Cluster 2: Difference between revisions

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Our new cluster at [[UCSF]] is described on this page.  The physical equipment in cluster [[Cluster 0]] will be subsumed into this cluster when it replicates all the functions of the original. We expect this to happen later in 2014.
Our new cluster at [[UCSF]] is described on this page.  The physical equipment in cluster [[Cluster 0]] will be subsumed into this cluster when it replicates all the functions of the original. We expect this to happen later in 2014.
   
   
{{TOCright}}. The roles of computers are classified below.
{{TOCright}}.  
 
= Getting started =
 
Welcome to the lab. Here is what you need to know to get started.
* 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/
 
 
= Roles =


= General =  
= General =  

Revision as of 22:58, 27 February 2014

Our new cluster at UCSF is described on this page. The physical equipment in cluster Cluster 0 will be subsumed into this cluster when it replicates all the functions of the original. We expect this to happen later in 2014.

.

Getting started

Welcome to the lab. Here is what you need to know to get started.

  • 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/


= Roles =

General

  • sgehead - access to the cluster from within the lab
    • pgf fortran compiler
    • submit jobs to queue
  • portal - access to the cluster from off campus
  • ppilot - our pipeline pilot license will be transferred here
  • www - static webserver VM
  • dock - dock licensing VM
  • drupal -
  • wordpress -
  • public - runs public services ZINC, DOCK Blaster, SEA, DUDE
  • happy - postgres production server
  • ark - intern psql, like raiders in yyz
  • nfs1 - disk server 1
  • nfs2 - disk server 2
  • nfs3 - disk server 3
  • fprint - fingerprinting server

Services

  • aleph - VM running core administrative functions
  • bet -
  • gimel -
  • dalet -
  • he -
  • vav -
  • zayin -


SEA server

  • fawlty
  • mysql server is on msqlserver aka inception
  • fingerprint server is on fingerprint aka darkcrystal


By rack

Rack 0 - 10.20.0.*

Location BH101, column 7 row 5

  • aleph
  • bet
  • happy

Rack 1 - 10.20.10.*

Location: BH101, column 1 row 0

Rack 2 - 10.20.30.*

Location: BH


About our cluster

Retrieved from "http://wiki.docking.org/index.php?title=Cluster_2&oldid=6347"