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Welcome to the lab. This page is designed for new group members, our collaborators and anyone else who wishes to access our cluster via ssh.
Welcome to the lab! This page organizes topics of interest to group members, our collaborators and anyone else who wishes to access our cluster via ssh. If you are not a member of the lab, please see [[Welcome web user]].  If you have ssh access, [[:Category:Internal]] articles may be of interest to you.


== Guides ==
=== [[New Lab Members]] ===
* [[Group Meeting]]
Please read this first to get started using the cluster!
* [[Tutorials]]
* [[Reimbursement Instructions]]
 
As you know, we have two labs, one in Toronto and one in San Francisco.  Moreover, in each location there are shared clusters that we have access to.  We take up each in turn.


{{TOCright}}
{{TOCright}}


* [[Cluster 1]] - Toronto Cluster
= Info =
* [[Apply for SciNet Account]] - if you need it
* [[Group Meeting]]
* [[Cluster 0]] - Legacy UCSF cluster
* [[Reimbursement Instructions]]
* [[Cluster 2]] - new UCSF cluster
* [[Lab Security Policy]]
 
* [[Disk space policy]]
* [[Backups]]
* [[Tutorials]]


= San Francisco - shared cluster =  
= Best Practices =  
* [[Best:SGE Usage]]
* [[Best:Disk Usage]]
* [[Best:Desktop Usage]]
* [[Best:More]]


Contact Teague who will ask Josh to set up an account for you.  
= Computers =
Please see our  [[:Category:Cluster | cluster]] page.
You might be interested to know about the [[Disk types | types of disk]] we currently support.


= San Francisco - new cluster =
In Cluster 2, you log in to sgehead.ucsf.bkslab.org aka  gimel.compbio.ucsf.edu. If you need fortran, ssh to fortran. If you need ppilot, ssh to ppilot. You should not need to log in to any other machine.


Welcome to the lab. Here is what you need to know to get started.
In Cluster 0, you log in to sgehead.bkslab.org. You should be able to do everything from there.
* 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/


= Access from home =  
= Access from home =  
 
* [[How to generate ssh keys securely]]
[[How to generate ssh keys securely]]
* [[How_to_create_a_vpn/ssh_tunnel]]
 
* [[ssh tunnel (Trent's way)]]
[[How_to_create_a_vpn/ssh_tunnel]]


= Good habits =  
= Good habits =  
Set aside a quiet time every month to review your disk usage, and compress, delete or move excessive usage.
Set aside a quiet hour once a month to review your disk usage, and compress, delete or move excessive usage. There are disk quotas and we do monitor them. We will make additional space available for needed lab work, but we need your cooperation to keep the signal to noise ratio high.  Ask us for a [[Personal backup disk]].


= Synchrotron trips =  
= Synchrotron trips =  
We can help arrange to store your data in a safe place. Ask before you leave.
We can help arrange to store your data in a safe place. Ask before you leave.
= Third party software and databases =
See the main article on [[:Category:Third party software | third party software]] that we maintain on our cluster.
= Updates =
Some software must be updated or at least attended to annually due to license expiry. Otherwise, we generally update software on an as-needed basis. If you want something updated, ask us and give us some time. Even better, if you can take the lead, it will get done faster almost for sure.


= When you leave the lab =  
= When you leave the lab =  
Please discuss with Teague or Therese or John one month before you leave the lab to agree on which of your files will remain.  
Please discuss with John one month before you leave the lab to agree on which of your files will remain, and where they will live.
We can provide you with portable disks so you can take software and data with you, if you like. If you want to take the lab software with you, we can help with that too.
We can provide you with portable disks so you can take software and data with you, if you like. If you want to take the lab software with you, we can help with that too.


= FOTL: Friends of the lab =
* [[Travel Depth]], [[qnifft DOCK 3.6 conversion| QNIFFT]] and [http://crystal.med.upenn.edu/software.html  related software] for structural analysis from the [http://crystal.med.upenn.edu/  Sharp lab]
* [[PLOP]] - protein modeling program from the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group].
* [[Modeller]] - comparative modeling program from the [http://salilab.org Sali Group].
* Software vendors: [[OpenEye]], [[ChemAxon]], [[Molinspiration]]
* Software providers: [[RDKit]], [[Knime]]
* [http://zinc.docking.org/browse/catalogs/purchasable.php Compound vendors] and [http://zinc.docking.org/browse/catalogs/annotated.php Annotated catalog providers]
* [[Contract Research Organizations]]
* Transformative databases: [[DrugBank]], [[HMDB]], [[ChEMBL]].


== Computational Resources ==
= Special pages for certain people =  
* CSD
* [[:Category:Internal]] - ssh-level access for group members, lab visitors, collaborators
* ppilot
* [[:Category:Sysadmin]] - cluster creator / software installer / system administrator
* openeye
* [[:Category:Developer]] - github user / software developer
* cactvs
* [[:Category:Curator]] - database curator
 
== Misc ==
Brenda is at /raid5/backonce/joha/DB3/5_BRENDA2SDF/ORG_BRENDA_MOL_FILES_PREP/brenda_031306.ism
mysql is at mysql -u joha -p*secret* -h (brenda-machine-name-ask-jji) brenda
wombat is at ~jerome/sets/wombat/wombat_20062/wombat.20062.sdf.gz
 
* [[Dock Users' Meeting Minutes (DUMM)|Dock Users' Meeting Minutes]]


[[Category:Internal]]
[[Category:Internal]]
[[Category:Tutorials]]
[[Category:FAQ]]
[[Category:UCSF]]
[[Category:YYZ]]

Revision as of 17:59, 16 April 2018

Welcome to the lab! This page organizes topics of interest to group members, our collaborators and anyone else who wishes to access our cluster via ssh. If you are not a member of the lab, please see Welcome web user. If you have ssh access, Category:Internal articles may be of interest to you.

New Lab Members

Please read this first to get started using the cluster!

Info

Best Practices

Computers

Please see our cluster page. You might be interested to know about the types of disk we currently support.

In Cluster 2, you log in to sgehead.ucsf.bkslab.org aka gimel.compbio.ucsf.edu. If you need fortran, ssh to fortran. If you need ppilot, ssh to ppilot. You should not need to log in to any other machine.

In Cluster 0, you log in to sgehead.bkslab.org. You should be able to do everything from there.

Access from home

Good habits

Set aside a quiet hour once a month to review your disk usage, and compress, delete or move excessive usage. There are disk quotas and we do monitor them. We will make additional space available for needed lab work, but we need your cooperation to keep the signal to noise ratio high. Ask us for a Personal backup disk.

Synchrotron trips

We can help arrange to store your data in a safe place. Ask before you leave.

Third party software and databases

See the main article on third party software that we maintain on our cluster.

Updates

Some software must be updated or at least attended to annually due to license expiry. Otherwise, we generally update software on an as-needed basis. If you want something updated, ask us and give us some time. Even better, if you can take the lead, it will get done faster almost for sure.

When you leave the lab

Please discuss with John one month before you leave the lab to agree on which of your files will remain, and where they will live. We can provide you with portable disks so you can take software and data with you, if you like. If you want to take the lab software with you, we can help with that too.

FOTL: Friends of the lab

Special pages for certain people

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