MATLAB: How to use Matlab Compiler to make a stand alone script including simFunction Objects

MATLAB CompilerSimBiologysimfunctionstandalone

Hi,
I am currently trying to make a standalone version of my Matlab scripts in order to run it on a cluster. Unfortunately I am running into problems, when calling simFunctions (supplied by the SimBiology Toolbox).
In the Matlab terminal everything works just fine, but as soon as I compile it and do a test run through the terminal I get this error:
Warning: Variable 'Model' originally saved as a SimBiology.Model cannot be instantiated as an object and will be read in as a cell.
> In TEST_Script (line 2)
Undefined function or variable 'createSimFunction'.
Error in TEST_Script (line 5)
MATLAB:UndefinedFunction
I read http://ch.mathworks.com/products/compiler/supported/compiler_support.html that simBiology Models and simFunctions can be compiled.
Here is the code
%%Load Model

load Model;
%%Generate SimFunction

mySimFunction = createSimFunction(Model, {'Parameter_1','Parameter_2','Parameter_3','Parameter_4','Parameter_5','Parameter_6'},...
    {'Output_1','Output_2','Output_3','Output_4','Output_5'},[], 'UseParallel',false);
%%Generate Input

Input = [1,10,10,5,5,1000];
%%Evaluate SimFunction

stopTime = 100000;
[~,y] = mySimFunction(Input,[],[],stopTime);
Similarly, when I import only the simFunctions and omit generating them in the script I get this error:
> In TEST_Script2 (line 2)
Insufficient number of outputs from right hand side of equal sign to satisfy assignment.
Error in TEST_Script2 (line 9)
When using feval() for createSimFunction
%%Load Model
load Model;
fun = 'createSimFunction';
%%Generate SimFunction
mySimFunction = feval(fun,Model, {'Parameter_1','Parameter_2','Parameter_3','Parameter_4','Parameter_5','Parameter_6'},...
      {'Output_1','Output_2','Output_3','Output_4','Output_5'},[], 'UseParallel',false);
%%Generate Input
Input = [1,10,10,5,5,1000];
%%Evaluate SimFunction
stopTime = 100000;
[~,y] = mySimFunction(Input,[],[],stopTime);
myResult = vertcat(y{:});
I get this error:
Undefined function 'createSimFunction' for input arguments of type 'cell'.
I am grateful for any kind of help.
Thanks, Christoph
PS I am using MATLAB2015b, MRCv90
PPS I attached files

Best Answer

Steven is right with respect to the link he is refering to. After the loading of your simfunction in your file TEST, you need the line
 %#function SimBiology.function.SimFunction

In order to compile your code you need the following kind of code:
load mysimfunction;
accelerate(mySimFunction) %to accelerate the simulation of the simfunction
save('new_simfunction','mySimFunction') %save the accelerated simfunction
out=mySimFunction.DependentFiles;
mccCommand = ['mcc -m TEST.m -N -p simbio -a new_simfunction.mat -a lacI_Repression.mat' ...
    sprintf(' -a %s', out{:})]; %mention the use of the two mat files so that they are compiled into TEST.exe.
% The mex file of the accelerated version of the
% SimFunction needs to be included (out{:})
eval(mccCommand)
Note that it uses the accelerated SimFunction. Hence you need to load new_simfunction in TEST.m. The complete script TEST.m looks like as follows:
%%Generate simFunction Object
% The Model was exported from Matlab SimBiology by the export to workspace
% function. Afterwards it was saved as a .mat file.
%load('lacI_Repression.mat')
%mySimFunction = createSimFunction(Model,{'unnamed.DNA','unnamed.lacI'},{'unnamed.DNA_lacI'},[],'UseParallel',false);
%%Load simFunction
% loads the previouse generated simFunction (saved as a workspace .mat)
load new_simfunction;
%#function SimBiology.function.SimFunction
% needed to load the class SimFunction
%%Generate Input
% arbitrary inputs
Input = [100,500];
%%Evaluate SimFunction
stopTime = 100; % stoptime for the model
[~,y] = mySimFunction(Input,[],[],stopTime); % simFunction evaluation
myResult = vertcat(y{:}) % extracting the results from the cell array
%%END
I hope this helps.
Ingrid
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