1  Onboarding and Setup

Author

Sean Taylor, Lindsay Clark, Yeji Bae and Glenn Morton

Published

May 7, 2026

This is intended as a quick start for Sasquatch, the high performance computing cluster at Company. For more detailed information, we highly recommend reading the full HPC Guide, attending our Intro to Scientific Computing course, and joining us during office hours.

1.1 Onboard as a Sasquatch user

To leverage resources or access to Sasquatch can be requested by submitting a ticket through Onboard a HPC User. *Access setup may take up to seven days after your request is submitted.

1.2 Optional: Request an association

What is the Association? For Sasquatch, associations define a set of users who have access to a shared set of compute and storage resources. If you anticipate doing heavy computation on Sasquatch, needing storage and scratch space beyond 100 GB, and/or needing storage space that is shared with other users, you will need to have an association.

To request a new association can be requested through Create a new Association or ask to be added to an existing one through Join an Association.

1.3 Optional: Request Posit Workbench access

If you plan to use R(Rstudio) or Python(VSC, Jupyter Lab) on a regular basis, we highly recommend getting a Posit Workbench license. You can request Posit Workbench access through Onboard a Posit Workbench User.

Once you are granted access, you can log in to Posit Workbench at link

1.3.1 Optional: R setup

If you are using R and are a member of an association, we highly recommend storing your R packages in your association space so that you don’t fill up your home directory with them. Using a text editor in the bash terminal, OpenOnDemand web interface, or RStudio, open the file ~/.Renviron for editing, creating it if it doesn’t exist yet.

To ~/.Renviron, add the line:

R_LIBS_USER_BASE_PATH="/data/hps/assoc/private/mylab/user/mmouse"

replacing “mylab” with your association name and “mmouse” with your user name. This is now your default location for installing R packages.

1.4 Optional: Request Posit Connect access

Posit Connect enables you to share HTML files, PowerPoint presentations, and Shiny applications developed in Posit Workbench. If you would like to use this service, please request a license through Onboard a Posit Connect User.

1.5 Logging on

We have two login nodes, login-1.hpc and login-2.hpc. You can use them interchangeably. The easiest way to log on is using Open On Demand. While connected to the Company network (on site or via Zscalar or Citrix), click one of those two links or paste the node name into your web browser. You will get prompted to sign in, which you can do with your Company password and short user name.

Once you are logged in, at the top of the screen click “Clusters” and then “Sasquatch HPC Shell Access”

After doing this, you will find yourself at a bash terminal on a login node.

1.6 Install Mamba

There are several options for getting the software you need, but mamba/conda is one of the more useful approaches. You are going to install a personal copy of mamba for your use. You only need to do this once.

First, download the installation script:

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh

Then run the installer.

bash Miniforge3-Linux-x86_64.sh
  • Follow the prompts on the screen, and accept the license agreement.
  • You will be prompted for an installation location, with the default being in your home directory.
    • IMPORTANT We recommend installing it in your association, e.g. /data/hps/assoc/private/mylab/user/mmouse/miniforge3.
    • If you don’t change this, your home will fill up with a bunch of small files unless you only make a couple tiny environments.
  • IMPORTANT Say yes to updating your shell profile.
  • Once you are done, the miniforge3 directory will exist.

Then set up your environment to use mamba:

source ~/.bashrc
mamba deactivate
conda config --set auto_activate_base false
conda config --set env_prompt '({name})'
source ~/.bashrc

Official install instructions at mamba.readthedocs.io and from their GitHub.

See Using Mamba/Conda for more information about using mamba on Sasquatch.

1.7 Optional: Connect to Bitbucket and configure Git

If you use Git (which we highly recommend if you write code regularly) you will want to be able to push and pull from the Company Bitbucket. Do this one-time setup on Sasquatch to make an SSH key:

ssh-keygen -t ed25519

Then print out your public key:

cat ~/.ssh/id_ed25519.pub

Go to https://ea-bitbucket-prod./, click on your avatar in the upper-right, go to “Manage account”, then “SSH keys”, then “Add key” and paste in the whole string from the public key, starting with “ssh-ed225519” and ending with “@login-1”. Click “Add key” after pasting it in, and you are all set.

If you have more questions about SSH keys, please see our chapter Using SSH keys.

You will also want to set your name and email for Git.

git config --global user.name "Doe, Jane"
git config --global user.email "Jane.Doe@company.org"

See Using Git for more information about using Bitbucket and version control on Sasquatch.

1.8 Logging off

  • Use the exit command to end a session on a worker node if you are done.
  • Use Ctrl + b d to detach from your tmux session.
  • Use exit do disconnect from the login node.