I wrote an algorithm to solve a set of PDE. There are some very long equations in the middle of while loop, and I tried to calculated these equations by GPU for speeding up, then the results from these equations are further employed. It runs successful, however, the gather() function takes almost 1/5 of total time (3000s). I tried to use [dk1,dk2,dk3,dk4,dk5,dk6,dk7,dk8,dk9] = dkfunction(S,T) in command window, it just cost 0.001s.
I am confused why this code in a big loop performs badly? I want to know if there is a way to speed up gather() function, or an alternative function? By the way, the size of array in mex file should be constant or not?
(Note: my code is very long, so I attatch the profiler and core part (simplified) of my question. dkfunction is related to cuda).
Profiler for following code operation time:
while t<n
%Omitted code for S and T calculation.
%%%
[dk1,dk2,dk3,dk4,dk5,dk6,dk7,dk8,dk9] = dkfunction(S,T);
[dkvTdT,dkvTdS,dkvhdT,dkvhdS,dphaivdT,dphaivdS,dkhdS,dkdS,dphaidS] = gather(dk1,dk2,dk3,dk4,dk5,dk6,dk7,dk8,dk9);
%%%
%Omitted code to use dkvTdt..... to calculate other variables and t steps.
%%%
end