MatLab DCS R2010b 2011a 2011b - Revision history

Tanthony@uab.edu: deprecated banner

2017-03-10T00:35:56Z

deprecated banner

← Older revision		Revision as of 00:35, 10 March 2017
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			{{Matlab_deprecated}}

	=== MATLAB DCS from Your Desktop ===		=== MATLAB DCS from Your Desktop ===

Tanthony@uab.edu: /* Validate the "cheaha" PCT Configuration */ new /scratch/user/location

2013-06-12T16:40:48Z

Validate the "cheaha" PCT Configuration: new /scratch/user/location

← Older revision		Revision as of 16:40, 12 June 2013
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	===== Validate the "cheaha" PCT Configuration =====		===== Validate the "cheaha" PCT Configuration =====

	# Before starting validation please make sure the directory 'lustre/scratch/YOURUSERID/matlab' exists on the ~~lustre~~ scratch space on the Cheaha. If it does not please SSH into Cheaha and create the directory before proceeding.		# Before starting validation please make sure the directory 'lustre/scratch/YOURUSERID/matlab' (please convert all settings to point to the new preferred location) or ''''/scratch/user/YOURUSERID/matlab'''' (preferred) exists on the scratch space on the Cheaha. If it does not please SSH into Cheaha and create the directory before proceeding.
	# Select Cheaha on the configuration manager page and click 'Start Validation'		# Select Cheaha on the configuration manager page and click 'Start Validation'
	# Wait for the validation to complete. This might take a few minutes and you ask for User credentials on Cheaha. All tests other than 'Matlabpool' validate on the Cheaha and the output is as shown.		# Wait for the validation to complete. This might take a few minutes and you ask for User credentials on Cheaha. All tests other than 'Matlabpool' validate on the Cheaha and the output is as shown.

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

2013-05-22T19:31:33Z

replaced all references to $UABGRID_SCRATCH with $USER_SCRATCH

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	#* '''SubmitFcn''' : Change the text "YOURUSERID" to your login id on Cheaha		#* '''SubmitFcn''' : Change the text "YOURUSERID" to your login id on Cheaha
	# Click 'OK'to save the configuration		# Click 'OK'to save the configuration
	# SSH to cheaha and make sure to create the $~~UABGRID_SCRATCH~~/matlab directory. If this directory does not exist, the parallel computing toolbox jobs will fail.		# SSH to cheaha and make sure to create the $USER_SCRATCH/matlab directory. If this directory does not exist, the parallel computing toolbox jobs will fail.

	The initial configuration will look similar to this screen shot. You will need to edit the fields as describe in the preceding steps before you can use the configuration. '''NOTE: be sure to replace the template user name settings "YOURUSERNAME" with the appropriate settings for your desktop and cluster account.'''		The initial configuration will look similar to this screen shot. You will need to edit the fields as describe in the preceding steps before you can use the configuration. '''NOTE: be sure to replace the template user name settings "YOURUSERNAME" with the appropriate settings for your desktop and cluster account.'''

Tanthony@uab.edu: added sub category matlab installation

2012-03-12T17:55:39Z

added sub category matlab installation

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

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

Tanthony@uab.edu: Page started :Added support and category

2012-03-08T16:54:06Z

Page started :Added support and category

New page

=== MATLAB DCS from Your Desktop ===

==== MATLAB Submit Functions ====

The MATLAB submit functions create a cluster job context for your code and are responsible for transferring your code and the data it analyzes to the cluster for processing.

These submit functions must be installed on your computer and must be accessible to MATLAB via the MATLAB PATH environment. The easiest way to accomplish this is to copy the submit functions to the default directory created for by MATLAB. These directories on the respective operating systems are listed below.

All operating systems (Windows, Linux and Mac) are supported by the same set of submit functions. The functions are written in MATLAB making them cross-platform and only dependent on the version of MATLAB in use.

# Download the MATLAB submit functions
#* [http://projects.uabgrid.uab.edu/matlab/browser/trunk/distributables/matlab-R2011b-nonshared.zip?format=raw Submit Functions for MATLAB R2010b, R2011a, R2011b] -(updated 02/21/2011)
# Unzip the files to a directory included in your MATLAB PATH setting. Recommended locations are:
#* Windows: <pre>My Documents\MATLAB</pre>
#* Linux: <pre>$HOME/Documents/MATLAB</pre>
#* Mac: <pre>$HOME/Documents/MATLAB</pre>

Once the submit function files have been downloaded and unzipped in the above paths, restart MATLAB to ensure they are properly loaded in your environment.

NOTE: If you choose not to use the above path recommendations, your MATLAB PATH may be viewed/altered by starting the MATLAB client on your workstation and clicking File -> Set Path and adding the path in which you unpacked the submit functions.

==== Parallel Computing Toolbox Configuration ====

The Parallel Computing Toolbox (PCT) enables language extensions in MATLAB that support dividing your application into tasks that can be executed in parallel. By default, all of these tasks will run on your local workstation using the pre-defined "local" PCT configuration.

To run these tasks on the Cheaha compute cluster, a new configuration for the PCT must be defined. In this section we will create the "cheaha" configuration and run a quick validation test to confirm its operation.

'''Prior to continuing''', make sure you:
* can establish an SSH connection to Cheaha
* have followed the steps in the previous section

===== Create the "cheaha" PCT Configuration =====
Download and save the Cheaha cluster configuration file for your MATLAB version
# [http://projects.uabgrid.uab.edu/matlab/browser/trunk/parallel-configs/cheaha-R2011b.mat?format=raw R2010b, R2011a, R2011b] cluster configuration file
#* Start MATLAB on your workstation
#* Click the "Parallel" menu
#* Click "Manage Configurations"
#* In the "Configurations Manager" window, click "File -> Import"
#* Browse to the location where you saved the '''cheaha-R2011b.mat''' file, select it, and click "Open"

[[Image:2011_config_mngr.png|none|x400px]]

===== Personalize the "cheaha" PCT Configuration =====

#Double click on cheaha in the Configuration Manager window to open the configuration editor. (Note: stretch the "Generic Scheduler Configuration Properties" window to the right so that you can view all of the text in the fields making it easier to read and edit correctly.)
# Edit the following fields to use your personal data directories
#* '''ClusterMatlabRoot''': Make sure that the Root directory of MATLAB installation for workers matches the exact version of MATLAB you are using on your workstation. In this example '''/share/apps/mathworks/R2011a''' matches a MATLAB R2011a workstation install. Change the "R2011a" to match your workstation MATLAB version.
#* '''DataLocation''' : Change the directory path where job data is stored to an existing directory on your workstation where MATLAB can stage job files.
#* '''ParallelSubmitFcn''': Change the text "YOURUSERID" to your login id on Cheaha
#* '''SubmitFcn''' : Change the text "YOURUSERID" to your login id on Cheaha
# Click 'OK'to save the configuration
# SSH to cheaha and make sure to create the $UABGRID_SCRATCH/matlab directory. If this directory does not exist, the parallel computing toolbox jobs will fail.

The initial configuration will look similar to this screen shot. You will need to edit the fields as describe in the preceding steps before you can use the configuration. '''NOTE: be sure to replace the template user name settings "YOURUSERNAME" with the appropriate settings for your desktop and cluster account.'''

[[Image:Cheaha_parallel_config.png|none|x650px]]

===== Validate the "cheaha" PCT Configuration =====

# Before starting validation please make sure the directory 'lustre/scratch/YOURUSERID/matlab' exists on the lustre scratch space on the Cheaha. If it does not please SSH into Cheaha and create the directory before proceeding.
# Select Cheaha on the configuration manager page and click 'Start Validation'
# Wait for the validation to complete. This might take a few minutes and you ask for User credentials on Cheaha. All tests other than 'Matlabpool' validate on the Cheaha and the output is as shown.

[[Image:Validation.png|none|x400px]]

===== Begin Using MATLAB DCS from your Desktop =====

The MATLAB DCS is now configured for Desktop usage. A simple parallel wave job "rParforWave" to test the configuration is described in [[MatLab_DCS_Examples]].

A summary of the above steps is available at [[MATLAB_workshop_2011]] with additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s | workshop demo ]] section.

{{MATLAB Support}}

[[Category:MATLAB]]