MatLab CLI - Revision history

Bhickson@uab.edu: /* Simple MATLAB Test */

2016-10-28T18:29:34Z

Simple MATLAB Test

← Older revision		Revision as of 18:29, 28 October 2016
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	Set up your environment with the command:		Set up your environment with the command:
	<pre>		<pre>
	$ module load rc/matlab/~~R2011a~~		$ module load rc/matlab/R2012a
	</pre>		</pre>
	As a test, you can run MatLab and access your license server with		As a test, you can run MatLab and access your license server with
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	For example:		For example:
	<pre>		<pre>
	$ module load rc/matlab/~~R2011a~~		$ module load rc/matlab/R2012a
	$ matlab -nodesktop -nojvm -r 'rand, pause(0), exit'		$ matlab -nodesktop -nojvm -r 'rand, pause(0), exit'

Bhickson@uab.edu: /* Simple MATLAB Test */

2016-10-28T18:28:59Z

Simple MATLAB Test

← Older revision		Revision as of 18:28, 28 October 2016
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	Set up your environment with the command:		Set up your environment with the command:
	<pre>		<pre>
	$ module load ~~mathworks~~/R2011a		$ module load rc/matlab/R2011a
	</pre>		</pre>
	As a test, you can run MatLab and access your license server with		As a test, you can run MatLab and access your license server with
Line 40:		Line 40:
	For example:		For example:
	<pre>		<pre>
	$ module load ~~mathworks~~/R2011a		$ module load rc/matlab/R2011a
	$ matlab -nodesktop -nojvm -r 'rand, pause(0), exit'		$ matlab -nodesktop -nojvm -r 'rand, pause(0), exit'

Bhickson@uab.edu: /* MATLAB Versions */

2016-10-28T18:28:31Z

MATLAB Versions

← Older revision		Revision as of 18:28, 28 October 2016
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	The following is an example output of the command and doesn't necessarily represent the currently installed versions:		The following is an example output of the command and doesn't necessarily represent the currently installed versions:
	<pre>		<pre>
	$ module avail ~~mathworks~~		$ module avail rc/matlab

	------------------------------------ /~~etc~~/modulefiles -------------------------------------		------------------------------------ /share/apps/modulefiles -------------------------------------
	~~mathworks~~/~~R2011b~~		rc/matlab/R2012a
	~~mathworks~~/~~R2011a~~		rc/matlab/R2012aa
	~~mathworks~~/~~R2010b~~		rc/matlab/R2013a
	~~mathworks~~/~~R2010a~~		rc/matlab/R2015a
	~~mathworks~~/~~R2010b~~		rc/matlab/R2015b
	~~mathworks~~/~~R2009b~~
	~~mathworks~~/~~R2009a~~

	</pre>		</pre>

Mhanby@uab.edu: replaced all references to $UABGRID_SCRATCH with $USER_SCRATCH

2013-05-22T19:27:18Z

replaced all references to $UABGRID_SCRATCH with $USER_SCRATCH

← Older revision		Revision as of 19:27, 22 May 2013
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	Note, the matlab command switch '-nojvm' dramatically decreases the amount of RAM needed to start MATLAB. The work performed by your job will determine whether or not it can be run with '-nojvm'		Note, the matlab command switch '-nojvm' dramatically decreases the amount of RAM needed to start MATLAB. The work performed by your job will determine whether or not it can be run with '-nojvm'
	<pre>		<pre>
	$ mkdir -p $~~UABGRID_SCRATCH~~/jobs/matlab/serial01/output		$ mkdir -p $USER_SCRATCH/jobs/matlab/serial01/output
	$ cd $~~UABGRID_SCRATCH~~/jobs/matlab/serial01		$ cd $USER_SCRATCH/jobs/matlab/serial01
	</pre>		</pre>
	<pre>		<pre>
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	Then submit the script to the scheduler with		Then submit the script to the scheduler with
	<pre>		<pre>
	$ cd $~~UABGRID_SCRATCH~~/jobs/matlab/serial01		$ cd $USER_SCRATCH/jobs/matlab/serial01
	$ qsub matlabtest.qsub		$ qsub matlabtest.qsub
	</pre>		</pre>
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	First, create the working directory for the job		First, create the working directory for the job
	<pre>		<pre>
	$ mkdir -p $~~UABGRID_SCRATCH~~/jobs/matlab/distrib01/output		$ mkdir -p $USER_SCRATCH/jobs/matlab/distrib01/output
	$ cd $~~UABGRID_SCRATCH~~/jobs/matlab/distrib01		$ cd $USER_SCRATCH/jobs/matlab/distrib01

	</pre>		</pre>
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	h_rt = '00:07:00'; % hard wall time		h_rt = '00:07:00'; % hard wall time
	vf = '1G'; % Amount of memory need per task		vf = '1G'; % Amount of memory need per task
	scratch = getenv('~~UABGRID_SCRATCH~~');		scratch = getenv('USER_SCRATCH');
	outputDirectory = [scratch, '/jobs/matlab/distrib01/output'];		outputDirectory = [scratch, '/jobs/matlab/distrib01/output'];

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	First, create the working directory for the job		First, create the working directory for the job
	<pre>		<pre>
	$ mkdir -p $~~UABGRID_SCRATCH~~/jobs/matlab/paralle01/output		$ mkdir -p $USER_SCRATCH/jobs/matlab/paralle01/output
	$ cd $~~UABGRID_SCRATCH~~/jobs/matlab/parallel01		$ cd $USER_SCRATCH/jobs/matlab/parallel01

	</pre>		</pre>
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	min_cpu_slots = 4; % Minimum number of cpu slots needed for the parallel job		min_cpu_slots = 4; % Minimum number of cpu slots needed for the parallel job
	max_cpu_slots = 8; % Maximum number of cpu slots needed for the parallel job		max_cpu_slots = 8; % Maximum number of cpu slots needed for the parallel job
	scratch = getenv('~~UABGRID_SCRATCH~~');		scratch = getenv('USER_SCRATCH');
	outputDirectory = [scratch, '/jobs/matlab/parallel01/output'];		outputDirectory = [scratch, '/jobs/matlab/parallel01/output'];

Tanthony@uab.edu: moved all changes to MATLAB R2011a

2011-11-14T18:08:56Z

moved all changes to MATLAB R2011a

← Older revision		Revision as of 18:08, 14 November 2011
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	------------------------------------ /etc/modulefiles -------------------------------------		------------------------------------ /etc/modulefiles -------------------------------------
			mathworks/R2011b
			mathworks/R2011a
	mathworks/R2010b		mathworks/R2010b
	mathworks/R2010a		mathworks/R2010a
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	Set up your environment with the command:		Set up your environment with the command:
	<pre>		<pre>
	$ module load mathworks/~~R2010b~~		$ module load mathworks/R2011a
	</pre>		</pre>
	As a test, you can run MatLab and access your license server with		As a test, you can run MatLab and access your license server with
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	For example:		For example:
	<pre>		<pre>
	$ module load mathworks/~~R2010b~~		$ module load mathworks/R2011a
	$ matlab -nodesktop -nojvm -r 'rand, pause(0), exit'		$ matlab -nodesktop -nojvm -r 'rand, pause(0), exit'

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	#$ -m eas		#$ -m eas
	#		#
	module load mathworks/~~R2010a~~		module load mathworks/R2011a
	#$ -V		#$ -V

	matlab ~~-c 27000@lmgr.uabgrid.uab.edu~~ -nodisplay -nojvm < matlab-script		matlab -nodisplay -nojvm < matlab-script
	</pre>		</pre>

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	<pre>		<pre>
	% Always set these variables		% Always set these variables
	matlab_ver = '~~R2010b~~'; % (MATLAB release supported by your license) R2009a R2009b R2010a		matlab_ver = 'R2011a'; % (MATLAB release supported by your license) R2009a R2009b R2010a
	email = 'YOUREMAIL'; % your email address		email = 'YOUREMAIL'; % your email address
	email_opt = 'eas'; % qsub email options		email_opt = 'eas'; % qsub email options
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	<pre>		<pre>
	$ module load mathworks/R2010a		$ module load mathworks/R2010a
	$ matlab ~~-c port@license-server~~ -nodisplay < sharedDistrib01.m		$ matlab -nodisplay < sharedDistrib01.m
	</pre>		</pre>

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	<pre>		<pre>
	% Always set these variables		% Always set these variables
	matlab_ver = '~~R2010a~~'; % (MATLAB release supported by your license) R2009a R2009b R2010a		matlab_ver = 'R2011a'; % (MATLAB release supported by your license) R2009a R2009b R2010a
	email = 'YOUREMAIL'; % your email address		email = 'YOUREMAIL'; % your email address
	email_opt = 'eas'; % qsub email options		email_opt = 'eas'; % qsub email options
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	Running the MATLAB script will submit 1 SGE job requesting 4 slots (cpu cores). The Parallel Computing Toolbox requires Java VM, so notice that for this job we do not include the "-nojvm" switch!		Running the MATLAB script will submit 1 SGE job requesting 4 slots (cpu cores). The Parallel Computing Toolbox requires Java VM, so notice that for this job we do not include the "-nojvm" switch!
	<pre>		<pre>
	$ module load mathworks/~~R2010a~~		$ module load mathworks/R2011a
	$ matlab ~~-c port@license-server~~ -nodisplay < sharedPar01.m		$ matlab -nodisplay < sharedPar01.m
	</pre>		</pre>

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	<pre>		<pre>
	1. Login to the Cheaha head node with X using: ssh -X USERID@cheaha.uabgrid.uab.edu		1. Login to the Cheaha head node with X using: ssh -X USERID@cheaha.uabgrid.uab.edu
	2. load the Matlab module: module load mathworks/~~R2010b~~		2. load the Matlab module: module load mathworks/R2011a
	3. Start Matlab in X using: matlab ~~-c 27000@lmgr.uabgrid.uab.edu~~		3. Start Matlab in X using: matlab
	</pre>		</pre>

Tanthony@uab.edu: /* Simple MATLAB Test */ chages to remove pointing to license server

2011-11-14T18:05:30Z

Simple MATLAB Test: chages to remove pointing to license server

← Older revision		Revision as of 18:05, 14 November 2011
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	As a test, you can run MatLab and access your license server with		As a test, you can run MatLab and access your license server with
	<pre>		<pre>
	$ matlab ~~-c port@license-server~~ -nodesktop -nojvm -r 'rand, pause(0), exit'		$ matlab -nodesktop -nojvm -r 'rand, pause(0), exit'
	</pre>		</pre>

			or create an 'm file' and run it as
			<pre>
			$ matlab -nodesktop -nojvm <temp.m
			</pre>

	For example:		For example:
	<pre>		<pre>
	$ module load mathworks/R2010b		$ module load mathworks/R2010b
	$ matlab ~~-c 27000@lmgr.uabgrid.uab.edu~~ -nodesktop -nojvm -r 'rand, pause(0), exit'		$ matlab -nodesktop -nojvm -r 'rand, pause(0), exit'

	< M A T L A B (R) >		< M A T L A B (R) >
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	</pre>		</pre>



	This will start matlab without a graphical display and without Java support. This is good just to		This will start matlab without a graphical display and without Java support. This is good just to
	verify things work, but do not run any significant computations on the Cheaha head node!		verify things work, but do not run any significant computations on the Cheaha head node!

Tanthony@uab.edu: /* Distributed MATLAB */

2011-11-14T18:02:55Z

Distributed MATLAB

← Older revision		Revision as of 18:02, 14 November 2011
Line 169:		Line 169:
	Running the MATLAB script will submit 2 SGE single slot (CPU) jobs, one for each task. The Parallel Computing Toolbox requires Java VM, so notice that for this job we do not include the "-nojvm" switch!		Running the MATLAB script will submit 2 SGE single slot (CPU) jobs, one for each task. The Parallel Computing Toolbox requires Java VM, so notice that for this job we do not include the "-nojvm" switch!

	Additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s \| workshop demo ]] ~~section~~.		Additional examples and submit scripts available on the [[MATLAB_workshop_2011#Workshop_Demo.27s \| MATLAB workshop 2011 demo ]] page.

	<pre>		<pre>

Tanthony@uab.edu: /* Distributed MATLAB */ added link to workshop demo

2011-11-14T18:01:36Z

Distributed MATLAB: added link to workshop demo

← Older revision		Revision as of 18:01, 14 November 2011
Line 168:		Line 168:

	Running the MATLAB script will submit 2 SGE single slot (CPU) jobs, one for each task. The Parallel Computing Toolbox requires Java VM, so notice that for this job we do not include the "-nojvm" switch!		Running the MATLAB script will submit 2 SGE single slot (CPU) jobs, one for each task. The Parallel Computing Toolbox requires Java VM, so notice that for this job we do not include the "-nojvm" switch!

			Additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s \| workshop demo ]] section.

	<pre>		<pre>
	$ module load mathworks/R2010a		$ module load mathworks/R2010a

Tanthony@uab.edu: /* Distributed MATLAB */

2011-11-14T17:58:34Z

Distributed MATLAB

← Older revision		Revision as of 17:58, 14 November 2011
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	createTask(job, @rand, 1, {3,3});		createTask(job, @rand, 1, {3,3});
	createTask(job, @rand, 1, {3,3});		createTask(job, @rand, 1, {3,3});
			% createTask(job, @USERFUNCTION, 1, {options}); % this can call a user m file instead of an inbuilt
			% function , please make sure that the user defined
			% function is in the MATLAB path)


	submit(job)		submit(job)

Mhanby@uab.edu at 20:04, 11 November 2011

2011-11-11T20:04:08Z

← Older revision		Revision as of 20:04, 11 November 2011
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	* YOUR_EMAIL_ADDRESS		* YOUR_EMAIL_ADDRESS
	* h_rt and s_rt to appropriate hard and soft runtime limits		* h_rt and s_rt to appropriate hard and soft runtime limits
	* ~~h_vmem~~ to the maximum amount of memory that your job will use		* vf to the maximum amount of memory that your job will use

	Note, the matlab command switch '-nojvm' dramatically decreases the amount of RAM needed to start MATLAB. The work performed by your job will determine whether or not it can be run with '-nojvm'		Note, the matlab command switch '-nojvm' dramatically decreases the amount of RAM needed to start MATLAB. The work performed by your job will determine whether or not it can be run with '-nojvm'
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	#		#
	#$ -N serialMatlab		#$ -N serialMatlab
	#$ -l h_rt=00:10:00,s_rt=00:08:00,~~h_vmem~~=2G		#$ -l h_rt=00:10:00,s_rt=00:08:00,vf=2G
	#$ -j y		#$ -j y
	#		#