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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
Using MATLAB on Sooner
  • MATLAB is available on sooner.oscer.ou.edu
  • You will need an OSCER 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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