1. Compiled Matlab on Condor: a recipe 30 th October 2007 Clare Giacomantonio

2. How to format your m-file function testfunction(input1,input2) % change arguments to numerics if necessary input1 = num2str(input1); input2 = num2str(input2); % computation sumofinputs = input1 + input2; % save output outputfilename = [ ' testfunction_ ' num2str(input1) ' _ ' num2str(input2)]; save(outputfilename, ' input1 ', ' inputs2 ', ' sumofinputs ' ) turn it into a function all arguments are strings - change to numerics if necessary use a dynamic filename for the output or make it one of the input arguments don’t create figures

3. Motivation Each instance of Matlab uses up a license so logging lots of Matlab jobs can quickly use up all the licenses stopping more of your jobs running and/or preventing others from using Matlab. Compiled Matlab does not use a license. - Matlab or the Matlab Component Runtime (MCR) still need to be installed. - All machines in the Condor pool have Matlab installed.

4. Compile your m-file Must compile on the same operating system as you want to run on. At the Matlab command line >> mcc -m testfunction.m -R -nojvm This creates a single executable and a testfunction.ctf file. - It also creates a lot of other files which we don’t need. There’s only one compiler license! - Don’t forget to close Matlab after you finish compiling to release the license. Not all Matlab functions compile. See list at http://www.mathworks.com/products/compiler/compiler_s upport.html

5. Running compiled Matlab from the terminal If you want to check that your function runs as desired from the command line, need to run from a script which sets the library path first. #!/bin/bash export MATLAB_ROOT=/opt/matlab-7.4 export LD_LIBRARY_PATH=${MATLAB_ROOT}/sys/opengl/lib/glnx86: ${MATLAB_ROOT}/sys/java/jre/glnx86/jre1.5.0/lib/i386: ${MATLAB_ROOT}/sys/java/jre/glnx86/jre1.5.0/lib/i386/ server:${MATLAB_ROOT}/sys/java/jre/glnx86/jre1.5.0/li b/i386/client:${MATLAB_ROOT}/sys/java/jre/glnx86/jre1.5.0/lib/i386/native_threads:${MATLAB_ROOT}/bin/glnx8 6:${MATLAB_ROOT}/sys/os/glnx86: export XAPPLRESDIR=${MATLAB_ROOT}/X11/app-defaults./testfunction 10 20

6. Condor submit script To schedule jobs in Condor you need a condor submit script. In this script - You must include executable and.ctf at transfer_input_files. - You must set the environment variable LD_LIBRARY_PATH. Other methods may work! This is just one way that I found works.

7. Now submit your jobs Put Matlab executable,.ctf, any data files used as inputs and condor_submit script in the directory InputDir. Make sure OutputDir exists. Submit your jobs to Condor at the command line condor_submit testfunction.sub

8. Outputs Any text normally written to the Matlab command window is saved in the output file. Any data files generated will appear in OutputDir.

9. What happens when an owner interrupts your job? The job re-starts again on another machine. It may be possible to implement checkpointing in your function by periodically saving the workspace and loading the workspace as a input if it exists.

10. Using Matlab on Condor Pros - Easy to set-up if your code compiles. - Can access DICE home directory. - Compiled Matlab doesn’t use up Matlab licenses. Cons - Some Matlab functions don’t compile. - Jobs restart if machine is reclaimed so only good for < 12 hour jobs.