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After opening a new notebook, you will be prompted to select a kernel

If you have never created a kernel to use, you will only see a list of default Jupyter kernels available on the cluster
You may check the box to start with the preferred kernel every time you open a notebook

Default Kernels on ARCC HPC Resources include:

Python Kernels
R Kernels

HPC-wide kernels are titled by packages installed and available when launched

Users can also create user-defined kernels from conda environments (Covered in a subsequent module. See: Launching Jupyter Kernels from Conda Environments)

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Open a New Blank Notebook

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We can use the cell type option in the toolbar to set cell type in the notebook body:

Code: Define computational code (language = from kernel) in the document.
- If the kernel is python cell type, the cell will expect input in the form of python code.
- This is our default code type when new cells are created.
Markdown: Uses Markdown language to build nicely formatted narratives around the code in the rest of the document. Click here for Markdown Cheat Sheet
Raw NBconvert: Used when text should be kept in raw form for conversion to another format (such as HTML or Latex). When you use these, cells marked as Raw are converted in a way specific to your targeted output format.
Heading: For making headings. Somewhat redundant - you can also make headings in a markdown cell.

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Code

Code cells allow you to write and run programming code in a language of your choosing (e.g., Python)
Languages supported in Jupyter include Python, R, Julia, and many others
On ARCC HPC resources, we support jupyter code in Python and R
After running, they can and usually do provide some form of output

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Markdown

Text Cells allowing you to write and render Markdown syntax
Where you describe and document your workflow

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Markdown

Text Cells allowing you to write and render Markdown syntax
Where you describe and document your workflow

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Raw NBConvert

Stands for “Raw Notebook Convert”
Retains any text in these cells in their raw form and does not run them
Enables the conversion of your notebook to another format as given by the FORMAT string using Jinja templates.
- Presenting: PDF
- Publishing: LaTeX
- Collaboration
- Sharing: HTML
Setting to “none” just makes it a “Raw” cell in which nothing is run on it.

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Where are we?

Previously, we said the file management tab shows the filesystem accessible to the user, rooted by the directory from which the notebook was launched.

In the file management tab we can see root directory, and within it, the Desktop, Documents, and Downloads, and ondemand directories.

We could just assume the file manager is showing our home directory. But how would we find out for certain?