Frequently Asked Questions (FAQ)

If my internet connection goes away or is intermittent - what happens to the running notebook?¶

If you have a running job and your internet is disrupted, the job should continue to run as long as the session does not expire (See JupyterLab Session Information). You can connect to a running session using the same browser or different browser. You can even connect to the same session from different machines.

I was logged out while having a running job. What happens to it?¶

Being logged-in and having a running job or server are independent. An active Server Session is running in the cloud regardless of whether you logged in or not (See JupyterLab Session Information). To access that active Server Session (to stop it or modify it), you need to be logged in. So your running job will not be affected.

How will my analysis be affected by CPU and memory limitations?¶

If your workload exceeds your server size, your server may be allowed to use additional resources temporarily. This can be convenient but should not be relied on. In particular, be aware that your job may be killed automatically and without warning if its RAM needs exceed the allotted memory. This behavior is not specific to Fornax or AWS but users may encounter it more often on the science console due to the flexible machine sizing options. (Your laptop needs to have the max amount of memory that you will ever use while working on it. On the science console, you can choose a different server size every time you start it up – this is much more efficient, but also requires you to be more aware of how much CPU and RAM your tasks need.)

Why was my session stopped?¶

The Fornax Science Console is currently intended for interactive use and will cull sessions which appear to be inactive. The team is working on tools to enable users to submit jobs to run asynchronously. For efficient resource usage, idle interactive sessions will be culled automatically. If you want to keep your session running for longer, you can use the Keep-alive feature in the Fornax menu. See the JupyterLab Session Information section for details.

how long is the period of inactivity that gets culled? It is set to 15 minutes, but it can take a few minutes longer for culling service to be triggered.

Why my html page is blank when opened inside Jupyterlab with Safari?¶

This is a known issue in displaying html files inside Jupyterlab in Safari. The workaround is to right-click (double finger tap) on the html file and select ‘Open in New Browser Tab’. The file should open correctly in a new browser tab.

How do I use Git from Fornax?¶

If you want to clone notebooks or code from a Git repository (repo) into the Fornax Science Console, you can use either the git command-line tool from the terminal or the Git extension UI.

Basic instructions to get started using Git on Fornax are below, including details that are specific to Fornax. For a detailed tutorial about how to use Git in any context, see https://git-scm.com/docs/gittutorial.

One-time setup¶

To set up Git on Fornax for the first time, configure your username and email by opening a terminal and running the following commands:

# Use the username and email associated with your Git account (not your Fornax account).
git config --global user.name "username"
git config --global user.email "your.email@example.com"

To be able to read (or clone) a private repo, or to write to any repo, you will need to use credentials. You can either use your username and password or an access token, both of which you would set up through your Git provider (for example, GitHub).

You can reduce the number of times you need to enter your credentials by configuring git to cache them. In a terminal on Fornax, execute the following command:

# Tell git to cache your credentials for all repos.
# To do this for a single repo instead, cd into the repo directory and remove '--global' before running the command.
git config --global credential.helper cache

Clone a repository¶

After setting up your credentials (if necessary; see above), you can clone a repo using a command similar to one of the following.

Option 1: Clone without passing credentials. (You will be asked to provide them later if/when doing something that requires them.)

git clone https://github.com/{repo-owner}/{repo-name}

Option 2: Pass your personal access token while cloning.

git clone https://{your-token}@github.com/{repo-owner}/{repo-name}