Your code for resetting "counter" is inside an if-test. You need to move it so that it always executes. E.g.,
%#Want to test numbers 2:n if they're prime
prompt = input('max number to test: ');
n = prompt;
l = 2; %#start of mod test
counter = 0;
tic
for i = 2:n %#cycle to test 2 up to n
t = floor(sqrt(i)); %#Only need to test up to root of number
counter = 0; % <-- Moved from below
for l = 2:t
if mod(i,l) == 0
break
else
counter = (counter + 1);
end
end
if counter == t-1 %# if tested up to the root of the number, it must be prime
prime = sprintf('%d is prime', round(i));
disp(prime)
% counter = 0; % <-- Moved to up above
end
end
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