Cluster 0 account

Getting started on the cluster

• 1. request an account from Therese or John.
• 2. Your home is on /raid1/people/<your_id>/. This area is backed up and is for important persistent files.
• 3. You should run docking jobs and other intense calculations in ~/work/, which Therese will set up for you and is generally not your home directory.
• 4. You should keep static data (e.g. crystallography data, results of published papers) in ~/store/ which is generally not your home directory.
• 5. Lab guests get 100GB in each of these areas, and lab members get 500GB. Ask if you need more.
• 6. If you go over your limit, you get emails for 2 weeks, then we impose a hard limit if you have not solved your overage.
• 7. You can choose bash or tcsh to be your default shell. We don't care. Everything should work equally well with both.
• 8. There is a special kind of static data, databases, for which you may request space. They will go in /nfs/db/<db_name>/. e.g. /nfs/db/zinc/ and /nfs/db/dude/ and /nfs/db/pdb and so on.
• 9. Please run large docking jobs on /nfs/work and not on /nfs/store or /nfs/home. When you publish a paper, please delete what you can, compress the rest, and move it to /store/. Do not leave it on /work/ if you are no longer using it actively.
• 10. Set up your account so that you can log in all across the cluster without a password. For instructions on how to securely generate ssh keys go here: http://wiki.uoft.bkslab.org/index.php/How_to_generate_ssh_keys_securely
• 11. Software lives in /nfs/software/. All our machines are 64 bit Centos 6.3 unless otherwise indicated.
• 12. Python 2.7 and 3.0 are installed. We currently recommend 2.7 because of library availability, but that may change soon. (Aug 2012)
• 13. If you use tcsh, copy .login and .cshrc from ~jji/  ; If you use bash, copy .bash_profile from ~jji/

• 1. cp /nfs/software/labenv/defaults.cshrc .cshrc

Note: if you are still in San Francisco, the path is /raid3/software/labenv/defaults.cshrc If you use bash or another shell, please see the Sysadmin.

• 2. Customize this file if you like.
• 3. Check out your own copy of dockenv, dock, sea, if you like.

By default you use the standard lab software.

• 4. Logout / login or source ~/.cshrc
• 5. You are now ready to use all the lab software, including docking.

Back to Cluster 0.