Matlab use cases - Revision history

Tanthony@uab.edu: /* Reserve your Computer */

2017-03-09T19:20:41Z

Reserve your Computer

← Older revision		Revision as of 19:20, 9 March 2017
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	<pre>		<pre>
	sinteractive --ntasks=4 --mem-per-cpu=1024 --time=8:00:00 --partition=medium		sinteractive --ntasks=1 --cpus-per-task=4 --mem-per-cpu=1024 --time=8:00:00 --partition=medium
	</pre>		</pre>
	The above resource request asks for a computer with 4 cores and 1 gigabyte of RAM/core (total 4GB ram) for 8 hours.		The above resource request asks for a computer with 4 cores and 1 gigabyte of RAM/core (total 4GB ram) for 8 hours.

Tanthony@uab.edu: /* Use Matlab on a compute node with a scheduled batch script */

2017-02-22T14:21:25Z

Use Matlab on a compute node with a scheduled batch script

← Older revision		Revision as of 14:21, 22 February 2017
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	#!/bin/bash		#!/bin/bash
	#		#
	#SBATCH --job-name=~~test~~		#SBATCH --job-name=matTest
	#SBATCH --output=res.txt		#SBATCH --output=res.txt
	#SBATCH --ntasks=1		#SBATCH --ntasks=1
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	module load rc/matlab/R2016b		module load rc/matlab/R2016b
	srun matlab -nodesktop -nodisplay -r Test1Fib.m		srun matlab -nodesktop -nodisplay -r Test1Fib
	srun sleep 60		srun sleep 60

	</pre>		</pre>
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	<pre>		<pre>
	$ squeue -u $USER		$ squeue -u $USER
	359705 express ~~test~~ tanthony R 0:03 1 c0005		359705 express matTest tanthony R 0:03 1 c0005
	</pre>		</pre>

Tanthony@uab.edu: /* Use Matlab on a compute node batch script */ added and tested

2017-02-22T14:07:51Z

Use Matlab on a compute node batch script: added and tested

← Older revision		Revision as of 14:07, 22 February 2017
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	Some use cases describing how to offload MATLAB computation to the cluster.		Some use cases describing how to offload MATLAB computation to the cluster.
	== Use Matlab on a compute node batch script ==		== Use Matlab on a compute node with a scheduled batch script ==
	A shared cluster environment like Cheaha uses a job scheduler to run tasks on the cluster to provide optimal resource sharing among users. Cheaha uses a job scheduling system call Slurm to schedule and manage jobs. A user needs to tell Slurm about resource requirements (e.g. CPU, memory) so that it can schedule jobs effectively. These resource requirements along with actual application code can be specified in a single file commonly referred as 'Job Script/File'. Following is a simple job script that prints job number and hostname.		A shared cluster environment like Cheaha uses a job scheduler to run tasks on the cluster to provide optimal resource sharing among users. Cheaha uses a job scheduling system call Slurm to schedule and manage jobs. A user needs to tell Slurm about resource requirements (e.g. CPU, memory) so that it can schedule jobs effectively. These resource requirements along with actual application code can be specified in a single file commonly referred as 'Job Script/File'. Following is a simple job script that prints job number and hostname.

Line 27:		Line 27:

	Following is the matlabSubmit.sbatch		Following is the matlabSubmit.sbatch
	Please edit he email address and the processor cores/memory requirement according to your jobs		Please edit the email address and the processor cores/memory requirement according to your jobs
	<pre>		<pre>
	#!/bin/bash		#!/bin/bash
Line 60:		Line 60:
	This shows that the job is running on compute node c0005		This shows that the job is running on compute node c0005
	The working directory should have two new files res.txt and out1.mat		The working directory should have two new files res.txt and out1.mat




	== Use Matlab on a compute node via VNC ==		== Use Matlab on a compute node via VNC ==

Tanthony@uab.edu: Added script for matlab

2017-02-22T14:06:53Z

Added script for matlab

← Older revision		Revision as of 14:06, 22 February 2017
Line 1:		Line 1:
	Some use cases describing how to offload MATLAB computation to the cluster.		Some use cases describing how to offload MATLAB computation to the cluster.
			== Use Matlab on a compute node batch script ==
			A shared cluster environment like Cheaha uses a job scheduler to run tasks on the cluster to provide optimal resource sharing among users. Cheaha uses a job scheduling system call Slurm to schedule and manage jobs. A user needs to tell Slurm about resource requirements (e.g. CPU, memory) so that it can schedule jobs effectively. These resource requirements along with actual application code can be specified in a single file commonly referred as 'Job Script/File'. Following is a simple job script that prints job number and hostname.


			Following is a sample script to generate Fibonacci series from 1-10 and save the output
			<pre>
			%% Job Test on Cheaha with SLURM - Test1Fib.m
			% Submit Job with matlabSubmit.sbatch
			% Output Files out.mat
			% Create Fibonacci Series upto 10

			% clear all
			% close all

			limit = 10 % Fibonacci series from 1 to limit
			c(1)=0; % first element
			c(2)=1; % second element

			for i=3:limit
			c(i)=c(i-1)+c(i-2);
			end
			c % Displays the output on screen
			save('out1.mat') % Saves the workspace to mat file
			exit
			</pre>

			Following is the matlabSubmit.sbatch
			Please edit he email address and the processor cores/memory requirement according to your jobs
			<pre>
			#!/bin/bash
			#
			#SBATCH --job-name=test
			#SBATCH --output=res.txt
			#SBATCH --ntasks=1
			#SBATCH --partition=express
			#SBATCH --time=10:00
			#SBATCH --mem-per-cpu=100
			#SBATCH --mail-type=FAIL
			#SBATCH --mail-user=YOUR_EMAIL_ADDRESS

			module load rc/matlab/R2016b
			srun matlab -nodesktop -nodisplay -r Test1Fib.m
			srun sleep 60

			</pre>

			The above job can be submitted by
			<pre>
			$ sbatch matlabSubmit.sbatch
			Submitted batch job 359705
			</pre>

			You can check the job status using squeue command
			<pre>
			$ squeue -u $USER
			359705 express test tanthony R 0:03 1 c0005
			</pre>

			This shows that the job is running on compute node c0005
			The working directory should have two new files res.txt and out1.mat




	== Use Matlab on a compute node via VNC ==		== Use Matlab on a compute node via VNC ==

Tanthony@uab.edu: /* Reserve your Computer */

2017-02-08T14:03:09Z

Reserve your Computer

← Older revision		Revision as of 14:03, 8 February 2017
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	<pre>		<pre>
	sinteractive --ntasks=4 --mem-per-cpu=1024 --time=14:00:00 --partition=medium		sinteractive --ntasks=4 --mem-per-cpu=1024 --time=8:00:00 --partition=medium
	</pre>		</pre>
	The above resource request asks for a computer with 4 cores and 1 gigabyte of RAM/core (total 4GB ram) for 4 hours.		The above resource request asks for a computer with 4 cores and 1 gigabyte of RAM/core (total 4GB ram) for 8 hours.

	=== Start Matlab ===		=== Start Matlab ===

Tanthony@uab.edu: edited pages for sitneractive

2017-02-08T14:02:43Z

edited pages for sitneractive

← Older revision		Revision as of 14:02, 8 February 2017
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	The third step is to request a computer on which you can run Matlab. In your cluster desktop terminal window, submit a resource request to reserve a compute node for running Matlab		The third step is to request a computer on which you can run Matlab. In your cluster desktop terminal window, submit a resource request to reserve a compute node for running Matlab
	<pre>		<pre>
	~~qlogin~~ -~~l vf~~=~~1G,h_rt~~=4:00:00 -~~now no~~		sinteractive --ntasks=1 --mem-per-cpu=1024 --time=4:00:00 --partition=medium
	</pre>		</pre>
	The above resource request asks for a computer with 1 gigabyte of RAM for 4 hours. You can adjust these values to suit your needs but you should try to make reasonable estimates to ensure that resources are shared fairly. WARNING: the specified time limit is a hard boundary and can't be changed after you start Matlab. When this time limit is reached, your Matlab session will be automatically stopped, without warning, by the cluster resource manager.		The above resource request asks for a computer with 1 gigabyte of RAM for 4 hours. You can adjust these values to suit your needs but you should try to make reasonable estimates to ensure that resources are shared fairly. WARNING: the specified time limit is a hard boundary and can't be changed after you start Matlab. When this time limit is reached, your Matlab session will be automatically stopped, without warning, by the cluster resource manager.

	<pre>		<pre>
	~~qlogin~~ -~~l vf~~=~~1G,h_rt~~=4:00:00 -~~pe smp 4~~ -~~now no~~		sinteractive --ntasks=4 --mem-per-cpu=1024 --time=14:00:00 --partition=medium
	</pre>		</pre>
	The above resource request asks for a computer with 4 cores and 1 gigabyte of RAM/core (total 4GB ram) for 4 hours.		The above resource request asks for a computer with 4 cores and 1 gigabyte of RAM/core (total 4GB ram) for 4 hours.
Line 28:		Line 28:
	The fourth and final step is to start Matlab on the compute resource you have reserved. In the same terminal window from which you made the resource request (ie. ran "qlogin"), run the following commands to start matlab.		The fourth and final step is to start Matlab on the compute resource you have reserved. In the same terminal window from which you made the resource request (ie. ran "qlogin"), run the following commands to start matlab.
	<pre>		<pre>
	module load ~~mathworks~~/~~R2012a~~		module load rc/matlab/R2016b
	matlab		matlab
	</pre>		</pre>

Tanthony@uab.edu: /* Reserve your Computer */

2014-03-20T14:08:43Z

Reserve your Computer

← Older revision		Revision as of 14:08, 20 March 2014
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	The third step is to request a computer on which you can run Matlab. In your cluster desktop terminal window, submit a resource request to reserve a compute node for running Matlab		The third step is to request a computer on which you can run Matlab. In your cluster desktop terminal window, submit a resource request to reserve a compute node for running Matlab
	<pre>		<pre>
	qlogin -l vf=1G,h_rt=4:00:00		qlogin -l vf=1G,h_rt=4:00:00 -now no
	</pre>		</pre>
	The above resource request asks for a computer with 1 gigabyte of RAM for 4 hours. You can adjust these values to suit your needs but you should try to make reasonable estimates to ensure that resources are shared fairly. WARNING: the specified time limit is a hard boundary and can't be changed after you start Matlab. When this time limit is reached, your Matlab session will be automatically stopped, without warning, by the cluster resource manager.		The above resource request asks for a computer with 1 gigabyte of RAM for 4 hours. You can adjust these values to suit your needs but you should try to make reasonable estimates to ensure that resources are shared fairly. WARNING: the specified time limit is a hard boundary and can't be changed after you start Matlab. When this time limit is reached, your Matlab session will be automatically stopped, without warning, by the cluster resource manager.

Tanthony@uab.edu: /* Reserve your Computer */ added for multiple cores

2014-03-20T14:08:13Z

Reserve your Computer: added for multiple cores

← Older revision		Revision as of 14:08, 20 March 2014
Line 19:		Line 19:
	</pre>		</pre>
	The above resource request asks for a computer with 1 gigabyte of RAM for 4 hours. You can adjust these values to suit your needs but you should try to make reasonable estimates to ensure that resources are shared fairly. WARNING: the specified time limit is a hard boundary and can't be changed after you start Matlab. When this time limit is reached, your Matlab session will be automatically stopped, without warning, by the cluster resource manager.		The above resource request asks for a computer with 1 gigabyte of RAM for 4 hours. You can adjust these values to suit your needs but you should try to make reasonable estimates to ensure that resources are shared fairly. WARNING: the specified time limit is a hard boundary and can't be changed after you start Matlab. When this time limit is reached, your Matlab session will be automatically stopped, without warning, by the cluster resource manager.

			<pre>
			qlogin -l vf=1G,h_rt=4:00:00 -pe smp 4 -now no
			</pre>
			The above resource request asks for a computer with 4 cores and 1 gigabyte of RAM/core (total 4GB ram) for 4 hours.

	=== Start Matlab ===		=== Start Matlab ===

Jpr@uab.edu: /* Use MATLAB on a compute node via VNC */ Updated text for easier navigation.

2013-02-06T17:53:32Z

Use MATLAB on a compute node via VNC: Updated text for easier navigation.

← Older revision		Revision as of 17:53, 6 February 2013
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	Some use cases describing how to offload MATLAB computation to the cluster.		Some use cases describing how to offload MATLAB computation to the cluster.

	== Use ~~MATLAB~~ on a compute node via VNC ==		== Use Matlab on a compute node via VNC ==

	This ~~entails~~ running a MATLAB ~~client (GUI) via VNC~~ on a compute node on [[Cheaha]].		This use case creates an ordinary Matlab session, just like you would on your desktop, however, instead of running MATLAB you your desktop, you run MATLAB on a compute node of the [[Cheaha\|cluster]] and access it's GUI via your cluster desktop.

	This is ~~a typical use case~~ in ~~the following scenarios~~		This is useful in situations where your personal desktop or laptop is not powerful enough to run your Matlab code or you simply want to offload a long-running computation so you can free your desktop or laptop for other activities.
	~~# Computation needs~~ to ~~be offloaded~~ to a ~~compute node on the cluster to~~ free ~~the user's~~ desktop for ~~development~~
	~~# Computation is too large to be performed on the user's desktop and needs more resources~~

	The ~~vnc~~ session ~~needs to be setup in two stages as described in~~ [[~~Setting_Up_VNC_Session~~]].		=== Connect to Your Cluster Desktop ===
			The first step is to connect to an existing cluster desktop session via VNC. Please follow the steps for [[Setting_Up_VNC_ Session\|setting up a VNC session]] to create your cluster desktop and connect to it.

	~~It will~~ open a ~~vnc~~ window ~~with a terminal~~ on the ~~cheaha~~.		=== Open a Terminal ===
			The second step is to open a terminal window on your cluster desktop. Once you are connected to your cluster desktop, start the Terminal application from the cluster desktop menu Applications->Accessories->Terminal.

	~~To portforward and login~~ to a compute node ~~use the following command from the terminal in the vnc session~~		=== Reserve your Computer ===
			The third step is to request a computer on which you can run Matlab. In your cluster desktop terminal window, submit a resource request to reserve a compute node for running Matlab
	<pre>		<pre>
	$ qlogin -l vf=~~memory~~,h_rt=hr:~~min~~:~~sec~~		qlogin -l vf=1G,h_rt=4:00:00
	</pre>		</pre>
			The above resource request asks for a computer with 1 gigabyte of RAM for 4 hours. You can adjust these values to suit your needs but you should try to make reasonable estimates to ensure that resources are shared fairly. WARNING: the specified time limit is a hard boundary and can't be changed after you start Matlab. When this time limit is reached, your Matlab session will be automatically stopped, without warning, by the cluster resource manager.

	~~Load~~ the ~~mathworks module and~~ start matlab		=== Start Matlab ===
	<pre>$ module load mathworks/R2012a		The fourth and final step is to start Matlab on the compute resource you have reserved. In the same terminal window from which you made the resource request (ie. ran "qlogin"), run the following commands to start matlab.
	$ matlab		<pre>
			module load mathworks/R2012a
			matlab
	</pre>		</pre>
	~~MATLAB will now start interactively in the VNC session and is running on the compute node on Cheaha.~~


			Matlab will be running your reserved compute resource and can be controlled interactively via the VNC session. This Matlab session works just like the Matlab sessions on your personal desktop or laptop. When you are finished using Matlab, simply exit the application as you normally would. Your compute resource will automatically return to the resource pool at the end of the your requested reservation time or you can type "exit" to return it immediately.

	{{MATLAB Support}}		{{MATLAB Support}}

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

Tanthony@uab.edu: /* Use MATLAB on a compute node via VNC */

2013-02-06T17:04:01Z

Use MATLAB on a compute node via VNC

@@ Line 9: / Line 9: @@
 # Computation is too large to be performed on the user's desktop and needs more resources
-The vnc session needs to be setup in two stages"
+The vnc session needs to be setup in two stages as described in [[Setting_Up_VNC_Session]].
 It will open a vnc window with a terminal on the cheaha.
@@ Line 54: / Line 18: @@
 </pre>
 Load the mathworks module and start matlab
-<pre>$ module load mathworks/R2011b
+<pre>$ module load mathworks/R2012a
 $ matlab
 </pre>
-MATLAB will now start interactively in the VNC session and is running ont he compute node on Cheaha.
+MATLAB will now start interactively in the VNC session and is running on the compute node on Cheaha.