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Using_matlab.md

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Adjusting the number of threads

  • In matlab CLI >>> feature('numThreads',6)
    • or maxNumCompThreads(6) may work
  • If you want to use OMP_NUM_THREADS from the system variable, then >>> feature('numThreads',str2num(getenv('OMP_NUM_THREADS')))
    • If you want to use hybrid parallel computing with par-for, feature() must be done per workersCompThreads(). See below
parpool(npool)
a = zeros(nloop);
parfor i = 1:nloop
    workersCompThreads(i) = feature('numThreads',nthreads);
    a(i) = max(abs(eig(rand(nsize))));
end
sum(a)
poolobj = gcp('nocreate');
delete(poolobj);

or

parpool(npool)
a = zeros(nloop);
parfor i = 1:nloop
    maxNumCompThreads(nthreads);
    workersCompThreads(i) = maxNumCompThreads;
    a(i) = max(abs(eig(rand(nsize))));
end
poolobj = gcp('nocreate');
delete(poolobj);
  • matlab -singleCompThread will enforce to use one thread / one core only

Checking License status

Windows

  • cd c:\program files\matlab2013a\etc\win64 (or installed directory)
  • run “lmutil lmstat –a”

Linux

/opt/apps/matlab/R2014a/etc/glnxa64/lmutil lmstat -a -c 27000@license_server

Debugging in Linux CLI

Making MATLAB code into DLL

-Install Windows SDK - May have to remove pre-installed VC++ 2010 redistribution - http://www.mathworks.com/matlabcentral/answers/95039-why-does-the-sdk-7-1-installation-fail-with-an-installation-failed-message-on-my-windows-system

  • Run MATLAB
    • mex -setup
    • deploytool

When graphics crashes due to opengl

  • matlab -softwareopengl

Introduction to MATLAB standalone applications

What is a stand-alone application?

  • Your MATLAB script or program can be compiled using MATLAB compiler, running stand-alone - without MATLAB
    • This stand-alone requires MATLAB runtime library, which is free
    • No license required
    • Highly recommended for parametric study
  • You can save licenses of MATLAB and toolboxes
  • Stand-alone application might be faster than running from MATLAB platform

Sample tutorial to produce a stand-alone application

  • Prepare a text-based input file to control parameters. Save it as input.txt
#parpool
10
#Loop
100
#numThreads
4
#matrix size
1000
  • Note that parpool size is 10 while numThreads is 4. We test on Atom cluster, which has 40 cpus per node as 10 parpool X 4 numthreads
  • MATLAB script file is shown below. Save it as run_test.m
tic
fid = fopen('./input.txt');
line = fgetl(fid);line = fgetl(fid);npool = str2num(line)
line = fgetl(fid);line = fgetl(fid);nloop = str2num(line)
line = fgetl(fid);line = fgetl(fid);nthreads = str2num(line)
line = fgetl(fid);line = fgetl(fid);nsize = str2num(line)
fclose(fid);
%feature('numThreads',nthreads)
parpool(npool)
a = zeros(nloop);
parfor i = 1:nloop
    workersCompThreads(i) = feature('numThreads',nthreads);
    a(i) = max(abs(eig(rand(nsize))));
end
sum(a)
poolobj = gcp('nocreate');
delete(poolobj);
toc
  • This MATLAB scripts will execute eigen solver as many as nloop is required (dumb test). nloop is divided by par-for loop and each par-for loop will use nthreads for parallel eigen solver
  • Steps to produce stand-alone application
    • Linux CLI
      • module load matlab
      • mcc -m run_test.m # this may take 1-2 min
      • Produces mccExcludedFiles.log, requiredMCRProducts.txt, run_run_test.sh,readme.txt,run_test
      • Distribute run_run_test.sh and run_test binary file
      • input.txt will be necessary to control inputs
    • MATLAB GUI
      • module load matlab
      • matlab
      • Run "deploytool" from MATLAB command line, and select Application Compiler
      • Select or include source files
      • Click Package
      • It may take a couple of minutes ...
        • Will produce 3 folders as
            1. for_redistribution: Installer enclosed
            1. for_redistribution_files_only: Executables and script. You may use as it is
            1. for_testing: might be slower than for_redistribution
      • External files to be parsed in the matlab app are automatically included in the stand-alone application compilation
      • Even deleting the choice from the menu, it updates automatically anyway
      • Manually move such files from the folder temporarily

Running MATLAB stand alone applications

  • Command:
    • stand_alone_app.sh MATLAB_Runtime/vXX
      • The version of MATLAB Runtime must match with the MATLAB which produced the stand-alone application
    • Sample command: ./run_run_test.sh /usr/local/matlab/MATLAB_Runtime/v95
  • Scratch space 
#!/bin/bash
#PBS -q @myserver
#PBS -l select=1:ncpus=20:mpiprocs=20
#PBS -l walltime=100:00:00
echo $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
export TMPDIR=/scratch/$USER/tmp 
export SCRATCH=$TMPDIR/$PBS_JOBID
mkdir -p $SCRATCH
export  MCR_CACHE_ROOT=$SCRATCH
export V95LIB=/usr/local/matlab/MATLAB_Runtime/v95
export EXE=/home/foo/some_app/for_redistribution_files_only/run_my_app.sh 
$EXE $V95LIB
  • Note that the version of compiling MATLAB will determine the library of the stand-alone application. If the matlab code is compiled by 2018/b, then the stand alone application needs v95.