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I a medical researcher with code written in MATLAB 2009b that runs very slowly because of a self-referential loop (not sure of the programming lingo here), i.e., the results of the first iteration is used during the second iteration, etc. (I have vectorized it to a fare-thee-well. I have run the Profiler.)

I d like to convert the slow parts of the code to a mex function. I learned Fortran in the early 1970s but haven t used it since. The code I need to convert doesn t do anything fancy, it is just a long numerical calculation.

My question is: what would be the easiest-to-relearn version of Fortran adequate for this purpose, and what compiler works best on the Intel Mac for this? I found information comparing syntax in MATLAB to Fortran 90 for example, and the conversion doesn t look like it would be too daunting for me. However, again, I am no programmer.

I am using a MacBook Pro with OS 10.6.

Appreciate any help, thanks.

Answer 1

I d recommend using modern Fortran, at least 90/95 as the syntax is much more forgiving and almost all compilers now support it.

On a Mac I would recommend gfortran from here. It s not the most recent version, but it s well integrated with Apple build tools (you will need to install Xcode from your Mac OS DVD) and works well. In the numerical python community, which depends a lot of Fortran extensions, this build is highly recommended.

I haven t actually used fortran mex on the mac - but I think it should be fairly straightforward if you follow the mex documentation - and as you say translating code from Matlab to Fortran shouldn t be too bad (it s better if you can avoid calling Matlab functions, but fortran has sensible slicing and array access).

Answer 2

Well, you have probably found a solution already. However, I will say this: Matlab has been getting faster and faster. However making full use of Matlab s JIT is sometimes not intuitive. Mathworks used to say vectorize code for speed. Then they said write everything in explicit loops. I m actually not certain what the current best practice is.

What I m saying is, before you go to fortran, find out the best practice and implement it. That may give you enough of a speed-up right there.

Also, are you absolutely certain that you have isolated the slowdown to a loop? Have you been using the profiler? You probably have, since you sound experienced. I just thought I d mention it.

Good luck, Ariel

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