Currently I am testing out the use of my mentat toolbox for parallel computing within Matlab in combination with GridEngine on our linux cluster. Initially it worked fine, but that was because I was testing it with simple level Matlab functions like “rand” and “fft”. However, I am now trying to get it to work with more complex real-world scripts for EEG and MEG analysis that use the FieldTrip toolbox and I am running into a few problems:

I had to edit the file /opt/matlab-6.5.1/toolbox/matlab/iofun/private/readavi.m and rename the output argument “varargin” into “varargout”. I think that this is a plain bug in that function, which only becomes apparent after translating the code to c. The original file resulted in a compilation error, changing the output variable name fixed that.

Somehow, the code wants to include the Matlab function wk1read in the stand-alone executable. I cannot determine where that happens, because all functions are very deeply nested: mcc generates ~350 c-files on which my analysis function depends. The problem is that, after compilation, wk1read results in a unresolved symbol error. Since I am not interested in reading Lotus database stuff (which is what that particular function does), I have simply replaced it on my own Matlab search path with an alternative (empty) implementation for wk1read. That solved the unresolved symbol error.

Furthermore, I encountered a problems with the exist function. In the stand-alone executable, it does not seem to detect the existence of a variable. Since I am using that function on multiple locations throughout the code, I have to think of a nice workaround. Related to this problem I found this page which gives some relevant hints on using the Matlab compiler:

1. The following things cause a warning in compilation and may cause a runtime error if the offending statement is executed: objects, most toolboxes, inline, whos, some graphics functions that are passed functions by string.
2. Program compiled with graphics will not run without X windows. This includes running on beowulf nodes from PBS scripts.
3. Program containing graphics commands and compiled without graphics will produce compile time warning but will run fine as long as the graphics commands are not executed.
4. The following commands work differently: eval, feval, exist, global.
5. Use handles to pass functions rather than strings.
6. Do not use exist to check for the presence of arguments in a function.