Speed up MATLAB code

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Speed up MATLAB code



In my code, I have a line where I calculate the cumulative sum of a vector, A, using the cumsum() function in MATLAB (R2017b). However, between each iteration, only one element in the vector A changes, and so really it's only the values from that point onwards that change. I was wondering if there was a faster way of doing this? I have tried A(elementNumber:end) = A(elementNumber:end) - oldValue + newValue, but this isn't any faster.



Additionally, I then use the find() function at each iteration to find the first index in this cumulative sum matrix where the value first exceeds a certain value.



I was wondering if there was a faster way to perform either of these in MATLAB?



An example of the kind of code I am using is given below:


beta = 0.05;
S = randi(130, 15000, 1); I = randi(130, 15000, 1);
tmax = 10000; n=1; t(1) = 0; t1=0;
rates = (beta.*S.*I); cums = cumsum(rates); numI = sum(I);
Rtot = cums(end);
n=1; t(1) = 0; t1=0;
while t1<tmax
if n>1
newRate = beta*S(eventHouseNum)*I(eventHouseNum);
% rates(eventHouseNum) = beta*S(eventHouseNum)*I(eventHouseNum);
cums(eventHouseNum:end) = cums(eventHouseNum:end) - rates(eventHouseNum) + newRate;
rates(eventHouseNum) = newRate
end
Rtot = cums(end);
if Rtot==0
return
end
randNums = rand(2,1);
dt=-log(randNums(1))/Rtot;
P=randNums(2)*Rtot;
eventHouseNum = find(cums>=P,1);
S(eventHouseNum) = S(eventHouseNum)-1;
I(eventHouseNum) = S(eventHouseNum)+1;
numI = numI+1; n=n+1;
t(n)=t(n-1)+dt; t1=t(n);
Iarray1(n) = numI;
end





@Wolfie I've added a shortened example of the code. Is that okay, or is there still too much there?
– user112495
Aug 10 at 14:26






Profile your code, then check what makes it slow.
– Ander Biguri
Aug 10 at 15:05





@AnderBiguri I know it's definitely the cumsums and the finds that are taking up the majority of the time (along with generating the random numbers - but there's nothing I can do about that).
– user112495
Aug 10 at 15:12






@user112495 you can then probably produce a considerably smaller code for us to test
– Ander Biguri
Aug 10 at 15:14





@AnderBiguri I've produced something a bit simpler. In the above example, about 50% of the time is spent on cumsum(), and about 40% on find().
– user112495
Aug 10 at 15:35










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