Using matlab on sooner
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Using MATLAB on Sooner. MATLAB is available on sooner.oscer.ou.edu You will need an OSCER account Contact [email protected] to request an account You must be OU Norman facutly, staff, or student or with affiliated programs at Tulsa campus OUHSC is not covered by our license

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Using MATLAB on Sooner

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Using matlab on sooner

Using MATLAB on Sooner

  • MATLAB is available on sooner.oscer.ou.edu

  • You will need an OSCER account

    • Contact [email protected] to request an account

  • You must be OU Norman facutly, staff, or student or with affiliated programs at Tulsa campus

    • OUHSC is not covered by our license

    • Verify that you are in the 'matlab' group on sooner

      • Run the command id – the matlab group should appear in your group list if you're allowed to use MATLAB


Support@oscer

[email protected]

  • If you have difficulties with running MATLAB or with any other aspect of OSCER systems, please send email to [email protected]


Two approaches

Two Approaches

  • Creating an Ad Hoc MATLAB cluster within Sooner

    • Reserve a pool of nodes for up to 48 hours

    • Cannot use toolboxes licensed on your workstation

  • Submitting Tasks From Your Workstation

    • Slightly slower

    • Allows you to use your personal toolboxes

    • Somewhat difficult to configure


Within the cluster

Within the Cluster

  • Submit a job to the distcomp queue

  • A sample submission script is available

    /home/hneeman/example_matlab_parallel.bsub

  • A job manager is created for that job

  • Discover the job manager with

    jm=findResource('scheduler','type','jobmanager','Name','JobManager_yourusernamehere','LookupURL','localhost');

  • Sample code is included in comments in the sample bsub file


From your workstation

From Your Workstation

  • Run MATLAB normally

  • Use Cluster resources to offload tasks

  • Requires some setup

  • Allows using locally licensed toolboxes


Procedure overview

Procedure Overview

  • Setup SSH to Connect to Sooner

    • Generate shared keys

    • Configure Putty for shared key access

  • Copy support files for MATLAB

  • Create needed directories


Install matlab

Install MATLAB

  • We're going to assume you already have a local MATLAB installation

  • Go to itstore.ou.edu to get MATLAB

  • Contact IT Support at 325-HELP for installation support with MATLAB


Install putty

Install PuTTY

  • Putty is a Windows SSH client

    • www.chiark.greenend.org.uk/~sgtatham/putty

  • You will need

    • PuTTY, PSCP, PSFTP, Plink, Pageant, PuTTYgen

  • All of these must be in your default path

    • The easiest way to do this is to copy them all to the c:\windows\system32 directory


Generate keys

Generate Keys

  • Login to sooner.oscer.ou.edu

  • Generate a key pair

    ssh-keygen -t rsa -f temp_key

  • Import the public key

    cat temp_key.pub >>~/.ssh/authorized_keys

    Copy the private key to your workstation

    (From Windows)pscp [email protected]:temp_key “c:\Documents and Settings\yourlocalaccount\My Documents\temp_key”


Import key

Import Key

  • Run PuTTYgen

  • Click 'Load' and select the temp_key file

  • Click 'Save Private Key' and save as 'private_key.ppk'


Create a connection

Create a Connection

  • Run Putty

  • Enter sooner.oscer.ou.edu for the hostname

  • Enter sooner.oscer.ou.edu in 'Saved Sessions' and click 'Save'


Setup putty to use key

Setup Putty to Use Key

  • Select Connection->SSH->Auth in the left panel

  • In the field marked 'Private key file for authentication' select the key you saved in PuTTYgen


Setup putty to login automatically

Setup Putty to Login Automatically

  • Select Connection->Data from the left panel

  • In the field marked Auto-login username enter your OSCER username

  • Click Session in the left panel and click save

  • Double click the sooner.oscer.ou.edu saved connection and verify you're able to login


Install client files

Install Client Files

  • Copy the file /home/hneeman/MATLAB_Client_Files.zip to your workstation

  • Unzip the files and move them to the local toolbox directory

    • Typically this will be c:\Program Files\MATLAB\R2008b\toolbox\local


Create directories

Create Directories

  • You'll need two temporary directories MATLAB will use for transferring files and managing jobs

  • On Sooner

    /scratch/yourusername/matlab_temp

  • On your workstation

    c:\Documents And Settings\localusername\My Documents\matlab_temp


Testing the connection

Testing the Connection

  • Copy the file /home/hneeman/soonertest.m to your local MATLAB directory on your workstation. Usually located in

  • C:\Documents and Settings\localusername\My Documents\MATLAB

  • Edit the file to use the correct usernames in the file paths

    • remoteDataLocation = '/scratch/yourusername/matlab_temp';

      set(sched, 'DataLocation', 'C:\Documents and Settings\localusername\My Documents\matlab_temp');

  • From within MATLAB run soonertest


Points to remember

Points to Remember

  • This information is available on the OSCER website: www.oscer.ou.edu

  • Sample bsub scripts are at /home/hneeman/example_matlab_parallel.bsub

  • You must be an OU Norman faculty, staff, or student (including affiliated Tulsa programs) to use MATLAB at OSCER

  • As always, contact [email protected] if you have any difficulty with this or any other aspect of OSCER systems


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