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How can I use Matlab Compiler to make a stand alone script including simFunction Objects

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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)
I read 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


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Accepted Answer

Ingrid Tigges
Ingrid Tigges on 24 Sep 2015
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
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{:})
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.
%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
I hope this helps.

More Answers (2)

Arthur Goldsipe
Arthur Goldsipe on 23 Sep 2015
Hi Christoph,
I believe you misread the compiler support page. "Regular" SimBiology models are listed in the "Cannot be compiled" column.
However, a SimFunction can be compiled. It looks like you tried this in TEST_Script2, but something went wrong. We should be able to get that to work, but I think you will need to provide the exact code (ideally including any MAT files loaded by the code). Can you attach those files to your question?

  1 Comment

Christoph Stelzer
Christoph Stelzer on 23 Sep 2015
Hi Arthur,
True, I did misread the page for the regular SimBiology Models.
Also, I attached the files.
Thank you, Christoph

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Steven Lord
Steven Lord on 23 Sep 2015
My suspicion is that you're running into the "Fixing Callback Problems: Missing Functions" problem described in the MATLAB Compiler documentation. Since the only places references to SimFunction appear are in the MAT-file (see the Tip in that section) or in the FEVAL statement, I think if you called createSimFunction directly (NOT via FEVAL) that would work.


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