If you use the "sim" command to run a simulink model, via matlab code, you can use tic & toc to measure how long it took to complete.
tic;
sim(... ) % make sure the inputs are right for what you want.
toc
Alternatively, there are the "clock" and "now" matlab functions. I expect that you'll be able to put them into the model via embedded matlab (though, this will slow the simulation down)
