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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 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

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Using MATLAB on Sooner

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  1. 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

  2. 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

  3. 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

  4. 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

  5. From Your Workstation • Run MATLAB normally • Use Cluster resources to offload tasks • Requires some setup • Allows using locally licensed toolboxes

  6. 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

  7. 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

  8. 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

  9. 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”

  10. Import Key • Run PuTTYgen • Click 'Load' and select the temp_key file • Click 'Save Private Key' and save as 'private_key.ppk'

  11. Create a Connection • Run Putty • Enter sooner.oscer.ou.edu for the hostname • Enter sooner.oscer.ou.edu in 'Saved Sessions' and click 'Save'

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

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