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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}}. | {{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