MatLab DCS R2012a

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Revision as of 17:25, 8 March 2012 by Tanthony@uab.edu (talk | contribs) (added cluster configs)
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Attention: Research Computing Documentation has Moved
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Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

Overview

The following outline highlights the steps involved to configure your MatLab install and write programs that submit tasks to the worker nodes of the Distributed Computing Server on Cheaha:

  • Configure the Task Submit Environment (One-time Setup)
    • Install MatLab with the Parallel Computing Toolbox on your Windows / Linux / Mac workstation
    • Download and extract the MatLab task submission functions to your workstation MatLab environment
    • Define the "cheaha" parallel configuration in your workstation MatLab environment to submit tasks to Cheaha
    • Run the validation tests to ensure your "cheaha" parallel configuration works
  • Develop and Run Parallel Computing Applications
    • Write, test and debug your parallel code on your local workstation using the default "local" parallel configuration
    • Once your code works, select the "cheaha" parallel configuration to submit tasks to the Cheaha cluster. Note: your workstation MatLab application does not need to keep running after the tasks are submitted.
    • You will receive an email when the tasks you submitted are complete
    • Use your workstation MatLab application to retrieve the results
    • When you are finished with your job contexts, clean up the job related content to free disk space

Using MATLAB DCS

The MATLAB Distributed Computing Services (DCS) are accessed via the Parallel Computing Toolbox (PCT) which is installed as part of your desktop MATLAB installation. The PCT allows MATLAB running on your workstation to send MATLAB code and data (tasks) to the cluster directly from the comfort of your familiar MATLAB environment on your desktop. This makes the expanded compute power of Cheaha available to processes work loads that exceed the capabilities of your desktop computer. Once your tasks are submitted to Cheaha, your desktop MATLAB is also free to move on to other tasks or be closed completely, freeing your desktop or laptop for your other activities.

Configuring the Parallel Computing Toolbox involves three steps documented below:

  1. install MATLAB submit functions on your workstation
  2. configure the "cheaha" parallel computing target to which PCT tasks can be submitted
  3. run the validation tests to confirm a working installation.

This page documents the DCS configuration for MATLAB 2012a and later. For DCS configuration instructions on previous versions of MATLAB, please see the page MatLab DCS R2010a and Earlier or Matlab DCS R2010b -R2011b

Using MATLAB DCS requires you have a cluster account on Cheaha. Please request an account by sending an email to [[1]] and include your campus affiliation and a brief statement of your research interests for using the cluster.

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.

  1. Download the MATLAB submit functions
  2. Unzip the files to a directory included in your MATLAB PATH setting. Recommended locations are:
    • Windows: 
      My Documents\MATLAB
    • Linux: 
      $HOME/Documents/MATLAB
    • Mac: 
      $HOME/Documents/MATLAB

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
  1. R2012a cluster configuration file
    • Start MATLAB R2012a on your workstation
    • Click the "Parallel" menu
    • Click "Manage Cluster Profiles"
    • In the "Cluster Profile Manager" window, click the "Import" button on the toolbar
    • Browse to the location where you saved the cheaha-R2012a.settings file, select it, and click "Open"
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