using matlab on sooner

Using MATLAB on Sooner

MATLAB is available on sooner.oscer.ou.edu You will need an OSCER account

Contact hneeman@ou.edu 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

If you have difficulties with running MATLAB or with any other aspect of OSCER systems, please send email to support@oscer.ou.edu

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

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 withjm=findResource('scheduler','type','jobmanager','Name','JobManage

r_yourusernamehere','LookupURL','localhost');

Sample code is included in comments in the sample bsub file

From Your Workstation

Run MATLAB normally Use Cluster resources to offload tasks Requires some setup Allows using locally licensed toolboxes

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

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

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

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 yourusername@sooner.oscer.ou.edu:temp_key “c:\Documents and

Settings\yourlocalaccount\My Documents\temp_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

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

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

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

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

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

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 pathsremoteDataLocation = '/scratch/yourusername/matlab_temp';

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

From within MATLAB run soonertest

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 support@oscer.ou.edu if you have any difficulty with this or any other aspect of OSCER systems