Cluster 2

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.

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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