Frodo at 14:47, 23 April 2014

2014-04-23T14:47:09Z

← Older revision		Revision as of 14:47, 23 April 2014
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	~~= Getting~~ started on the ~~cluster =~~		Get started on Cluster 0. Return to the main article about [[Cluster 0]].

			Franky, if you are joining the group now (April 23, 2014), we would rather set you up on [[Cluster 2]] and not have you use [[Cluster 0]] at all. That may not be pragmatic, so here are the legacy instructions.

	* 1. request an account from Therese or John.		* 1. request an account from Therese or John.
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	* 4. You should keep static data (e.g. crystallography data, results of published papers) in ~/store/ which 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.		* 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.		* 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. '''not done'''
	* 7. You can choose bash or tcsh to be your default shell. We don't care. Everything should work equally well with both.		* 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.		* 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.

Frodo: Created page with "= Getting started on the cluster = * 1. request an account from Therese or John. * 2. Your home is on /raid1/people//. This area is backed up and is for important p..."

2014-04-23T14:45:10Z

Created page with "= 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 p..."

New page

= 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]].
[[Category:Internal]]

Cluster 0 account - Revision history

Frodo at 14:47, 23 April 2014

Frodo: Created page with "= Getting started on the cluster = * 1. request an account from Therese or John. * 2. Your home is on /raid1/people//. This area is backed up and is for important p..."