Why don't I see a significant speed-up when using the MATLAB compiler?
I have a lot of nice MATLAB code that runs too slowly and would be a pain to write over in C. The MATLAB compiler for C does not seem to help much, if at all. Should it be speeding execution up more? Am I screwed?
I'll echo what dwj said: if your MATLAB code is slow, this is probably because it is not sufficiently vectorized. If you're doing explicit loops when you could be doing operations on whole arrays, that's the culprit.
This applies equally to all array-oriented dynamic languages: Perl Data Language, Numeric Python, MATLAB/Octave, etc. It's even true to some extent in compiled C and FORTRAN compiled code: specially-designed vectorization libraries generally use carefully hand-coded inner loops and SIMD instructions (e.g. MMX, SSE, AltiVec).
If you are using the MATLAB complier (on a recent version of MATLAB) then you will almost certainly not see any speedups at all. This is because all the compiler actually does is give you a way of packaging up your code so that it can be distributed to people who don't have MATLAB. It doesn't convert it to anything faster (such as machine code or C) - it merely wraps it in C so you can call it.
It does this by getting your code to run on the MATLAB Compiler Runtime (MCR) which is essentially the MATLAB computational kernel - your code is still being interpreted. Thanks to the penalty incurred by having to invoke the MCR you may find that compiled code runs more slowly than if you simply ran it on MATLAB.
Put another way - you might say that the compiler doesn't actually compile - in the traditional sense of the word at least.
Older versions of the compiler worked differently and speedups could occur in certain situations. For Mathwork's take on this go to
In my experience slow MATLAB code usually comes from not vectorizing your code (i.e., writing for-loops instead of just multiplying arrays (simple example)).
If you are doing file I/O look out for reading data in one piece at a time. Look in the help files for the vectorized version of fscanf.
Don't forget that MATLAB includes a profiler, too!