Using Git on Quest

Quest RHEL8 Pilot Environment

The RHEL8 Pilot Environment is available for use now.

Ahead of the March 2025 Downtime, Quest users have the opportunity to test their software and research workflows on CPU nodes and NVIDIA H100 GPU nodes which are running the new RHEL8 OS. Detailed instructions are available on how to submit jobs for the new Operating System in the Knowledge Base article, RHEL8 Pilot Environment.

RHEL8 Pilot Quest log-in nodes can be access via ssh or FastX through using the hostname login.quest.northwestern.edu. Please note that the new hostname login.quest.northwestern.edu will require the GlobalProtect VPN when outside of the United States.

RHEL8 Pilot Quest Analytics nodes can be access via: rstudio.quest.northwestern.edu, jupyterhub.quest.northwestern.edu, and sasstudio.quest.northwestern.edu.

Starting Tuesday, December 10, seventy of the latest Intel Emerald Rapids CPU nodes (128 cores and 512GB of RAM) will be available to the RHEL8 Pilot, significantly increasing the compute capacity of this environment. With this expansion, the pilot environment will consist of twenty-four NVIDIA H100 GPU nodes (totaling ninety-six H100 cards) and 140 CPU nodes totaling 12,600 cores. Quest users are encouraged to test their workflows in RHEL8 Pilot environment to prepare for Quest moving completely to RHEL8 in March 2025. Detailed instructions are available on how to submit jobs for the new Operating System in the Knowledge Base article, RHEL8 Pilot Environment.

Git is an open source, distributed version control system that is commonly used for collaboration on code or documents. While it is often used with a hosting service like GitHub, Git can be used locally to track changes within a single repository stored on disk.

Making Git Available

Git is available as part of the operating system, but that version of Git is old. It is strongly recommended that you load a newer version of Git with the git module before using Git:

module load git

Setting up Git

Before you use Git for the first time on Quest, you need to set the user name and email address it will use when it records your commits. Use the following commands to set this information:

git config --global user.name "John Doe"
git config --global user.email johndoe@northwestern.edu

You only need to do this one time. Git will remember your name and email.

To view your Git settings, at any time you can run this command:

git config --list

Repositories

You can create repositories at any time in any directory on Quest you have write access to with the git init command. However, if you wish to clone a repository from a remote server such as GitHub or Bitbucket, you have a choice of using either HTTPS or SSH to clone.

Cloning from GitHub with HTTPS

To clone a repository from GitHub on Quest using the HTTPS protocol, click the "Clone or download" button:

Then copy the URL that appears below it:

Finally, in your Quest terminal, run this command (pasting in the URL you copied):

git clone https://github.com/<organization>/<repository>.git

That will download the repository from GitHub into a directory with the same name as the repository.

If the repository is private (and you have access to it), you will be asked to provide your GitHub username and password. Similarly, if you push to a repository you have cloned from GitHub using the HTTPS protocol, you will have to provide your username and password. Because it is annoying to have to type your username and password over and over again, Git provides a way to cache your credentials.

Type the following command to enable username and password caching:

git config --global credential.helper cache

By default Git will remember your credentials for 15 minutes. To set a different timeout (in seconds), use a command like this one:

git config --global credential.helper 'cache --timeout=3600'

This will allow Git to remember your credentials for one hour.

Cloning from GitHub with SSH

To clone a repository from GitHub on Quest using the SSH protocol, you must first load your SSH key from Quest into GitHub.

First, in your Quest terminal, print out the contents of your SSH public key:

cat ~/.ssh/id_rsa.pub

This will display several lines of text. Copy it to your computer's clipboard, then go to GitHub and click your profile in the upper right corner, then click "Settings":

In the left sidebar, click "SSH and GPG Keys"

Click "New SSH Key"

In the "Title" field, enter a descriptive name for the key, such as "Quest". Paste the public key you copied earlier into the "Key" field, then click the "Add SSH Key" button. If prompted, confirm your GitHub password.

Now you are able to clone using the SSH protocol.

On the page of a repository you want to clone on GitHub, click "Clone or Download".

Then click the "Use SSH" link.

Next, copy the repository URL.

Finally, in your Quest terminal, run this command (pasting in the URL you copied):

git clone git@github.com/<organization>/<repository>.git

That will download the repository from GitHub into a directory with the same name as the repository. You will now be able to push and pull from this remote repository without having to enter a username and password.

Git Resources

There are many resources for learning Git on the web. See the Research Computing Git Workshop page for a list of resources.