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

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

Answer 1

[Ingrid Tigges]

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

[Christoph Stelzer]

Great! Thanks a lot!

Answer 2

[Arthur Goldsipe]

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?

[Christoph Stelzer]

Hi Arthur,

True, I did misread the page for the regular SimBiology Models.

Also, I attached the files.

Thank you, Christoph

Answer 3

[Steven Lord]

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.