CBS Server - Getting started with using the server

Tutorials
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Using the Virtual Desktops

The compute server uses a VMware Virtual Desktop Infrastructure (VDI) to instantiate virtual clones of the linux machine each time a user logs in.

Logging in to the VDI

The server is accessed as a virtual machine.

  1. Users will need to connect to: https://vsecurity.robarts.ca
  2. Download and install the VMWare Horizon Client (link near bottom of https://vsecurity.robarts.ca).
  3. Launch the VMWare Horizon Client software and set up a new connection server.
  4. Use vsecurity.robarts.ca as the connection server address.
  5. You should then be prompted to log in with your server username and password.
  6. You will use the same server username and password to log into Ubuntu.

Changing your password

From a terminal inside of the VM type:

  1. kinit [username]
  2. Enter your password when prompted.
  3. kpasswd
  4. Enter your old password when prompted.
  5. Enter your new password when prompted.
  6. Re-enter your new password when prompted.

Shutting down vs. disconnecting from virtual machine

  • If you wish to keep your virutal machine running (e.g., you still have a process running), then either just quit the VMWare Horizon application or select “Disconnect” from the VMWare Horizion application “Connection” pull-down menu.
  • If you do not have any active processes running, please be considerate of the shared resources and shut down your virutal machine either by selecting “Log Out” from your account menu in Ubuntu or selecting “Log Out” from the VMWare Horizon application “Connection” pull-down menu.

Note: While there is no formal policy, the CBS server administrators reserve the right to shut down virtual machines that have been left running for at least 8 hours. Leaving an idle virtual machine running takes resources away from other users.

Mounting datashares on the VDI

Manually mouting datashares on VDI

As datashare access is tied to a user’s credentials, users will need to manually mount datashares each time they start up a VM. To mount your PI’s datashare, use the following command:

mount /srv/<pi_last_name>

You will be prompted to enter your password. Afterwards, you will see the contents of the datashare in /srv/<pi_last_name>. The datashare will remain mounted until you log out of the VM, shutting it down.

Note: Replace <pi_last_name> with your PI’s last name all in lowercase.

Automatically mounting datashares on VDI at log-in

Ali has written a script that will allow users to automatically mount their PI’s datashare at log-in. The script creates a master key using Passphrase and links it to a user’s server credentials.

  1. Start up the VDI and log into the Ubuntu VM.
  2. Open a terminal and type: /srv/software/deps/cbs-vdi-utils/setup_automount
  3. The script will check if a Passphrase master key already exists. If none is found, the user will be prompted to type Y to continue creating a master key for the user’s account.
  4. A Passphrase GUI window will open asking the user to enter a new password for their master key. This can be the same as their server password, or something completely different. Pick something you will remember.
  5. After clicking OK in the password GUI window to accept your master key password and closing the window, the user will be prompted to enter and re-enter their Robarts password (e.g., same password you use to log into the VDI and Ubuntu VM).
  6. A GUI window will open up allowing the user to select the datashare directory they would like to have automounted. Note: users can only automount their PI(s) datashares.
  7. After clicking OK in the upper right-hand corner of the GUI, the user will be prompted in a second Passphrase GUI to enter the password they created in step 4. Make sure you check the Save in password manager. box before clicking okay.
  8. Users who have access to multiple datashares will need to re-run this script for every datashare they wish to have automounted.

Mounting Compute Canada on the VDI

Ali has written a script that will set up a sshfs to allow users to mount a Compute Canada machine (e.g., graham) on the VDI.

N.B.: Users must have an active Compute Canada account before running this script.

  1. From your home directory, type: setup_sshfs_alias.
  2. Follow the prompts. Users looking to mount graham on the VDI can accept all of the defaults. Users looking to mount a different Compute Canada machine should consult the Compute Canada to find the relevant system addresses.
  3. When prompted to save the ssh keypair, please enter your CBS server password.
  4. Once the ssh keypair has been saved, type graham to mount the Compute Canada system, graham, to your home directory (/home/ROBARTS/<user>/graham/).
  5. Type unmount graham to unmount graham.
  6. Note: graham is not set to automount upon log in, so users will need to manually run step 4 to mount graham at log in and step 5 to unmount graham when finished.

Storage on the VDI

This system should only be used to store data and files related to research. It should not be used as a primary backup for lab computers.

There is really only one directory in which to store data and files permanently on the server, and this is your PI’s datashare (/srv/<pi_last_name>).

Small text files (e.g., console login information) or python environments may be stored in a user’s home directory (/home/ROBARTS/<username>), but home directories are not meant to store large files or large numbers of files. Users are responsible for ensuring that their home directories do not exceed 10GB in size.

To check the size of your home directory at any time, run: du -h /home/ROBARTS/<user>

All files and data stored anywhere on the system outside of a PI’s datashare or a user’s home directory will be deleted when the virtual machine is shut down.

Software on the VDI

The VDI system is running Ubuntu 18.04.4 LTS, with a variety of software pre-installed. For those that have not used Ubuntu before, please see Ubuntu Getting Started. Some software is accessible through the application launcher, but most is available through the command-line, via the Terminal application.

Users of the VDI do not have admin (sudo) access to install software directly onto the VDI system, but can either install software into a folder they can access (home directory or /srv/<pi_last_name>), or make a software install request.

Environment modules

Most software, wherever possible, will be installed into the /srv/software NFS share, and can be added or removed from each user’s environment using the module command.

To show the modules installed:
module list

To unload all modules:
module purge

To list the available modules:
module avail

To load a module:
module load matlab

To load a specific version:
module load matlab/2019b

To get more extensive help on module:
module

User-specific or group-specific module files can also be created, please see the lmod documentation or contact support-cbs-server -at- uwo -dot- ca for help.

Using Python on the VDI

Python3 and virtualenv is installed on the server. You can also use Microsoft VS Code (available in launcher), or Pycharm Educational (available as a module), to manage your environment.

Instructions for setting up virtualenv:

virtualenv ~/myenv
source ~/myenv/bin/activate
pip install ...

Use of Anaconda is discouraged since it does not work well in multi-user environments. If you want your own conda environment, you can install miniconda in your home directory:

Instructions for local install of miniconda:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh ./Miniconda3-latest-Linux-x86_64.sh
conda init

Now after logging out and back in, or source ~/.bashrc, you can conda install ... or pip install ... into your base conda environment

Software install requests

Please e-mail support-cbs-server@uwo.ca for software install requests.

Using the storage without VDI (i.e. mounting locally)

It is possible to mount your PI’s datashare on your local machine. This will allow you to access files and folders on the datashare and use them with applications installed on your local machine. This will also allow you to transfer files between the server and local machines or other mounted drives.

Use of the tsclient is not recommended for transferring data; it is an inherently unstable connection.

Mounting a datashare on your local machine is best done from a Western network. When on Western campus, mounting a datashare on your local machine can be done from the wired Western network, uwosecure-v2 wifi, and eduroam wifi.

Note:

  • Replace <PI_Last_Name> with your PI’s last name with the first letter capitalized (e.g., Smith).
  • Replace <pi_last_name> with your PI’s last name all lowercase (e.g., smith).
  • Replace <username> with your BMI server username (e.g., jsmith7). This should be the same as your UWO username.

Mac OS

  1. Use ‘Connect to Server…’ under the ‘Go’ menu and enter either of the following:
  • cifs://bmisrv.robarts.ca/<PI_Last_Name>_data$
  • smb://bmisrv.robarts.ca/<PI_Last_Name>_data$
  1. When prompted to log in, use the following as your username:<username>@robarts.ca

Note: Both cifs and smb protocols should work, however, it is preferred to use cifs.

Windows

  1. From Windows Explorer, navigate to:\\bmisrv.robarts.ca\<PI_Last_Name>_data$\
  2. When prompted to log in, use the following as your username:<username>@robarts.ca

Linux

  1. Make sure you have cifs-utils installed on your local Linux machine.
sudo apt install cifs-utils
  1. Create the mount point:
sudo mkdir -p /srv/<PI_Last_Name>
  1. Mount the network drive:
sudo mount -t cifs -o <your_user_name> //bmisrv.robarts.ca/<PI_Last_Name>_data$ /srv/<PI_Last_Name>

Note: you will have to perform step 3 if you reboot your machine. Alternatively, you can add a line to your /etc/fstab file (see the /etc/fstab file on the CBS server for an example)

Off-campus mounting of datashares

Mounting datashares locally is not available from non-Western networks, due to Western ITS regulations of Western network firewalls. To access files stored on CBS server datashares, users will either need to use the Western VPN (Pulse Secure) with the above instructions, or use the VDI or remote desktop into a computer on the Western network and access the datashares from there. Note: We have discovered that using VPN access does not appear to work for users without Robarts affiliation. We are working to resolve this.

Need help?

support-cbs-server -at- uwo -dot- ca

Glossary

  • Default user account: Standard, free user account with access to 4 cores/8 GB
  • Power user account: Fee-based user account with access to 12 cores/32 GB + GPU
  • VDI-client: VMWare Horizon application
  • VM: Ubuntu virutal machine accessed via VMWare Horizon application
  • datashares: Backed-up storage drive tied to a PI’s account.
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