using matlab on sooner
DESCRIPTION
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 - PowerPoint PPT PresentationTRANSCRIPT
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
If you have difficulties with running MATLAB or with any other aspect of OSCER systems, please send email to [email protected]
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 [email protected]: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 [email protected] if you have any difficulty with this or any other aspect of OSCER systems