How to solve a compiler related problem to make a Parameter Fit run

I'm using simbiology Desktop in Matlab 2011a on OSX Mountain Lion. I just build a quite complicated model für an enzym-reaction-cascade an like to fit some of the unknown parameters to some data. The raw data is read in in a .xls-sheet and consists of one column for time and columns for intermediates and products.

T tried the individual fit function but i get a warning saying that "The reaction rates could not be accelerated du to a compiler related problem. Run the command "mex -setup" or ..." and an error message concerning the Fit Summary Plot Type - Line 17: Java exception occured... As I am using OSX i have already installed the latest Xcode Version and downloaded the patch as described in the Mathworks Compiler Help page. Could the problem be in the rate-equations? I already have changed the scope to the model. Any ideas?

Thanks!

Answer 1

[Arthur Goldsipe]

Hi Martin,

My guess is that MATLAB has still not been properly set up for use with Xcode. Were you following the instructions on the following page? http://www.mathworks.com/support/solutions/en/data/1-FR6LXJ/

My advice would be to check that mex is properly set up by trying to create one of the example MEX files. For example, try the following commands:

cd(matlabroot)
cd extern/examples/mex/
mex yprime.c

If the mex command givens an error, your compiler has not been set up correctly, and SimBiology will not be able to accelerate your model during fitting. In that case, double-check that you have followed the latest instructions posted on the page above, including the suggestion to install the old patch if the newer patch does not work correctly. (I had to use the old patch on the computer I tried.)

Once you have verified that mex is working correctly, try running the parameter fit again. I hope that will take care of the Java error as well.

If you are still running into problems, can you send me an email that includes your project? (I'm one of the SimBiology developers, so perhaps I can help diagnose the problem.)

-Arthur

[Martin]

Hi Arthur, Thank you very much for this answer. It helped me a lot to solve the problem. The prog finally runs.

Martin

[Paul]

Does the patch described work with Xcode v5.0.1, Matlab R2013b and OSX 10.9 (Mavericks)? What are the risks of applying an older patch with the sofware I have mentioned?

Many Thanks

Paul

[Ingrid Tigges]

Hi Paul,

did you have a look at this solution Can I use Xcode 5 as my C or C++ compiler in MATLAB 8.1 (R2013a) or MATLAB 8.2 (R2013b)? (1-OAMYBZ) already?

Ingrid