaN) ,count) > ;print,' index is ',index > if (count ne 0) then G[index] = 0. > ; non_zero = where(G,count) > ; print,'non zero value is',non_zero > ; > ; if count ne 0. then G = G[non_zero] > > ;print,' last log part',alog((a/rp_scld)^2.) > ;print,' G_in - G_out is ',G_in - G_out > ;print,'G inside rp loop is ',G(i_r,i_rp),' for i_r =',i_r,' > and i_rp =',i_rp > > endfor ;end of rp loop > > ;G_p= G_in > ;G_h= G_out > ;print,'G_p is',G_p,'and G_h is',G_h > ;G(i_r,i_rp)= G_p(i_rp) - G_h(i_rp) - alog((a/rp_scld)^2.) > > ;print,'rp_scld is ',rp_scld > > ; print,' G inside the r loop is',G > > ; if i_r eq (n_radial_points-1) then print,'Last r_scld value is=', > r_scld > > ;if i_r eq ( (n_radial_points-1)/10.) then print,'First 1/10th > r_scld value is=', r_scld > ;if i_r eq ( (n_radial_points-1)/2.) then print,'First 1/2th > r_scld value is=', r_scld > ;if i_r eq ( (n_radial_points-1)*3./4.) then print,'3/4 th r_scld > value is=', r_scld > ;if i_r eq (n_radial_points-1) then print,'Last r_scld value is=', > r_scld > > if i_r eq (n_radial_points - 1.) then begin > > print,'The time it took to finish ',i_r,'th loop is', systime(1) - > loop_time,'seconds' > > endif > > endfor ; end of r loop > > ;print,'here is the PROFILER report for r prefered loop' > > ;print,'G is ',G ;[n_radial_points - 1] > > if ignore_realdata eq 1 then begin > > r_vec=(findgen(n_radial_points)/(n_radial_points)) > potential=fltarr(n_radial_points) > prod = fltarr(n_radial_points) > > endif else begin > > r_vec=(findgen(n_theta_points)/(n_theta_points)) > potential=fltarr(n_theta_points) > prod = fltarr(n_theta_points) > endelse > > if ignore_realdata eq 1 then p= n_radial_points else p= n_theta_points > > for k = 0,100 do begin ;p -1 do begin > ;rp_mat = randomn(1,n_radial_points,/double) > ;print,' amp_vec is',amp_vec > ;print,'amp_vec is',amp_vec[k] > ;print,'G[*,k] is',G[*,k] > prod =amp_vec[k] * G(*,k) > prod_invfft = abs( fft(prod,/inverse)) > potential[k] = int_tabulated(r_vec,prod_invfft) > ;print,'potential is',potential > > ===== > So as u can see there are 4 for loops running. the m loop with > running index i_m should be 200. But setting it to 200 slows down the > program. > > My supervisor said that, this should be a very fast way of calculating > green function than the traditional way(which my group-mate is doing). > > what I am doing wrong? > Any help will be HIGHLY appreciated! > > Best, > > Tareque Looking back over your code again, I noticed that your whole code looks like essentially one big nested set of for loops. Of course, nested for loops are a bit harder to separate from eachother. In general when you are trying to optimize nested for loops the trick is to start from the inside and work your way out. Looking at your phi loop (which seems to be the innermost loop) I would do something like this. Your code says (getting rid of comments and empty space): for i_phi=0,i_phi_max - 1 do begin count= i_phi + 1. phi=(count*2*!PI)/(i_phi_max) a= 1 gp(i_phi) = 2.0*(1./i_m)*(r_minus/r_plus)^i_m *cos(i_m*(phi)) gh(i_phi) = 2.0*(1./i_m)*(r_minus * r_plus/a^2)^i_m *cos(i_m*(phi)) endfor That can be re-written: phis = findgen(i_phi_max)+1 gp = 2.0*(1./i_m)*(r_minus/r_plus)^i_m * cos(i_m * phis*2*!PI/ i_phi_max ) gh = 2.0*(1./i_m)*(r_minus*r_plus/a^2)^i_m * cos(i_m * phis*2*!PI/ i_phi_max ) and your for loop is gone (assuming that I got everything right), as long as i_m, r_minus, r_plus, and a are all simple variables, and not arrays. I have to go to class now, so you'll have to do without any additional comments.
On Nov 6, 8:13 am, Conor <cmanc...@gmail.com> wrote: > On Nov 6, 1:31 am, tarequea...@gmail.com wrote: > >> Hello all, > >> help me! I am running a code 'infested' with for loops.And as u can >> guess, its painfully slow. The part of my code with loop looks like >> the following: > >> jump1: > >> ;Setting up the Green functions array which will have the same number >> of elements as of amp_vec > >> G=fltarr(n_elements(amp_vec),n_elements(amp_vec)) >> G_phi=fltarr(n_elements(amp_vec)) >> G_rp=fltarr(n_elements(amp_vec)) >> G_r=fltarr(n_elements(amp_vec)) >> G_in=fltarr(n_elements(amp_vec)) >> G_out=fltarr(n_elements(amp_vec)) >> G_p=fltarr(n_elements(amp_vec)) >> G_h=fltarr(n_elements(amp_vec)) >> gp=fltarr(n_elements(amp_vec)) >> gh=fltarr(n_elements(amp_vec)) >> G_in_msum = fltarr(n_elements(amp_vec)) >> G_out_msum = fltarr(n_elements(amp_vec)) >> G_in_phisum = fltarr(n_elements(amp_vec)) >> G_out_phisum = fltarr(n_elements(amp_vec)) > >> if ignore_realdata eq 1. then begin >> amp_vec= abs(randomn(0.5,n_radial_points,/double)) >> a=1. >> ;print,' amp_vec is',amp_vec >> endif > >> do_u_like_to_start_with_rp_loop = 0 ; Set 1 if YES,0 if NO > >> if do_u_like_to_start_with_rp_loop eq 1. then BEGIN >> PRINT,' WE ARE USING rp PREFERED LOOP' >> goto,jump2 > >> ENDIF > >> PRINT,' WE ARE USING r PREFERED LOOP' >> for i_r= 0,n_radial_points-1 do begin > >> loop_time = systime(1) > >> if ignore_realdata eq 1. then begin > >> r_scld=( i_r*2.)/(n_radial_points -1) ;---------> We took off >> trap radius from here for scaling purpose,see note > >> ;---------> Also note the use of factor 2. This is because, we >> want to get values outside >> ;----------> the cylinder. But this is just for demonstration purpose!!!! > >> endif else begin > >> r_scld=( i_r)/(n_radial_points -1) ; took off the factor 2 > >> endelse >> ;r_scld = 2. > >> ;print,'r_scld value is ',r_scld > >> for i_rp= 0,n_radial_points-1 do begin > >> if ignore_realdata eq 1. then begin > >> rp_mat = randomn(1,n_radial_points,/double) >> ;print,'rp_mat is',rp_mat > >> rp_scld = rp_mat(i_rp) > >> endif else begin > >> ;rp_scld=( i_rp/((n_radial_points-1))) * float(amp_vec(i_rp)) >> rp_scld= float(amp_vec(i_rp)) >> ;print,' amp_vec is',amp_vec > >> endelse > >> ; rp_scld=( i_rp/((n_radial_points-1))) * float(amp_vec(i_rp)) > >> ;rp_mat = randomn(1,n_radial_points,/double) >> ; print,'rp_mat is',rp_mat > >> ;rp_scld = rp_mat(i_rp) > >> ;rp_scld = 0.5 > >> ;;print,'rp_scld for i_rp= ',i_rp,' is, ',rp_scld > >> if (r_scld gt rp_scld) then begin >> r_plus = r_scld >> r_minus = rp_scld >> endif else begin >> r_minus = r_scld >> r_plus = rp_scld >> endelse > >> ;print,'r_plus value is ',r_plus >> ;print,'r_minus value is ',r_minus > >> for i_m=1,20 do begin ;n_radial_points do begin > >> ;;print,'starting i_m value is ',i_m > >> ;if (n_radial_points le 5) then i_phi_max = 20 else i_phi_max = >> n_radial_points >> ;print,'i phi max is = ',i_phi_max >> i_phi_max = 20. > >> for i_phi=0,i_phi_max - 1 do begin >> ; print,'starting i_phi value is',i_phi > >> count= i_phi + 1. >> ;print,'count is ',count >> phi=(count*2*!PI)/(i_phi_max) > >> ; print,'phi value is= ',phi >> ; phi= 0.785398163 ; <----- In radian > >> a= 1. ; -----> Scaled trap radius > >> gp(i_phi) = 2.0*(1./i_m)*(r_minus/r_plus)^i_m * >> cos(i_m*(phi)) >> gh(i_phi) = 2.0*(1./i_m)*(r_minus * r_plus/a^2)^i_m * >> cos(i_m*(phi)) > >> ;print,'cos(i_m*phi) is',cos(i_m*phi) > >> ;if (i_r eq 0.) && (i_rp eq 0.) && (i_m eq 1.) then begin > >> ;print,' the 1st gp is ',gp(i_phi) >> ;print,' the 1st gh is ',gh(i_phi) >> ;endif > >> ;if (i_r eq n_radial_points - 1.) && (i_rp eq >> n_radial_points -1.) && (i_m eq n_radial_points -1.) then begin > >> ;print,' the Last gp is ',gp(i_phi) >> ;print,' the Last gh is ',gh(i_phi) > >> ;endif > >> endfor ; end of phi loop > >> G_in_phisum [i_m -1] = total(gp) ; Add up the phi elements >> for a specific m >> G_out_phisum [i_m -1] = total(gh) > >> endfor ; end of m-loop > >> G_in_msum(i_rp) = total(G_in_phisum) ; Add up all m values for >> a specific rp value >> G_out_msum(i_rp) = total(G_out_phisum) > >> G_in(i_rp) = -alog((r_plus)^2.) + G_in_msum[i_rp] >> G_out(i_rp) = -alog((a^2./rp_scld)^2.) + G_out_msum[i_rp] > >> ;print,'G_in is',G_in >> ;print,'G_out is',G_out > >> G(i_r,i_rp)= G_in(i_rp) - G_out(i_rp) - alog((a/rp_scld)^2.) > >> index=where(finite(G,/NaN) ,count) >> ;print,' index is ',index >> if (count ne 0) then G[index] = 0. >> ; non_zero = where(G,count) >> ; print,'non zero value is',non_zero >> ; >> ; if count ne 0. then G = G[non_zero] > >> ;print,' last log part',alog((a/rp_scld)^2.) >> ;print,' G_in - G_out is ',G_in - G_out >> ;print,'G inside rp loop is ',G(i_r,i_rp),' for i_r =',i_r,' >> and i_rp =',i_rp > >> endfor ;end of rp loop > >> ;G_p= G_in >> ;G_h= G_out >> ;print,'G_p is',G_p,'and G_h is',G_h >> ;G(i_r,i_rp)= G_p(i_rp) - G_h(i_rp) - alog((a/rp_scld)^2.) > >> ;print,'rp_scld is ',rp_scld > >> ; print,' G inside the r loop is',G > >> ; if i_r eq (n_radial_points-1) then print,'Last r_scld value is=', >> r_scld > >> ;if i_r eq ( (n_radial_points-1)/10.) then print,'First 1/10th >> r_scld value is=', r_scld >> ;if i_r eq ( (n_radial_points-1)/2.) then print,'First 1/2th >> r_scld value is=', r_scld >> ;if i_r eq ( (n_radial_points-1)*3./4.) then print,'3/4 th r_scld >> value is=', r_scld >> ;if i_r eq (n_radial_points-1) then print,'Last r_scld value is=', >> r_scld > >> if i_r eq (n_radial_points - 1.) then begin > >> print,'The time it took to finish ',i_r,'th loop is', systime(1) - >> loop_time,'seconds' > >> endif > >> endfor ; end of r loop > >> ;print,'here is the PROFILER report for r prefered loop' > >> ;print,'G is ',G ;[n_radial_points - 1] > >> if ignore_realdata eq 1 then begin > >> r_vec=(findgen(n_radial_points)/(n_radial_points)) >> potential=fltarr(n_radial_points) >> prod = fltarr(n_radial_points) > >> endif else begin > >> r_vec=(findgen(n_theta_points)/(n_theta_points)) >> potential=fltarr(n_theta_points) >> prod = fltarr(n_theta_points) >> endelse > >> if ignore_realdata eq 1 then p= n_radial_points else p= n_theta_points > >> for k = 0,100 do begin ;p -1 do begin >> ;rp_mat = randomn(1,n_radial_points,/double) >> ;print,' amp_vec is',amp_vec >> ;print,'amp_vec is',amp_vec[k] >> ;print,'G[*,k] is',G[*,k] >> prod =amp_vec[k] * G(*,k) >> prod_invfft = abs( fft(prod,/inverse)) >> potential[k] = int_tabulated(r_vec,prod_invfft) >> ;print,'potential is',potential > >> ===== >> So as u can see there are 4 for loops running. the m loop with >> running index i_m should be 200. But setting it to 200 slows down the >> program. > >> My supervisor said that, this should be a very fast way of calculating >> green function than the traditional way(which my group-mate is doing). > >> what I am doing wrong? >> Any help will be HIGHLY appreciated! > >> Best, > >> Tareque > > Well, the first thing you are doing wrong is posting a gigantic chunk > of code for people to go over! I'd love to help, but I really don't > have time to re-write the whole thing for you. Can you break it down > into a couple smaller sections? If you can summarize what each chunk > of code is actually trying to do, isolated from the rest of the code > as a whole, that will be extremely helpful. > > For a first suggestion for now (I have class to teach in a couple > minutes) I'd point out that your array declarations can be sped up, > even though those aren't in a for loop. Look: > > G=fltarr(n_elements(amp_vec),n_elements(amp_vec)) > G_phi=fltarr(n_elements(amp_vec)) > G_rp=fltarr(n_elements(amp_vec)) > G_r=fltarr(n_elements(amp_vec)) > > should be: > > namp_vec = n_elements(amp_vec) > g = fltarr(namp_vec,namp_vec) > g_phi = fltarr(namp_vec) > g_rp = fltarr(namp_vec) > g_r = fltarr(namp_vec) > > or even: > > namp_vec = n_elements(amp_vec) > g = fltarr(namp_vec,namp_vec) > g_phi = fltarr(namp_vec) > g_rp = g_phi & g_r = g_phi > > In the long run this won't make a big difference for the speed of your > code, but it does help highlight a very important lesson when you are > trying to optimize your code for speed - avoid all unnecessary > computation. Something like that in a for loop that iterates many > times can make a difference. > > Anyway, please, try to extract a few sections of your code and explain > what they are doing indpendent of the rest of your code. I really > doubt anyone will have the time to look through the whole thing for > you. Thanks for the reply. Really appreciated it. I am going to cut down the code into smaller pieces and post it here. Tareque
On Nov 6, 8:23 am, Conor <cmanc...@gmail.com> wrote: > On Nov 6, 1:31 am, tarequea...@gmail.com wrote: > >> Hello all, > >> help me! I am running a code 'infested' with for loops.And as u can >> guess, its painfully slow. The part of my code with loop looks like >> the following: > >> jump1: > >> ;Setting up the Green functions array which will have the same number >> of elements as of amp_vec > >> G=fltarr(n_elements(amp_vec),n_elements(amp_vec)) >> G_phi=fltarr(n_elements(amp_vec)) >> G_rp=fltarr(n_elements(amp_vec)) >> G_r=fltarr(n_elements(amp_vec)) >> G_in=fltarr(n_elements(amp_vec)) >> G_out=fltarr(n_elements(amp_vec)) >> G_p=fltarr(n_elements(amp_vec)) >> G_h=fltarr(n_elements(amp_vec)) >> gp=fltarr(n_elements(amp_vec)) >> gh=fltarr(n_elements(amp_vec)) >> G_in_msum = fltarr(n_elements(amp_vec)) >> G_out_msum = fltarr(n_elements(amp_vec)) >> G_in_phisum = fltarr(n_elements(amp_vec)) >> G_out_phisum = fltarr(n_elements(amp_vec)) > >> if ignore_realdata eq 1. then begin >> amp_vec= abs(randomn(0.5,n_radial_points,/double)) >> a=1. >> ;print,' amp_vec is',amp_vec >> endif > >> do_u_like_to_start_with_rp_loop = 0 ; Set 1 if YES,0 if NO > >> if do_u_like_to_start_with_rp_loop eq 1. then BEGIN >> PRINT,' WE ARE USING rp PREFERED LOOP' >> goto,jump2 > >> ENDIF > >> PRINT,' WE ARE USING r PREFERED LOOP' >> for i_r= 0,n_radial_points-1 do begin > >> loop_time = systime(1) > >> if ignore_realdata eq 1. then begin > >> r_scld=( i_r*2.)/(n_radial_points -1) ;---------> We took off >> trap radius from here for scaling purpose,see note > >> ;---------> Also note the use of factor 2. This is because, we >> want to get values outside >> ;----------> the cylinder. But this is just for demonstration purpose!!!! > >> endif else begin > >> r_scld=( i_r)/(n_radial_points -1) ; took off the factor 2 > >> endelse >> ;r_scld = 2. > >> ;print,'r_scld value is ',r_scld > >> for i_rp= 0,n_radial_points-1 do begin > >> if ignore_realdata eq 1. then begin > >> rp_mat = randomn(1,n_radial_points,/double) >> ;print,'rp_mat is',rp_mat > >> rp_scld = rp_mat(i_rp) > >> endif else begin > >> ;rp_scld=( i_rp/((n_radial_points-1))) * float(amp_vec(i_rp)) >> rp_scld= float(amp_vec(i_rp)) >> ;print,' amp_vec is',amp_vec > >> endelse > >> ; rp_scld=( i_rp/((n_radial_points-1))) * float(amp_vec(i_rp)) > >> ;rp_mat = randomn(1,n_radial_points,/double) >> ; print,'rp_mat is',rp_mat > >> ;rp_scld = rp_mat(i_rp) > >> ;rp_scld = 0.5 > >> ;;print,'rp_scld for i_rp= ',i_rp,' is, ',rp_scld > >> if (r_scld gt rp_scld) then begin >> r_plus = r_scld >> r_minus = rp_scld >> endif else begin >> r_minus = r_scld >> r_plus = rp_scld >> endelse > >> ;print,'r_plus value is ',r_plus >> ;print,'r_minus value is ',r_minus > >> for i_m=1,20 do begin ;n_radial_points do begin > >> ;;print,'starting i_m value is ',i_m > >> ;if (n_radial_points le 5) then i_phi_max = 20 else i_phi_max = >> n_radial_points >> ;print,'i phi max is = ',i_phi_max >> i_phi_max = 20. > >> for i_phi=0,i_phi_max - 1 do begin >> ; print,'starting i_phi value is',i_phi > >> count= i_phi + 1. >> ;print,'count is ',count >> phi=(count*2*!PI)/(i_phi_max) > >> ; print,'phi value is= ',phi >> ; phi= 0.785398163 ; <----- In radian > >> a= 1. ; -----> Scaled trap radius > >> gp(i_phi) = 2.0*(1./i_m)*(r_minus/r_plus)^i_m * >> cos(i_m*(phi)) >> gh(i_phi) = 2.0*(1./i_m)*(r_minus * r_plus/a^2)^i_m * >> cos(i_m*(phi)) > >> ;print,'cos(i_m*phi) is',cos(i_m*phi) > >> ;if (i_r eq 0.) && (i_rp eq 0.) && (i_m eq 1.) then begin > >> ;print,' the 1st gp is ',gp(i_phi) >> ;print,' the 1st gh is ',gh(i_phi) >> ;endif > >> ;if (i_r eq n_radial_points - 1.) && (i_rp eq >> n_radial_points -1.) && (i_m eq n_radial_points -1.) then begin > >> ;print,' the Last gp is ',gp(i_phi) >> ;print,' the Last gh is ',gh(i_phi) > >> ;endif > >> endfor ; end of phi loop > >> G_in_phisum [i_m -1] = total(gp) ; Add up the phi elements >> for a specific m >> G_out_phisum [i_m -1] = total(gh) > >> endfor ; end of m-loop > >> G_in_msum(i_rp) = total(G_in_phisum) ; Add up all m values for >> a specific rp value >> G_out_msum(i_rp) = total(G_out_phisum) > >> G_in(i_rp) = -alog((r_plus)^2.) + G_in_msum[i_rp] >> G_out(i_rp) = -alog((a^2./rp_scld)^2.) + G_out_msum[i_rp] > >> ;print,'G_in is',G_in >> ;print,'G_out is',G_out > >> G(i_r,i_rp)= G_in(i_rp) - G_out(i_rp) - alog((a/rp_scld)^2.) > >> index=where(finite(G,/NaN) ,count) >> ;print,' index is ',index >> if (count ne 0) then G[index] = 0. >> ; non_zero = where(G,count) >> ; print,'non zero value is',non_zero >> ; >> ; if count ne 0. then G = G[non_zero] > >> ;print,' last log part',alog((a/rp_scld)^2.) >> ;print,' G_in - G_out is ',G_in - G_out >> ;print,'G inside rp loop is ',G(i_r,i_rp),' for i_r =',i_r,' >> and i_rp =',i_rp > >> endfor ;end of rp loop > >> ;G_p= G_in >> ;G_h= G_out >> ;print,'G_p is',G_p,'and G_h is',G_h >> ;G(i_r,i_rp)= G_p(i_rp) - G_h(i_rp) - alog((a/rp_scld)^2.) > >> ;print,'rp_scld is ',rp_scld > >> ; print,' G inside the r loop is',G > >> ; if i_r eq (n_radial_points-1) then print,'Last r_scld value is=', >> r_scld > >> ;if i_r eq ( (n_radial_points-1)/10.) then print,'First 1/10th >> r_scld value is=', r_scld >> ;if i_r eq ( (n_radial_points-1)/2.) then print,'First 1/2th >> r_scld value is=', r_scld >> ;if i_r eq ( (n_radial_points-1)*3./4.) then print,'3/4 th r_scld >> value is=', r_scld >> ;if i_r eq (n_radial_points-1) then print,'Last r_scld value is=', >> r_scld > >> if i_r eq (n_radial_points - 1.) then begin > >> print,'The time it took to finish ',i_r,'th loop is', systime(1) - >> loop_time,'seconds' > >> endif > >> endfor ; end of r loop > >> ;print,'here is the PROFILER report for r prefered loop' > >> ;print,'G is ',G ;[n_radial_points - 1] > >> if ignore_realdata eq 1 then begin > >> r_vec=(findgen(n_radial_points)/(n_radial_points)) >> potential=fltarr(n_radial_points) >> prod = fltarr(n_radial_points) > >> endif else begin > >> r_vec=(findgen(n_theta_points)/(n_theta_points)) >> potential=fltarr(n_theta_points) >> prod = fltarr(n_theta_points) >> endelse > >> if ignore_realdata eq 1 then p= n_radial_points else p= n_theta_points > >> for k = 0,100 do begin ;p -1 do begin >> ;rp_mat = randomn(1,n_radial_points,/double) >> ;print,' amp_vec is',amp_vec >> ;print,'amp_vec is',amp_vec[k] >> ;print,'G[*,k] is',G[*,k] >> prod =amp_vec[k] * G(*,k) >> prod_invfft = abs( fft(prod,/inverse)) >> potential[k] = int_tabulated(r_vec,prod_invfft) >> ;print,'potential is',potential > >> ===== >> So as u can see there are 4 for loops running. the m loop with >> running index i_m should be 200. But setting it to 200 slows down the >> program. > >> My supervisor said that, this should be a very fast way of calculating >> green function than the traditional way(which my group-mate is doing). > >> what I am doing wrong? >> Any help will be HIGHLY appreciated! > >> Best, > >> Tareque > > Looking back over your code again, I noticed that your whole code > looks like essentially one big nested set of for loops. Of course, > nested for loops are a bit harder to separate from eachother. In > general when you are trying to optimize nested for loops the trick is > to start from the inside and work your way out. Looking at your phi > loop (which seems to be the innermost loop) I would do something like > this. Your code says (getting rid of comments and empty space): > > for i_phi=0,i_phi_max - 1 do begin > count= i_phi + 1. > phi=(count*2*!PI)/(i_phi_max) > a= 1 > gp(i_phi) = 2.0*(1./i_m)*(r_minus/r_plus)^i_m *cos(i_m*(phi)) > gh(i_phi) = 2.0*(1./i_m)*(r_minus * r_plus/a^2)^i_m *cos(i_m*(phi)) > endfor > > That can be re-written: > > phis = findgen(i_phi_max)+1 > gp = 2.0*(1./i_m)*(r_minus/r_plus)^i_m * cos(i_m * phis*2*!PI/ > i_phi_max ) > gh = 2.0*(1./i_m)*(r_minus*r_plus/a^2)^i_m * cos(i_m * phis*2*!PI/ > i_phi_max ) > > and your for loop is gone (assuming that I got everything right), as > long as i_m, r_minus, r_plus, and a are all simple variables, and not > arrays. I have to go to class now, so you'll have to do without any > additional comments. Thank u thank u thank u thank u....or may be I should write a program which should keep sending u 'thank u' note for rest of your life! You guys are awesome!!!!!!! Tareque
Also, you might find this website handy: http://www.dfanning.com/tips/rebin_magic.html In general what I've done can be extended into 3 dimensions to eliminate another for loop, but at some point you start to run into issues with filling up your memory with gigantic arrays.