HPC Bootcamp Fall 2024

Introduce users to typing commands using the command line to work with the Linux operating system. Focusing on hands-on exercises, it will introduce the basic structure and use of the file system, and how to find help.

Introduce how to work with, view, find and search the content of text files. The workshop is aimed at beginners with basic command-line experience of the Linux file system and will focus on hands-on exercises.

Prerequisites: Basic command-line experience or attendance at Intro to Linux Command Line: The File System

Introduce the various text editors available on our Services. Using emacs as a GUI via an OnDemand interactive desktop, and vim/nano from a terminal command line.

Prerequisites: Basic command-line experience or attendance at either Intro to Command Line module

Introduce UW ARCC, our core services, and how we can help.
Introduce the core concepts behind High Performance Computing and clusters.
Introduce available HPC Resources to UW Researchers

Introduce users on how to remotely access the clusters

• Over the web using OnDemand

• Accessing Beartooth with traditional SSH and 2 factor authentication

• Accessing MedicineBow using passwordless authentication

Introduce users to LMOD, ARCC’s HPC software module system.
Introduce how to set up and personalize their environment and software for their computational needs.

Introduce users to job management using the Slurm system - demonstrating how to create interactive jobs and submit jobs to the cluster queue that follow a basic workflow.

Introduce OnDemand

Show users how to navigate remote web access to HPC Services.

Introducing the concept of data management with a focus on some common best practices of working with data on ARCC systems.

The practical options for transferring data from onto HPC systems from local computers and remote servers.

 Introduce what Conda is and how it can be used to create a variety of environments, such as Python/R and contained applications.

Discuss how the various Python related tools work together on the cluster and introduce a series of best practices for managing these environments. (**Note: This is not an introduction to programming in Python. It covers how to use Python, Conda and Pip on an HPC cluster)

Prerequisites: Intermediate users of HPC or attendance at prior modules, and experience programming in Python

Discuss how the various R related tools and RStudio work together on the cluster and introduce a series of best practices for managing these environments. (**Note: This is not an introduction to programming in R. It covers how to use R and RStudio on an HPC cluster)

Prerequisites: Intermediate users of HPC or attendance at prior modules, and experience programming in R or RStudio

• Demonstrate how to use the OnDemand Jupyter Service across a variety of available languages and kernels.

• Demonstrate how to convert an existing Conda environment into a kernel that can be used within a notebook.

Prerequisites: Intermediate users of HPC or attendance at Using Python, Conda and Pip on the Cluster

If you have any questions or need help with something that wasn’t covered in the bootcamp, we have allocated some of the morning to go over concepts that were not covered, or things you may want additional help with.