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software:matlab [2019/09/09 11:21] jrutte02 [Usage] 
— (current) 
====== Mathworks MATLAB ======  
{{ http://upload.wikimedia.org/wikipedia/commons/thumb/2/21/Matlab_Logo.png/267pxMatlab_Logo.png?100&nocache}} MATLAB (matrix laboratory) is a multiparadigm numerical computing environment and fourthgeneration programming language. Developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, and Fortran. (taken from http://en.wikipedia.org/wiki/MATLAB, more details there)  
 
[[http://www.mathworks.de/products/matlab/]]\\  
 
 
 
^ Matlab ^^  
**Version:**R2017a  
**Lizenz:**[[http://www.unimainz.deUniversity of Mainz]]  
**Developer**:Mathworks  
**Toolboxes:**Curve Fitting, Fuzzy Logic, Image Processing, Mapping, Compiler, Compiler SDK, Optimization, Parallel Computing, Partial Differential Equation, Signal Processing, Statistics and Machine Learning, Symbolic Math, Wavelet  
 
====== Usage ======  
Use  
<code shell>  
$ module load math/MATLAB  
</code>  
 
to load the most recent version available.  
 
See the vendor documentation: [[https://www.mathworks.com/help/matlab/]]  
 
====== Using MatlabCompiler ======  
 
There are several options to compile your Matlab code to standalone executables/libraries. Being independent of licenses is one of the major advantages here, of course. But when running compiled code with the Matlab Runtime Envirenment (MRE) on the cluster you have to consider the threading of your code just as well as when you run Matlab itself.  
Generally, Matlab detects the number of physical cores and opens the same amount of threads to make full use of the multithreading implemented in the builtin functions. So, if you call  
<code> mcc m my_mfile.m </code> you obtain multithread code. Often this might be wanted, but you have to make sure that you select the appropriate resources for this then  namely, the appropriate coreaffinity. Since Matlab wants to use everything on a host you'll have to call '' bsub n 1 R 'affinity[cores(64)]' '' and an appropriate memory reservation.  
On the other hand, if your code doesn't need the full multithreading capability, which often is the case, you should compile your code with the flag 'singleCompThread' <code> mcc m R singleCompThread my_mfile.m </code>. This makes sure that your standalone code will run on a single computational thread, which not only doesn't frustrate the core scheduler and the other users less but improves performance of your code because less time is spent in scheduling all the threads on one core.  
 
====== Examples ======  
===== Submitting a Matlab job =====  
 
The flag ''nojvm'' starts Matlab without the Java virtual machine, ''nodisplay'' instructs Matlab to run without the GUI, ''nosplash'' prevents Matlab from displaying the Matlab logo and ''r'' defines the name of the script you want to run.\\  
**Notice:** Save your file with the ''.m'' extension, but call it without the ''.m'' extension.  
 
For full nodes consider  
 
<code shell>  
#SBATCH p nodeshort # Queue name  
#SBATCH n 32 # Total number of tasks  
#SBATCH c 2 # Total number of cores  
</code>  
as Matlab will not be able to fully utilize the node, but considers every FPU equal to a CPU.  
===== Compiling a mfile on a node =====  
 
Using the following shell script you can compile a mfile into a standalone c application. It's a variation of the script for [[:local_scratchusing local scratch on a node]].  
 
<file bash compileFile.sh>  
#!/bin/bash  
 
# Store working directory to be safe  
SAVEDPWD=`pwd`  
FILENAME=$1  
 
# We define a bash function to do the cleaning when the signal is caught  
cleanup(){  
cp /jobdir/${LSB_JOBID}/*$FILENAME.sh ${SAVEDPWD}/  
cp /jobdir/${LSB_JOBID}/$FILENAME ${SAVEDPWD}/  
exit 0  
}  
 
# Register the cleanup function when SIGUSR2 is sent, ten minutes before the job gets killed  
trap 'cleanup' SIGUSR2  
 
# Copy input file  
cp ${SAVEDPWD}/$FILENAME.m /jobdir/${LSB_JOBID}/  
 
# Go to jobdir and start the program  
cd /jobdir/${LSB_JOBID}  
mcc m $FILENAME.m  
 
# Call the cleanup function when everything went fine  
cleanup  
</file>  
 