I used MATLAB to write a simulation engine for the simulation of product flows in a production environment. I inherited all used class from handle and used these handles (quite excessively, I guess) to link between e.g. products and work systems, orders, etc.
Now, to run multiple instances of my model, I create a simulation object that contains all other objects and their relations, run the model and free the simulation variable.
Creating and running the model takes ~50 seconds (this including the generation of all objects, their relations and of course the calculation over the course of the simulation run). Freeing the variable before the next run, currently takes ~3-4 minutes!
I tried clear, delete and plain overwriting of the old simulation object, without notifying significant differences in performance.
Is there a way to improve the performance without rewriting the code?
Do you happen to use cell arrays to store other handle objects from within a handle object? This can cause serious slowdowns prior to Matlab R2011A. See http://www.mathworks.com/support/solutions/en/data/1-6VVMS0/index.html?product=ML
A workaround is to use a temp local variable to manipulate cell array, then assign this tmp variable back to your handle object property. I saw ~ 100X improvement in performance after doing this in one case.