One way is performing a time control with the tic and toc functions. For example, if code takes an hour, then break the loop:
% for loop
time0 = tic;
timeLimit = 60*60*1; % 1 hour == 3600 seconds
for ...
...
if toc(time0)>timeLimit
break
end
end
or using while loop:
time0 = tic;
timeLimit = 60*60*1; % 1 hour == 3600 seconds
while conds && toc(time0)<timeLimit
...
end