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MATLAB Release (Patch level)

MATLAB Compiler Runtime

Comment
R2020bR2021a


Code Block
languagebash
> module remove intel-mpi
> module load intel-mpi/2018-intel
> module load matlab/R2020bR2021a-generic



Code Block
languagebash
> module remove intel-mpi
> module load intel-mpi/2018-intel
> module load matlab-mcr/R2020bR2021a-generic


R2020bR2021a

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.


R2020aR2020b
(Update 5)


Code Block
languagebash
> module remove intel-mpi
> module load intel-mpi/2018-intel
> module load matlab/R2020aR2020b_Update5-generic



Code Block
languagebash
> module remove intel-mpi
> module load intel-mpi/2018-intel
> module load matlab-mcr/R2020aR2020b_Update5Update3-generic


R2020aR2020b
(Update 53)


Warning

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


R2019bR2020a
(Update 75)


Code Block
languagebash
> module remove intel-mpi
> module load intel-mpi/2018-intel
> module load matlab/R2019bR2020a_Update7Update5-generic



Code Block
languagebash
> module remove intel-mpi
> module load intel-mpi/2018-intel
> module load matlab-mcr/R2019bR2020a_Update7Update5-generic


R2019aR2020a
(Update 7)5)


Warning

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


Trouble Loading MATLAB Module

...

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/%x.%j.%N.out
#SBATCH -e ./out/%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=10000M
#SBATCH --time=0:30:00
# As needed, remove/adjust memory requirement "--mem" in MB

module load slurm_setup
module load matlab/R2020bR2021a-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/%x.%j.%N.out
#SBATCH -e ./out/%x.%j.%N.err
#SBATCH -D ./
#SBATCH -J matlab_threading_batch_job
#SBATCH --get-user-env
#SBATCH --export=NONE
#SBATCH --clusters=cm2_tiny
#SBATCH --partition=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/R2020bR2021a-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/%x.%j.%N.out
#SBATCH -e ./out/%x.%j.%N.err
#SBATCH -D ./
#SBATCH -J matlab_pct_batch_job
#SBATCH --get-user-env
#SBATCH --export=NONE
#SBATCH --clusters=cm2_tiny
#SBATCH --partition=cm2_tiny
#SBATCH --nodes=1
#SBATCH --tasks-per-node=4
#SBATCH --cpus-per-task=1
#SBATCH --time=00:30:00

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

module load slurm_setup
module load matlab/R2020bR2021a-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, 'serial') || ...
       strcmp(cluster, 'mpp3') || ...
       strcmp(cluster, 'ivymuc')
    % batch job
    nw = str2num(getenv('SLURM_NTASKS'));
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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