Matlab < BETA

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---+ Using Matlab 

This page is part of the EmpiricalAlgorithmics web.

---++ Compiling Matlab

   * Code modification:
      * the 'main' function is an m-file (myFunction.m) that needs to be a function.
      * since all arguments are passed as strings, you need to convert numeric arguments to double when 'deployed':  

=if isdeployed=

=myArg1 !== str2double(myArg1); 

=end=

      * no 'addpath' calls allowed
      * for functions called by 'feval', you need to get them included by adding the following to myFunction.m:   =%#function myAnnonymousFunction=


   * Compilation:
To compile a function for stand-alone execution, start Matlab in the appropriate directory and type:   

=addpath(genpath(pwd)); % Add stuff to the path so compiler can find functions=

=mcc -m myFunction.m % Compile into a stand-alone=

(you can call mcc from outside matlab, but it needs to be called from within matlab to add anything to the path)


   * Execution:
      * Set the library environment variable so that it can find the matlab libraries: 

=setenv LD_LIBRARY_PATH /cs/local/generic/lib/pkg/matlab-7.3/bin/glnx86=  (or wherever matlab is installed, this can be added to .cshrc)

      * Run the stand-alone:   =myFunction=

---++ Submitting Compiled Matlab to the Arrow Cluster
The configuration that has worked was compiling on
arrow50@cs with Matlab 7.3 compiler/libraries.

Here is a compile.sh file (run from the 'root' code directory, where
$1 is the function you want to compile):

=#!/bin/sh=

=/cs/local/generic/lib/pkg/matlab-7.3/bin/matlab -nojvm -nosplash -nodesktop -nodisplay -r "addpath(genpath(pwd));mcc -m $1;exit;"=

Also, the arrow cluster uses bash instead of cshell, so the library
command needs to be:

=export LD_LIBRARY_PATH=/cs/local/generic/lib/pkg/matlab-7.3/bin/glnx86=

It appears that the right way to get environment variables set is to
set them on the qsub command line.  So on samos, set your
LD_LIBRARY_PATH to be what you want (adding in the matlab directory)
and then use the command

=qsub -v LD_LIBRARY_PATH=$LD_LIBRARY_PATH -o . -e . -cwd -t 4 ./script=

to submit the job.  $SGE_TASK_ID causes a complaint from Matlab, so you may need to send explicit integers instead.

-- Main.jtillett - 19 Apr 2007

---++ Common Errors
*Problem:* You compiled initially without a problem. You try recompiling and you get this:

=??? Error: File: somefile Line: 1 Column: 25=

=The input character is not valid in MATLAB statements or expressions.=

*Solution:* Delete the mcr directory.

*Problem:* You're trying to load a file that has an array of user objects, and when you run it you get an error message like:

=Warning: Class ':all:' is an unknown object class.  Element(s) of this class in array '' have been converted to structures.=

*Solution:* Use the line "%#function my_object" in your code

*Problem:* You're trying to compile a MATLAB code, and you get error like:

=connect xxx.cs.ubc.ca port 6000: Connection refused.=

*Solution:* run "setenv DISPLAY fake_display" before run MATLAB
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Topic revision: r5 - 2009-03-06 - xulin730