Welcome group members

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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.

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

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/project/<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/repos/<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.
  • 2. Your home is on /raid1/people/<your_id>/. This area is backed up and is for important persistent files.
  • 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.
  • 4. You should keep static data (e.g. crystallography data, results of published papers) in ~/store/ which is generally not your home directory.
  • 5. Lab guests get 100GB in each of these areas, and lab members get 500GB. Ask if you need 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.
  • 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/


  • 1. cp /nfs/software/labenv/defaults.cshrc .cshrc

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

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

How to generate ssh keys securely

How_to_create_a_vpn/ssh_tunnel

Good habits

Set aside a quiet time every month to review your disk usage, and compress, delete or move excessive usage.

Synchrotron trips

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

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. 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.

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