Cluster 2 account - Revision history

Benrwong at 00:13, 10 November 2016

2016-11-10T00:13:04Z

← Older revision		Revision as of 00:13, 10 November 2016
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	Get started on Cluster 2.		Get started on Cluster 2.

	* 1. Your account. Get it from your system administrator ~~Therese Demers~~ (or John Irwin).		* 1. Your account. Get it from your system administrator Benjamin Wong (or John Irwin).
	* 2. Your home is on /nfs/home/<your_id>/. This area is backed up and is for important persistent files.		* 2. Your home is on /nfs/home/<your_id>/. This area is backed up and is for important persistent files.
	* 3. You should run docking jobs and other intense calculations in /nfs/work/<your_id>/ which is symlinked to ~/work by default.		* 3. You should run docking jobs and other intense calculations in /nfs/work/<your_id>/ which is symlinked to ~/work by default.

Frodo at 14:18, 23 April 2014

2014-04-23T14:18:52Z

← Older revision		Revision as of 14:18, 23 April 2014
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	* 13. If you use tcsh, begin by copying .cshrc from /nfs/soft/labenv/cshrc. If you use bash, start with .bashrc from /nfs/soft/labenv/bashrc.		* 13. If you use tcsh, begin by copying .cshrc from /nfs/soft/labenv/cshrc. If you use bash, start with .bashrc from /nfs/soft/labenv/bashrc.

	[[Category:~~Cluster 2~~]]		Back to [[Cluster 2]].

			[[Category:Internal]]

Frodo at 14:18, 23 April 2014

2014-04-23T14:18:06Z

Frodo: Created page with "Get started on Cluster 2. * 1. Your account. Get it from your system administrator Therese Demers (or John Irwin). * 2. Your home is on /nfs/home//. This area is bac..."

2014-04-23T14:03:53Z

Created page with "Get started on Cluster 2. * 1. Your account. Get it from your system administrator Therese Demers (or John Irwin). * 2. Your home is on /nfs/home/<your_id>/. This area is bac..."

New page

Get started on Cluster 2.

* 1. Your account. Get it from your system administrator Therese Demers (or John Irwin).
* 2. Your home is on /nfs/home/<your_id>/. This area is backed up and is for important persistent files.
* 3. You should run docking jobs and other intense calculations in /nfs/work/<your_id>/.
* 4. You should keep static data (e.g. crystallography data, results of published papers) in /nfs/store/<your_id>/.
* 5. Lab guests get 100GB in each of these areas, and lab members get 500GB. You may request more, just ask!
* 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. ssh-keygen; cd .ssh; cp id_rsa.pub authorized_keys; chmod 600 authorized_keys;
* 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/

← Older revision		Revision as of 14:18, 23 April 2014
Line 3:		Line 3:
	* 1. Your account. Get it from your system administrator Therese Demers (or John Irwin).		* 1. Your account. Get it from your system administrator Therese Demers (or John Irwin).
	* 2. Your home is on /nfs/home/<your_id>/. This area is backed up and is for important persistent files.		* 2. Your home is on /nfs/home/<your_id>/. This area is backed up and is for important persistent files.
	* 3. You should run docking jobs and other intense calculations in /nfs/work/<your_id>/.		* 3. You should run docking jobs and other intense calculations in /nfs/work/<your_id>/ which is symlinked to ~/work by default.
	* 4. You should keep static data (e.g. crystallography data, results of published papers) in /nfs/store/<your_id>/.		* 4. You should keep static data (e.g. crystallography data, results of published papers) in /nfs/store/<your_id>/, which is symlinked to ~/store by default.
	* 5. Lab guests get 100GB in each of these areas, and lab members get 500GB. You may request more, just ask!		* 5. Lab guests get 100GB in each of these areas, and lab members get 500GB. You may request more, just ask!
	* 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 email warnings for 2 weeks. If the problem remains unresolved after two weeks, the sysadmin will have a chat with you.
	* 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 may 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/<your_id>/ or perhaps /nfs/db/<dbname>/ 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.		* 9. Please run large docking jobs on /nfs/work and not on /nfs/store or /nfs/home. Find a way to archive key input files and possibly output files to your home or store directories. To be clear, these disk are all top quality with two levels of redundancy, so we are really not expecting you to experience a disk failure. But we cannot say it won't happen, so please take precautions. 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. ssh-keygen; cd .ssh; cp id_rsa.pub authorized_keys; chmod 600 authorized_keys;		* 10. Set up your account so that you can log in all across the cluster without a password. ssh-keygen; cd .ssh; cp id_rsa.pub authorized_keys; chmod 600 authorized_keys;
	* 11. Software lives in /nfs/~~software~~/. All our machines are 64 bit Centos 6.3 unless otherwise indicated.		* 11. Software lives in /nfs/soft/. All our machines are 64 bit Centos 6.5 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~~)		* 12. Python 2.7 and 3.0 are installed. We currently recommend 2.7 because of library availability, but that may change soon. (April 2014)
	* 13. If you use tcsh, ~~copy .login and~~ .cshrc from ~~~jji~~/ ; If you use bash, ~~copy~~ .~~bash_profile~~ from ~~~jji~~/		* 13. If you use tcsh, begin by copying .cshrc from /nfs/soft/labenv/cshrc. If you use bash, start with .bashrc from /nfs/soft/labenv/bashrc.

			[[Category:Cluster 2]]