MATLAB - Revision history

Dmitri: /* Support */

2023-10-18T19:36:29Z

Support

← Older revision		Revision as of 19:36, 18 October 2023
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	Please send any questions regarding using MATLAB on ARC to support@hpc.ucalgary.ca.		Please send any questions regarding using MATLAB on ARC to support@hpc.ucalgary.ca.

			= Links =

			[[ARC Software pages]]

	[[Category:MATLAB]]		[[Category:MATLAB]]

Lleung: Show ARC navbox

2023-09-21T18:14:59Z

Show ARC navbox

← Older revision		Revision as of 18:14, 21 September 2023
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	~~[[Category:MATLAB]]~~		= Introduction =
	~~[[Category:Software]]~~
	~~[[Category:ARC]]~~
	~~<span id~~=~~"contents"></span>~~
	~~= <span id="intro"></span>~~Introduction =

	[http://www.mathworks.com/ MATLAB] is a general-purpose high-level programming package for numerical work such as linear algebra, signal processing and other calculations involving matrices or vectors of data. Visualization tools are also included for presentation of results. The basic MATLAB package is extended through add-on components including SIMULINK, and the Image Processing, Optimization, Neural Network, Signal Processing, Statistics and Wavelet Toolboxes, among others.		[http://www.mathworks.com/ MATLAB] is a general-purpose high-level programming package for numerical work such as linear algebra, signal processing and other calculations involving matrices or vectors of data. Visualization tools are also included for presentation of results. The basic MATLAB package is extended through add-on components including SIMULINK, and the Image Processing, Optimization, Neural Network, Signal Processing, Statistics and Wavelet Toolboxes, among others.
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	Please send any questions regarding using MATLAB on ARC to support@hpc.ucalgary.ca.		Please send any questions regarding using MATLAB on ARC to support@hpc.ucalgary.ca.

	{{Navbox ~~Software~~}}		[[Category:MATLAB]]
			[[Category:Software]]
			[[Category:ARC]]
			{{Navbox ARC}}

Lleung: Added navbox

2023-09-20T22:28:14Z

Added navbox

← Older revision		Revision as of 22:28, 20 September 2023
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	Please send any questions regarding using MATLAB on ARC to support@hpc.ucalgary.ca.		Please send any questions regarding using MATLAB on ARC to support@hpc.ucalgary.ca.

			{{Navbox Software}}

Dmitri: /* Serial MATLAB example */

2022-11-24T16:48:12Z

Serial MATLAB example

← Older revision		Revision as of 16:48, 24 November 2022
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	end		end
	</syntaxhighlight>		</syntaxhighlight>
	In preparation to run the sawtooth.m code, create a batch job script, sawtooth.slurm of the form:		In preparation to run the <code>sawtooth.m</code> code, create a batch job script, <code>sawtooth.slurm</code> of the form:
	<syntaxhighlight lang=bash>		<syntaxhighlight lang=bash>
	#!/bin/bash		#!/bin/bash

Dmitri: /* Serial MATLAB example */

2022-11-24T16:46:40Z

Serial MATLAB example

← Older revision		Revision as of 16:46, 24 November 2022
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	<syntaxhighlight lang=bash>		<syntaxhighlight lang=bash>
	#!/bin/bash		#!/bin/bash
			# ==============================================================================
	#SBATCH --time=03:00:00 # Adjust this to match the walltime of your job		#SBATCH --time=03:00:00 # Adjust this to match the walltime of your job
	#SBATCH --nodes=1 # For serial code, always specify just one node.		#SBATCH --nodes=1 # For serial code, always specify just one node.
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	#SBATCH --cpus-per-task=1 # For serial code, always specify just one CPU per task.		#SBATCH --cpus-per-task=1 # For serial code, always specify just one CPU per task.
	#SBATCH --mem=4000m # Adjust to match total memory required, in MB.		#SBATCH --mem=4000m # Adjust to match total memory required, in MB.
			# ==============================================================================
	# Sample batch job script for running a MATLAB function with both numerical and string arguments		# Sample batch job script for running a MATLAB function with both numerical and string arguments
	~~# 2020-05-14~~

	~~# Specify the name of the main MATLAB function to be run.~~
	~~# This would normally be the same as the MATLAB source code file name without a .m suffix).~~
	~~MAIN="sawtooth"~~

	~~# Define key parameters for the example calculation.~~
	~~NTERMS=100~~
	~~NPPCYCLE=20~~
	~~NCYCLE=3~~
	~~PNGFILEBASE="sawtooth"~~

	~~# Contruct a complete function call to pass to MATLAB~~
	~~# Note, string arguments should appear to MATLAB enclosed in single quotes~~
	~~ARGS="($NTERMS,$NPPCYCLE,$NCYCLE,'$PNGFILEBASE')"~~
	~~MAIN_WITH_ARGS=${MAIN}${ARGS}~~

	~~echo "Calling MATLAB function: ${MAIN_WITH_ARGS}"~~

	~~echo "Starting run at $(date)"~~
	~~echo "Running on compute node $(hostname)"~~
	~~echo "Running from directory $(pwd)"~~

	~~# Choose a version of MATLAB by loading a module:~~
	module load matlab/r2019b		module load matlab/r2019b
	~~echo "Using MATLAB version: $(which matlab)"~~

	# Use -singleCompThread below for serial MATLAB code:		# Use -singleCompThread below for serial MATLAB code:
	matlab -singleCompThread -batch "~~${MAIN_WITH_ARGS}~~" ~~> ${MAIN}_${SLURM_JOB_ID}.out 2>&1~~		# Function call: sawtooth(NTerms, NPPCycles, NCycle, PNGFileBase)

			matlab -singleCompThread -batch "sawtooth(100,20,3,'sawtooth')"

	~~echo "Finished run at $(date)"~~		# ==============================================================================
	</syntaxhighlight>		</syntaxhighlight>

	Note that the above script uses the -batch option on the matlab command line. The MathWorks web page on [https://www.mathworks.com/help/matlab/ref/matlablinux.html running MATLAB on Linux (external link)] starting with Release 2019a of MATLAB, recommends using the -batch option for non-interactive use instead of the similar -r option that is recommended in interactive sessions.		Note that the above script uses the -batch option on the matlab command line. The MathWorks web page on [https://www.mathworks.com/help/matlab/ref/matlablinux.html running MATLAB on Linux (external link)] starting with Release 2019a of MATLAB, recommends using the -batch option for non-interactive use instead of the similar -r option that is recommended in interactive sessions.

Dmitri: /* Running MATLAB from command line */

2022-11-16T19:13:50Z

Running MATLAB from command line

← Older revision		Revision as of 19:13, 16 November 2022
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	$ matlab -batch "my_code(1, 2, 3)"		$ matlab -batch "my_code(1, 2, 3)"
	Note, that there is no extension <code>.m</code> (ending).		Note, that there is no extension <code>.m</code> (ending).

			If the function does not take any arguments, then this command will work too:
			$ matlab -batch my_code

	= Running MATLAB on the ARC cluster =		= Running MATLAB on the ARC cluster =

Dmitri: /* Running MATLAB from command line */

2022-11-16T16:31:45Z

Running MATLAB from command line

← Older revision		Revision as of 16:31, 16 November 2022
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	You can run such code from the '''command line''' with a command:		You can run such code from the '''command line''' with a command:
	$ matlab -batch my_code		$ matlab -batch "my_code(1, 2, 3)"
	Note, that there is no extension <code>.m</code> (ending).		Note, that there is no extension <code>.m</code> (ending).

Dmitri: /* Running MATLAB from command line */

2022-11-16T16:31:10Z

Running MATLAB from command line

← Older revision		Revision as of 16:31, 16 November 2022
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	= Running MATLAB from command line =		= Running MATLAB from command line =

	~~On the cluster the command line interface is the main way to run software.~~		Before you begin using '''MATLAB''' on a cluster, you have to know how to run your '''MATLAB''' programs (codes) from the '''command line'''.
	If you ~~have your~~ MATLAB ~~code in~~ a ~~text file, say <code>my_code.m</code>~~, you ~~can~~ run ~~it with a command:~~
	~~$ matlab -batch my_code~~

	~~Note, that there is no extension <code>.m</code>~~ (~~ending~~).

	The MATLAB code ~~in the~~ <code>my_code.m</code> must define a function with the same name and should end with the <code>quit; end</code> commands		The '''MATLAB''' code you want to run, say <code>my_code.m</code>, must define a function with the same name and should end with the <code>quit; end</code> commands
	<syntaxhighlight lang=matlab>		<syntaxhighlight lang=matlab>
	function my_code(arg1, arg2, arg3)		function my_code(arg1, arg2, arg3)
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	</syntaxhighlight>		</syntaxhighlight>
	to make sure that MATLAB exits at the end of the computation.		to make sure that MATLAB exits at the end of the computation.

			You can run such code from the '''command line''' with a command:
			$ matlab -batch my_code
			Note, that there is no extension <code>.m</code> (ending).

	= Running MATLAB on the ARC cluster =		= Running MATLAB on the ARC cluster =

Dmitri: /* Running MATLAB from command line */

2022-11-16T16:16:24Z

Running MATLAB from command line

← Older revision		Revision as of 16:16, 16 November 2022
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	Note, that there is no extension <code>.m</code> (ending).		Note, that there is no extension <code>.m</code> (ending).

	The MATLAB code in the <code>my_code.m</code> should end with the commands		The MATLAB code in the <code>my_code.m</code> must define a function with the same name and should end with the <code>quit; end</code> commands
	<syntaxhighlight lang=matlab>		<syntaxhighlight lang=matlab>
			function my_code(arg1, arg2, arg3)
			.....
			.....
	quit		quit
	end		end

Dmitri: /* Running a standalone application */

2022-11-16T16:12:01Z

Running a standalone application

← Older revision		Revision as of 16:12, 16 November 2022
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	echo "Finished run at $(date)"		echo "Finished run at $(date)"
	</~~pre~~>		</syntaxhighlight>

	The job is then submitted with sbatch:		The job is then submitted with sbatch:

	<pre>		<pre>
	sbatch sawtooth_standalone.slurm		$ sbatch sawtooth_standalone.slurm
	</~~syntaxhighlight~~>		</pre>

	An important part of the above script is the definition of the variable '''MCR''', which defines the location of the MATLAB Compiler Runtime (MCR) directory. This directory contains files necessary for the standalone application to run. The version of the MCR files specified (v97 in the example, which corresponds to MATLAB R2019b) must match the version of MATLAB used to compile the code.		An important part of the above script is the definition of the variable '''MCR''', which defines the location of the MATLAB Compiler Runtime (MCR) directory. This directory contains files necessary for the standalone application to run. The version of the MCR files specified (v97 in the example, which corresponds to MATLAB R2019b) must match the version of MATLAB used to compile the code.