I have no general advice. Perhaps if we saw a small snippet of your code we could help.
It is possible that your Jacobian is sparse, meaning it has a lot of zeros. In that case, it might be possible to avoid using matlabFunction at all, and simply use the JacobPattern option to have sparse finite differencing instead of time-consuming analytic calculations. Or perhaps there could be a hybrid sort of solution, where you explicitly calculate analytically (with matlabFunction) only the nonzero terms in the Jacobian. But this would require you to write a custom program.
Or it could be something as simple as declaring your symbolic variables to be real, which sometimes (but not often) saves time in matlabFunction.
Sorry I have nothing so helpful. There is simply a lot of calculation to be done, and it uses a lot of memory and time.
Alan Weiss
MATLAB mathematical toolbox documentation
