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MATLAB can be used by loading its module. We highly recommend to choose a particular – better: the newest – version, e. g.:

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languagebash

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Supported Releases of MATLAB and MATLAB Compiler Runtime

R2019bloadmatlab/R2019b-genericmatlabmcrR2019b-genericR2019a_Update5matlab-R2019a

MATLAB Release (Patch level)

MATLAB Compiler Runtime

Comment
R2021a


Code Block
languagebash
> module 
remove 
Code Block
languagebash
intel-mpi
> module load 
intel-
mpi/
R2019brecommended versionR2019a (Update 5)
Code Block
languagebash
2018-intel
> module load matlab/
R2021a-generic



Code Block
languagebash
> module remove intel-mpi
> module load 
intel-mpi/2018-intel
> module matlab-mcr/
R2021a-generic


R2021aR2019a

Trouble Loading MATLAB Module

The MATLAB module is not visible and, thus, cannot be loaded. Try to get access to the current software stack via following command. Then continue using "module avail" or "module load".

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recommended version

Warning

Using the default Intel-MPI module (Version 2019), unintended crashes of parallel MATLAB jobs might occur. Please switch to Intel MPI 2018.


R2020b
(Update 5)


Code Block
languagebash
> module 

...

remove 

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intel-mpi
> module load intel-mpi/2018-intel
> module load matlab/R2020b_Update5-generic



Code Block
languagebash
> module 

...

remove intel-

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Note

This is a fallback solution! Old software stacks are not supported anymore! Some MATLAB features might not work because according configurations refer to the CoolMUC-2 system used before March 2020!

Useful MATLAB Commands

Please consider: All MATLAB commandline arguments are case-sensitive!

Start MATLAB GUI:

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languagebash

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mpi
> module load intel-mpi/2018-intel
> module load matlab-mcr/R2020b_Update3-generic


R2020b
(Update 3)


Warning

Using the default Intel-MPI module (Version 2019), unintended crashes of parallel MATLAB jobs might occur. Please switch to Intel MPI 2018.


R2020a
(Update 5)


Code Block
languagebash
> module remove intel-mpi
> module load intel-mpi/2018-intel
> module load matlab/R2020a_Update5-generic



Code Block
languagebash
> module remove intel-mpi
> module load intel-mpi/2018-intel
> module load matlab-mcr/R2020a_Update5-generic


R2020a
(Update 5)


Warning

Using the default Intel-MPI module (Version 2019), unintended crashes of parallel MATLAB jobs might occur. Please switch to Intel MPI 2018.


Useful MATLAB Commands

Run MATLAB via the "matlab" command only or add command-line arguments. Please consider: All MATLAB command-line arguments are case-sensitive!

Code Block
languagebash
> matlab arg_1 ... arg_N


Command-line argumentMeaning
no argumentStart MATLAB GUI.
-nodesktop
Start MATLAB without desktop but allow GUI and graphics output

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languagebash

...

.
-nodisplay
Start MATLAB without any GUI support

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languagebash

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.
Code Block
languagebash
> matlab -nodisplay

Some intrinsic MATLAB functions automatically exploit multithreading. MATLAB can be forced to disable this feature, which is important on login nodes:

-singleCompThread

Some intrinsic MATLAB functions automatically exploit multithreading. MATLAB can be forced to disable this feature.


Warning

Use this option for any work on the login nodes!

Involving multiple threads (many MATLAB functions/operators use that by default) might cause a high load on the node and handicapping other users! MATLAB applications, which use multiple threads or multiple processes on login nodes, will be terminated by system administrators!


-r myfunc
Run a MATLAB script or function

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languagebash

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, e. g. myfunc.m.

Interactive MATLAB Jobs in a Nutshell – the Convenient Way

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Usecases

Depending on the purpose, there are different possibilities to use MATLAB interactively:

  • MATLAB computations with focus on visualisation: We recommend to use our Remote Visualisation System.
  • Pure MATLAB computations: Interactive MATLAB sessions may be started on compute nodes of CoolMUC-2 or CoolMUC-3 by employing interactive Slurm jobs (see Slurm documentation).

Constraints

  • Interactive jobs depend on the availability of compute resources. Matlab may not start immediately.
  • Matlab will run on 1 compute node.
  • The time limit is set to 2 hours (= maximum time for interactive Slurm sessions).

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Slurm job scriptMatlab script

Serial batch job

Warning

No parallelization at all, MATLAB is intended to run on a single core.
Please , use the "serial" cluster of the Linux Cluster!



Code Block
languagebash
titlematmul_serial.slurm
linenumberstrue
collapsetrue
#!/bin/bash
#SBATCH -o ./out/matlab_job%x.%j.%N.out
#SBATCH -e ./out/matlab_job%x.%j.%N.err
#SBATCH -D ./
#SBATCH -J matlab_serial_batch_job
#SBATCH --get-user-env
#SBATCH --export=NONE
#SBATCH --clusters=serial
#SBATCH --partition=serial_std
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=1000010000M
#SBATCH --time=0:30:00
# As needed, remove/adjust memory requirement "--mem" in MB

module load slurm_setup
module load matlab/R2019bR2021a-generic

# Example: matrix-matrix multiplication C = A*B
#          with A of size NROWA x NCOLA and
#          B of size NROWB x NCOLB
NROWA=1000
NCOLA=2000
NROWB=2000
NCOLB=5000

# Run MATLAB
# => Using option -r don't add file extension .m to the function call!
# => MATLAB commandline arguments are case-sensitive!
matlab -nodisplay -singleCompThread \
       -r "matmul_serial([$NROWA $NCOLA], [$NROWB $NCOLB]);"



Code Block
languagetext
titlematmul_serial.m
linenumberstrue
collapsetrue
function [C, comptime] = matmul_serial(size_A, size_B)

%===============================================================================
% MATLAB EXAMPLE: SERIAL HELLO WORLD
%                 -> matrix-matrix multiplication C = A*B
%
% INPUT
%   size_A, size_B ... 2-element row vectors defining sizes of A and B
% OUTPUT
%   C ................ result
%   comptime ......... computation time (matrix product only)
%===============================================================================

%===============================================================================
% Check input
%===============================================================================
if nargin~=2
    error('Invalid number of input arguments!');
end
if size_A(2)~=size_B(1)
    error(sprintf('Dimension mismatch of A (%d columns) and B (%d rows)!',...
                  size_A(2), size_B(1)));
end

%===============================================================================
% Work
%===============================================================================
% Hello message from compute node
fprintf('Hello from MATLAB process PID=%d running on node %s!\n',...
        feature('getpid'),...
        strtrim(evalc('system(''hostname'');')));

% generate well-defined matrices
NA = prod(size_A);
NB = prod(size_B);
A = reshape( linspace( 1,NA, NA), size_A );
B = reshape( linspace(NB, 1, NB), size_B );

% compute
tic;
C = A*B;
comptime = toc;
fprintf('serial computation of matrix-matrix product:\n');
fprintf('\ttime = %.2f s\n', comptime);


Parallel job using multithreading

Warning

MATLAB will run on a single compute node.
Please use the partition "cm2_tiny" in cluster "cm2_tiny"!



Code Block
languagebash
titlematmul_mthread.slurm
linenumberstrue
collapsetrue
#!/bin/bash
#SBATCH -o ./out/matlab_job%x.%j.%N.out
#SBATCH -e ./out/matlab_job%x.%j.%N.err
#SBATCH -D ./
#SBATCH -J matlab_threading_batch_job
#SBATCH --get-user-env
#SBATCH --export=NONE
#SBATCH --clusters=cm2
#SBATCH --partition=cm2_tiny
#SBATCH --qospartition=cm2_tiny
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task=14
#SBATCH --time=00:30:00

module load slurm_setup
module load matlab/R2019bR2021a-generic

# Example: matrix-matrix multiplication C = A*B
#          with A of size NROWA x NCOLA and
#          B of size NROWB x NCOLB
NROWA=1000
NCOLA=2000
NROWB=2000
NCOLB=5000

# Run MATLAB
# => Using option -r don't add file extension .m to the function call!
# => MATLAB commandline arguments are case-sensitive!
matlab -nodisplay \
       -r "matmul_mthread([$NROWA $NCOLA], [$NROWB $NCOLB]);"



Code Block
languagetext
titlematmul_mthread.m
linenumberstrue
collapsetrue
function [C, comptime] = parallel_mthread(size_A, size_B)

%===============================================================================
% MATLAB EXAMPLE: PARALLEL HELLO WORLD USING MULTITHREADING
%                 -> matrix-matrix multiplication C = A*B
%
% INPUT
%   size_A, size_B ... 2-element row vectors defining sizes of A and B
% OUTPUT
%   C ................ result
%   comptime ......... computation time (matrix product only)
%===============================================================================

%===============================================================================
% Check input
%===============================================================================
if nargin~=2
    error('Invalid number of input arguments!');
end
if size_A(2)~=size_B(1)
    error(sprintf('Dimension mismatch of A (%d columns) and B (%d rows)!',...
                  size_A(2), size_B(1)));
end

%===============================================================================
% Manage multithreading
%===============================================================================
% Get number of threads depending on job type (batch job or interactive job).
% In batch jobs 1 MATLAB task will use "nw" threads. 
%
% obtain number of threads from Slurm environment variables
cluster = getenv('SLURM_CLUSTER_NAME');
if strcmp(cluster, 'inter')
    % interactive job
    nw = str2num(getenv('SLURM_JOB_CPUS_PER_NODE'));
elseif strcmp(cluster, 'cm2_tiny') || ...
       strcmp(cluster, 'mpp3') || ...
       strcmp(cluster, 'ivymuc')
    % batch job
    nw = str2num(getenv('SLURM_CPUS_PER_TASK'));
else
    % default
    nw = 1;
end
% set threads
maxNumCompThreads(nw);

%===============================================================================
% Work
%===============================================================================
fprintf('Hello from MATLAB process PID=%d running on node %s!\n',...
        feature('getpid'),...
        strtrim(evalc('system(''hostname'');')));

% generate well-defined matrices
NA = prod(size_A);
NB = prod(size_B);
A = reshape( linspace( 1,NA, NA), size_A );
B = reshape( linspace(NB, 1, NB), size_B );

% compute
tic;
C = A*B;
comptime = toc;
fprintf('parallel computation (multithreading) of matrix-matrix product:\n');
fprintf('\tnumber of threads = %d\n', nw);
fprintf('\ttime = %.2f s\n', comptime);


Parallel batch job using Parallel Computing Toolbox (PCT)

Warning

MATLAB will run on a single compute node.
Please use the partition "cm2_tiny" in cluster "cm2_tiny"!



Code Block
languagebash
titlematmul_pct.slurm
linenumberstrue
collapsetrue
#!/bin/bash
#SBATCH -o ./out/matlab_job%x.%j.%N.out
#SBATCH -e ./out/matlab_job%x.%j.%N.err
#SBATCH -D ./
#SBATCH -J matlab_pct_batch_job
#SBATCH --get-user-env
#SBATCH --export=NONE
#SBATCH --clusters=cm2
#SBATCH --partition=cm2_tiny
#SBATCH --qospartition=cm2_tiny
#SBATCH --nodes=1
#SBATCH --tasks-per-node=4
#SBATCH --cpus-per-task=1
#SBATCH --time=00:30:00

module load slurm_setup

# IMPORTANT
# Default settings of Intel MPI module may disrupt 
# functionality of Parallel-Computing-Toolbox!
# Do one of the following solutions:  
# (1) Unload Intel MPI module:
module mpi.intel:rm intel-mpi
module rm mpi.intel
# (2) If Intel MPI module is mandatory, adduncomment next line 2 lines
# module load intel-mpi/2018-intel
# export KMP_AFFINITY=granularity=thread,none

module load slurm_setup
module load matlab/R2019bR2021a-generic

# Example: matrix-matrix multiplication C = A*B
#          with A of size NROWA x NCOLA and
#          B of size NROWB x NCOLB
NROWA=1000
NCOLA=2000
NROWB=2000
NCOLB=5000

# Run MATLAB
# => Using option -r don't add file extension .m to the function call!
# => MATLAB commandline arguments are case-sensitive!
matlab -nodisplay -singleCompThread \
       -r "matmul_pct([$NROWA $NCOLA], [$NROWB $NCOLB]);"



Code Block
languagetext
titlematmul_pct.m
linenumberstrue
collapsetrue
function [Cglob, comptime] = matmul_pct(size_A, size_B)

%===============================================================================
% MATLAB EXAMPLE: PARALLEL HELLO WORLD USING PCT TOOLBOX
%                 -> matrix-matrix multiplication C = A*B
%
% INPUT
%   size_A, size_B ... 2-element row vectors defining sizes of A and B
% OUTPUT
%   C ................ result
%   comptime ......... computation time (matrix product only)
%===============================================================================

%===============================================================================
% Check input
%===============================================================================
if nargin~=2
    error('Invalid number of input arguments!');
end
if size_A(2)~=size_B(1)
    error(sprintf('Dimension mismatch of A (%d columns) and B (%d rows)!',...
                  size_A(2), size_B(1)));
end

%===============================================================================
% Verify that no parallel pool is initialized by creating/deleting a dummy pool
%===============================================================================
if ~isempty(gcp('nocreate'))
    poolobj = gcp('nocreate');
    delete(poolobj);
end

%===============================================================================
% Start parallel pool
%===============================================================================
% Get number of workers depending on job type. Start parallel pool via "local"
% cluster object.
%
% obtain number of tasks from Slurm environment variables
cluster = getenv('SLURM_CLUSTER_NAME');
if strcmp(cluster, 'inter')
    % interactive job
    nw = str2num(getenv('SLURM_JOB_CPUS_PER_NODE'));
elseif strcmp(cluster, 'cm2_tiny') || ...
          strcmp(cluster, 'serialcm2') || ...
       strcmp(cluster, 'mpp3serial') || ...
       strcmp(cluster, 'ivymucmpp3')
    % batch job
    nw = str2num(getenv('SLURM_NTASKS_PER_NODE'));
else
    % default
    nw = 1;
end

% disallow Threading
if maxNumCompThreads > 1
    maxNumCompThreads(1);
    warning('MultiThreading: number of threads has been set to 1!');
end

% create a local cluster object
pc = parcluster('local');
% set number of workers
pc.NumWorkers = nw;
% set the JobStorageLocation to SCRATCH (default: HOME -> not recommended)
pc.JobStorageLocation = strcat(getenv('SCRATCH'));
% start the parallel pool
poolobj = parpool(pc, nw);

%===============================================================================
% Work
%===============================================================================
spmd
    fprintf('Hello from MATLAB process PID=%d running on node %s!\n',...
            feature('getpid'),...
            getenv('HOSTNAME'));
end

% generate well-defined matrices
NA = prod(size_A);
NB = prod(size_B);
A = reshape( linspace( 1,NA, NA), size_A );
B = reshape( linspace(NB, 1, NB), size_B );

% distribute data to workers and do parallel computation
spmd
    Aloc = codistributed(A, codistributor2dbc([nw 1]));
    Bloc = codistributed(B, codistributor2dbc([1 nw]));
    tic;
    Cloc = Aloc*Bloc;
    t = toc;
end

comptime = max(cell2mat(t(:)));
fprintf('parallel computation (MPI) of matrix-matrix product:\n');
fprintf('\tnumber of tasks (MATLAB workers) = %d\n', nw);
fprintf('\ttime = %.2f s\n', comptime);

Cglob = gather(Cloc);

%===============================================================================
% Close parallel pool
%===============================================================================
delete(poolobj);


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