The files I would like to run are found here:
http://www.mathworks.co.uk/matlabcentral/fileexchange/12552-multicanonical-monte-carlo-scheme-for-finding-rare-growth-factors/content/mcmc2.m
it consists of 3 files, one of which is called a driver.
I have tried running each individual one in Matlab and each one gets an error, I think this is because I need to run them all simultaneously or something?
At the beginning of the driver script it says "This is the driver script to be run from the command line. Also requires functions mcmc1 and mcmc2". Where mcmc1 and mcmc2 are the other two files I tried running it in command line but I kept getting error messages..
Any idea how I get these files to run?
You should just be able to run gf_mmc_driver from the command line in Matlab. The mcmc1.m and mcmc2.m files need to be in your matlab path, but do not need to be called directly.
However, I do notice in the driver file the following comment:
% Telling the Distributed Computing Toolbox to complete one job with
% 'numberchain' tasks. Each task is comprised of running a MCMC
% for the burnin time (mcmc1.m) with a different initial matrix.
Do you have the Distributed Computing Toolbox? The driver file appears to require it.
Related
Matlab provides the sim command that can be used in a Matlab script to call and execute a Simulink model. But the function seems to be restricted to models that only run in Normal mode. When I try to call a Simulink model that runs in External mode, Matlab halts the script and flags it as an error. Besides being a nuisance it seems to me an unnecessary restriction on what could be a very useful application.
In any event is there a work around, perhaps a different command that I can use to run the Simulink diagram in External mode from the Matlab script?
I did try using the Matlab DOS shell command (using !) but it requires opening another instance of Matlab.
External Mode doesn't run a simulation, rather it is a mechanism for using the Simulink model's front end as a way of changing and viewing data that is running elsewhere (e.g. an executable running on the same machine as the model, or code running on an external processor).
To do that from the command line (or within code) you need to use a combination of the following commands:
>> set_param(gcs,'SimulationMode','external') % put model into External Mode
>> set_param(gcs,'SimulationCommand','connect') % connect to the executable
>> set_param(gcs,'SimulationCommand','start') % Start the executable
>> set_param(gcs,'SimulationCommand','stop') % Stop the executable
I need to use a toolbox in Matlab that depends on a external program written in C and using OpenCV. I'm using Ubuntu 14.04 64 bits and Matlab R2014b.
The m-script calls it with the system function and after the C program runs, it reads some output files that the C program should generate. This is failing to happen. I observed that the files are not being generated.
Then, the first thing I did was verify if the C program was working properly, by directly calling it in the terminal, with the same parameters that the m-script has used to call it. Then it worked and the files where generated. Thus, the C program is correct and working.
Coming back to Matlab, it failed again. Then, I started debugging the C program and had find out that the OpenCV function cvLoadImage is failing to open the file, when called from Matlab. It works if I call it outside.
I verified the string that is passed to the function both running from Matlab and externally and it is rigorously the same, but the Matlab call fails ever. I verified with ldconfig -p | grep opencv from the Matlab command window and it shows the libraries. More amusing, there are other calls to other ocv functions before the problematic one that are working. Just this is failing.
The question is: is this a problem of some misconfiguration of my part or maybe it is a bug in Matlab?
Thanks in advance.
EDIT
Actually, calling from inside Matlab with sudo appended to the system call got the job done. What is strange, because I used chmod 777 -Rf as last resource in the whole folder and verified that my user was the owner of both the folder and Matlab processes. Strange... It stills bothers me having to type my password whenever I use the script though, but my schedule is tight, I'll consider this workaround as satisfactory by now.
Instead of calling the C function from MATLAB, you can try to call MATLAB from your C code with MATLAB Engine API for C:
https://es.mathworks.com/help/matlab/calling-matlab-engine-from-c-programs-1.html
I got a problem when executing batch file commands through matlab. This batch file includes commands to run simulations in Adams. When I execute the batch file directly from DOS window, it works well. But if I use matlab to execute it (using command dos()), it gives error saying 'cannot check out the license for Adams'.
This confuses me: if the license is incorrect, it should not work no matter I execute the batch file directly in DOS or ask MATLAB to execute it. I also tried to execute other DOS commands through matlab using dos() and it worked well.
Does anyone know what the problem may be?
Such issues are commonly caused by some environment variables being changed or cleared by MATLAB. I have very similar experience on Linux and Mac OS X, where this causes havoc when using system or unix.
In Unix-like systems, MATLAB is started from a shell script where all of this happens. So you can either incorporate missing variables there or in the .matlab7rc.sh in your home directory (the latter is preserved when you upgrade MATLAB and it is much easier to use). I won't go into all the Unix details here.
An alternative workaround is to explicitly set those variables when you issue a system command (e.g. system('export variable=value ; ...')). It is quite a bit of work, but you can then use that MATLAB code on different computers with ease.
On Windows, I'm not completely sure about the exact location of the corresponding files (and whether MATLAB starts in quite a similar way as on Unix). But if they exist, you can probably find it in the MATLAB documentation.
Anyhow, the alternative fix should work here as well.
First you need to diagnose which system variables you need (likely a PATH or anything that has a name related to Adams).
To do so in Windows, run set from the Windows command prompt (cmd.exe) and from within MATLAB. Whatever differs in the output is a possible suspect for your problem.
To inspect just a single variable, you can use the command echo %variablename%.
I will assume that you have found that the suspect environment variable is missing and should be set to value.
The workaround fix is then to run your command in MATLAB as system('set suspect=value & ...') where you replace ... with your original command.
For a project I am working on I'm preparing data in MATLAB, then running the data through a separate external application (written in C++) named Model v2.exe, then performing further analysis with the output in MATLAB. I'm trying to create an M-file which does all of this, but I am struggling to get the C++ program to launch from my MATLAB code.
How can I launch an external application from within my MATLAB code?
You can either make use of the ! operator, or the system() command.
First, rename you application to something that has no spaces in the name, like modelv2.exe. Next, either make sure it is in the system path, as defined by your system environment variables, or generate a full path to it (eg: C:\Users\Phil\Desktop\modelv2.exe).
You can call an executable program from the command line using the exclamation point or the system command:
!modelv2
or:
!C:\Users\Phil\Desktop\modelv2.exe
will cause Windows to execute the program hello.exe if there is such a file in the current directory or on the system path. Alternatively:
system('modelv2');
or
system('C:\Users\Phil\Desktop\modelv2.exe');
will do the same thing.
References
"MATLAB Central - call and run an external program in matlab under windows", Accessed 2014-03-19, <http://www.mathworks.com/matlabcentral/answers/11568-call-and-run-an-external-program-in-matlab-under-windows>
I am trying to start Matlab and run a script scheduled at a specific time using the windows Task Scheduler.
If I use a scheduled task I can see Matlab starting, but this last fails to load the script and returns me the error below
??? Unexpected Matlab operator.
Do you know what it is and why?
I am using the following syntax
c:\app\matlab\bin\matlab.exe -r c:\MyURL\ScriptFile.m
If I load the script manually and run it it tells me that the file is not in the path so give ms a choice between
Change Current Directory
Add Folder to the Path
Either choices are fine and the script runs fine.
Matlab is starting in its main directory and -r requires your function to be in quotation marks, thats why you get the error.
And you need to change to your workspace first, the syntax is as follows:
matlab -sd pathToYourWorkspace -r "function(parameters)"
Maybe you also want to avoid the complete loading of the whole Matlab working environment, so add at the end:
-nodesktop -nosplash
If you run your task sheduled, are you doing it multiple times? Are you aware that every function call like above opens a new instance of Matlab? This question may be helpful then.
From the comments: of course you could just use the command run to call a script wherever it is.
"run('c:\MyURL\ScriptFile.m')" is an example for "functionName(YourArgs)"
as run is a function and the string 'c:\MyURL\ScriptFile.m' its argument. In this case it is usually not necessary to change the workspace before.