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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 =
If you have just joined the lab, here's what you need to know:
 
# Ask the [[sysadmin]]s for an account on the cluster, and a workstation.  Tell us what account name you prefer.
# Set up a [[How_to_generate_ssh_keys_securely|public key]] so you can login from off campus.
# Make sure you are on the mailing list yall, ask a [[sysadmin]] if you are not.
# Get set up with github / lab tools.
 
= Info =
* [[Group Meeting]]
* [[Group Meeting]]
* [[Reimbursement Instructions]]
* [[Lab Security Policy]]
* [[Disk space policy]]
* [[Backups]]
* [[Tutorials]]
* [[Tutorials]]
* [[Testcase repository]]
* [[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.
= Toronto - our cluster =
{{TOCright}}
== Obtaining credentials ==
For command line access to our cluster, please contact Teague, Therese or John for credentials.
For your main email address, you may well use your gmail account or other public account for most purposes.
== Disk usage conventions ==
We differentiate dockers from everyone else. If you are a full time member of the group, your disk space allocation will be like this:
Your home directory is for important or small files. 500 GB default. Backed up.
/nfs/home/<userid>/
We expect you to run docking calculations in /project/. 1TB default. Not backed up.
/nfs/work/<userid>/
If you have large amounts of data you want kept, e.g. from the synchrotron, you may request repository space to keep it.  Backed up. Size by agreement.
/nfs/store/<userid>/
If you generate private databases, you may request /db/ space. Backup by arrangement. Size by agreement.
/nfs/db/<userid>/
If you have software you want to share, you may request /software/ space. backed up. 500 GB.
/nfs/software/<userid>/
== Getting set up with lab software ==
svn co dockenv
cp $SOFT/labenv.csh ~/.csh
OR
cp $SOFT/labenv.sh ~/.bashrc
for bash users.
= Toronto - SciNet cluster =
If you need personal access to the SciNet cluster, you will need a U of T email address.  If you do not need access to SciNet, then you may well not need a U of T email address.
* 1. Contact Lilita, who can get you a U of T email address.
* 2. Get a Compute Canada Role Identifier (CCRI) from me.
* 3. Register on SciNet (page here).
= San Francisco - our lab =


* 1. request an account from Therese or John.
= Best Practices =
* 2. Your home is on /raid1/people/<your_id>/. This area is backed up and is for important persistent files.
* [[Best:SGE Usage]]
* 3. You should run docking jobs and other intense calculations in ~/work/, which Therese will set up for you and is generally not your home directory.
* [[Best:Disk Usage]]
* 4. You should keep static data (e.g. crystallography data, results of published papers) in ~/store/ which is generally not your home directory.
* [[Best:Desktop Usage]]
* 5. Lab guests get 100GB in each of these areas, and lab members get 500GB. Ask if you need more.
* [[Best:More]]
* 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.
* 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]].
* 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. For instructions on how to securely generate ssh keys go here: http://wiki.uoft.bkslab.org/index.php/How_to_generate_ssh_keys_securely
* 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/


= Computers =
Please see our  [[:Category:Cluster | cluster]] page.
You might be interested to know about the [[Disk types | types of disk]] we currently support.


* 1. cp /nfs/software/labenv/defaults.cshrc .cshrc
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.
Note: if you are still in San Francisco, the path is /raid3/software/labenv/defaults.cshrc
If you use bash or another shell, please see the Sysadmin.
* 2. Customize this file if you like.
* 3. Check out your own copy of dockenv, dock, sea, if you like.
By default you use the standard lab software.
* 4. Logout / login or source ~/.cshrc
* 5. You are now ready to use all the lab software, including docking.


= San Francisco - shared cluster =
In Cluster 0, you log in to sgehead.bkslab.org. You should be able to do everything from there.
 
Contact Teague who will ask Josh to set up an account for you.
 
= San Francisco - new cluster =
 
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/


= Access from home =  
= Access from home =  
* [[How to generate ssh keys securely | First, generate an ssh key securely]]
* [[How_to_create_a_vpn/ssh_tunnel | Second, create a vpn/ssh tunnel]]
* [[ssh tunnel (Trent's way)]]


[[How to generate ssh keys securely]]
= Synchrotron trips =
We can help arrange to store your data in a safe place. Ask before you leave.


[[How_to_create_a_vpn/ssh_tunnel]]
= Third party software and databases =
See the main article on [[:Category:Third party software | third party software]] that we maintain on our cluster.


= Good habits =  
= Updates =  
Set aside a quiet time every month to review your disk usage, and compress, delete or move excessive usage.
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.
 
= Synchrotron trips =
We can help arrange to store your data in a safe place. Ask before you leave.


= 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]]

Latest revision as of 21:06, 30 December 2020

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

If you have just joined the lab, here's what you need to know:

  1. Ask the sysadmins for an account on the cluster, and a workstation. Tell us what account name you prefer.
  2. Set up a public key so you can login from off campus.
  3. Make sure you are on the mailing list yall, ask a sysadmin if you are not.
  4. Get set up with github / lab tools.

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

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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