Introduction to HPC Systems

Welcome to Workshop 0: Introduction to HPC Systems

This workshop is your gateway to high-performance computing at Pomona College. Whether you’re a first-time HPC user or transitioning from personal computers to cluster computing, this introductory workshop will guide you through everything you need to know to begin using Sagehen HPC, our powerful research computing cluster.

What You’ll Learn

By the end of this workshop, you will be able to:

  • Understand what high-performance computing (HPC) is and why it matters for research
  • Connect securely to Sagehen using SSH and navigate the two-factor authentication process
  • Navigate the Sagehen filesystem and understand the different storage spaces available
  • Recognize Sagehen’s hardware architecture, including compute nodes and GPU nodes
  • Use the module system to load and manage software packages
  • Submit and monitor your first computational job

About Sagehen HPC

Sagehen (sagehen.hpc.pomona.edu) is Pomona College’s research computing cluster managed by Information Technology Services (ITS). It features:

  • 12 AMD EPYC compute nodes: 128 cores and 500 GB RAM each
  • GPU-enabled nodes: Sagehen has 10 GPUs across multiple nodes (4× NVIDIA A100 80 GB, 4× L40S 48 GB, 2× RTX PRO 6000 96 GB; confirmed May 2026 — see Workshop 16 for full hardware breakdown)
  • Multiple storage systems: Home directories (100 GB), lab storage (1 TB), and high-speed scratch space
  • SLURM job scheduler: Manage computational jobs efficiently across all users
  • Lmod software environment: A managed Lmod environment with hundreds of pre-built software modules
  • OnDemand web portal: Access via browser without SSH

Workshop Structure

This 10-episode workshop is organized as follows:

  1. What is HPC? - Understand high-performance computing concepts and Sagehen’s role
  2. Why Use HPC? - Recognize when an HPC cluster is the right tool for your research
  3. Connecting to Sagehen - SSH access, DUO authentication, and your first login
  4. Navigating the Filesystem - Understanding directories, storage spaces, and Linux basics
  5. Files and Directories - Working with files, directories, and basic commands on Sagehen
  6. Cluster Architecture - Learn about nodes, partitions, and hardware specifications
  7. Nodes and Partitions - Survey Sagehen’s compute, GPU, and login nodes and how SLURM partitions group them
  8. Software Modules - Discover and use the Lmod module system
  9. Running Your First Job - Submit and monitor a SLURM batch job
  10. Next Steps - Build on this foundation with the rest of the Pomona HPC workshop series
Prerequisite

Prerequisites

This workshop assumes no prior HPC experience, but you should have: - Pomona College credentials: Your @pomona.edu email and password - DUO authentication: Access to your Pomona DUO account for two-factor authentication - A computer with SSH: macOS and Linux have SSH built-in; Windows users can use PowerShell, WSL, or PuTTY - An HPC account: Contact to request one if needed

How to Use This Workshop

  • For learners: Work through each episode in order. We recommend having a terminal open so you can follow along with examples on Sagehen.
  • For instructors: See the Instructor Notes for detailed timing, common questions, and teaching strategies.
  • For quick reference: Check the Quick Reference Card for command syntax and useful information.

Getting Help

Callout

Important: This is a Shared Resource

Sagehen is used by hundreds of researchers. Please be a good neighbor: - Don’t run computationally intensive jobs on the head node - Clean up your temporary files regularly - Respect resource quotas and time limits - Report issues to

About The Carpentries

This workshop follows The Carpentries approach to teaching, emphasizing hands-on learning, realistic examples, and community collaboration. Learn more at carpentries.org.

Ready to get started? Begin with Episode 1: What is HPC?.

Acknowledgments

Developed by Andrew Wilson, Director of Research Computing and Digital Scholarship at Pomona College, with Andrei Motchenko, who tested, edited and produced screenshots for the workshop series.

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Getting Started with Sagehen HPC

This workshop assumes you have access to Sagehen, Pomona College’s research computing cluster. By the end of this setup process, you’ll have everything needed to connect and run your first job.

Prerequisites

Before you start, you’ll need:

  1. Pomona College credentials: Your @pomona.edu email and password
  2. DUO authentication: Access to your registered DUO account (for two-factor authentication)
  3. A computer with a terminal/SSH client: See below for your operating system
  4. An HPC account on Sagehen: request one via the HPC account request form if you don’t have one yet

Step 1: Request an HPC Account

If you don’t already have access to Sagehen, there are two ways to request an account:

  1. Preferred: submit the HPC account request form on the ITS Service Desk.

  2. Or email with:

    • Your full name
    • Your @pomona.edu email address
    • Your department/major
    • Your faculty advisor or PI (if applicable)
    • A brief description of your research or coursework

Either way, the HPC team will respond within 1-2 business days confirming your account is ready

  1. You’ll receive instructions to complete your first login

Step 2: Set Up SSH Access

SSH (Secure Shell) is how you connect to Sagehen. Choose your operating system below:

Discussion

SSH Setup for Your Operating System

SSH clients allow you to securely connect to Sagehen. Most systems have SSH built-in. Follow the instructions for your operating system.

macOS includes SSH built-in. No installation needed!

To connect to Sagehen: 1. Open Terminal (Applications > Utilities > Terminal) 2. Type the command:

BASH 

ssh <myusername>@sagehen.hpc.pomona.edu

Replace username with your Pomona username (the part before @pomona.edu) 3. On first connection, you’ll see a prompt about the host key. Type yes to continue. 4. Enter your Pomona password 5. Complete DUO authentication (see Step 3 below)

Option A: PowerShell (Recommended)

Windows 10 and 11 include SSH in PowerShell natively. 1. Open PowerShell (Windows key + X, select Windows PowerShell, or search “PowerShell”) 2. Type:

POWERSHELL 

ssh <myusername>@sagehen.hpc.pomona.edu
  1. Enter your Pomona password
  2. Complete DUO authentication

Option B: Windows Subsystem for Linux (WSL)

For a full Linux environment: 1. Open PowerShell as Administrator 2. Run: wsl --install 3. Restart your computer 4. Open WSL Terminal and follow the Linux instructions (below)

Option C: PuTTY (Graphical)

For a graphical interface: 1. Download PuTTY from https://www.putty.org/ 2. Open PuTTY 3. In “Host Name”, enter: sagehen.hpc.pomona.edu 4. Leave Port as 22 5. Click “Open” 6. Enter your username and password 7. Complete DUO authentication

Linux includes SSH by default. 1. Open your terminal (usually Ctrl+Alt+T) 2. Type: bash ssh <myusername>@sagehen.hpc.pomona.edu 3. Enter your Pomona password 4. Complete DUO authentication

Step 3: Complete DUO Authentication

When you connect to Sagehen, you’ll see a DUO prompt:

Duo Authentication

1. Push (Duo app)
2. SMS
3. Backup Code

Passcode or option (1-3):

Recommended: Use Push Notification

  1. Type 1 and press Enter
  2. Look at your phone for a notification from “Duo Mobile”
  3. Tap “Approve”
  4. You’ll be logged in!

Alternative: Use SMS

If you don’t have the Duo app:

  1. Type 2 and press Enter
  2. Check your phone for a text with a 6-digit code
  3. Type the code and press Enter
  4. You’ll be logged in

Step 4: Test Your Connection

Once connected, you should see:

[<myusername>@sagehen ~]$

Verify everything works by running:

BASH 

# Check your username
whoami

# Confirm you're on Sagehen
hostname

# View available modules
module avail | head -20

You should see your username, “sagehen”, and a list of available software modules.

Create directories for organizing your work:

BASH 

# Navigate to your home directory
cd

# Create directories for this workshop
mkdir -p workshop-0

# Verify they exist
ls -la

You can also customize your shell by editing ~/.bashrc:

BASH 

nano ~/.bashrc

Jump to end of file with Alt + / (or Ctrl+End)

Add these useful aliases at the end with Right-click or Ctrl+Shift+V:

BASH 

# Useful aliases
alias ll='ls -lah'
alias sq='squeue -u $USER'
alias sa='sacct -u $USER'

# Useful module setup (optional). Loading without a version picks up the
# current default, so this keeps working when modules are updated:
module load miniconda3

Save with Ctrl+O, Enter, Ctrl+X.

Troubleshooting Connection Issues

“Permission denied (publickey)”

Problem: Can’t log in

Solutions: - Check your username is correct (not your email) - Verify hostname: sagehen.hpc.pomona.edu - Confirm your password is correct - Ensure your Pomona account is active

“DUO authentication failed”

Problem: DUO won’t authenticate

Solutions: - Ensure Duo Mobile app is installed and registered - Check your phone volume isn’t muted - Try SMS option if push notification fails - Verify your phone number is correct in Pomona account settings - Contact Pomona IT if continuing to fail: (909) 621-8061 or

“Connection timeout” or “Network unreachable”

Problem: Can’t connect to Sagehen

Solutions:

  • Check your internet connection
  • Verify you can reach other Pomona services (email, Canvas)
  • If off-campus, try using Pomona VPN
  • Confirm your HPC account is active (check email from )

Commands Not Found

Problem: After login, common commands don’t work

Solution: Load modules! HPC clusters require loading software. First find what’s available:

BASH 

module avail              # list everything available
module spider conda       # search for a specific package

Then load what you found, using the full name including the version:

BASH 

module load miniconda3/py313_26.3.2-2
python --version
module list               # confirm what's loaded

Next Steps

Once you can successfully connect to Sagehen:

  1. Start with Episode 1: What is HPC?
  2. Work through each episode in order
  3. Refer to the Quick Reference Card as needed
  4. Complete the challenges to build your skills

Getting Help

If you’re stuck:

Account Checklist

Before you begin the workshop, confirm you have:

Once all these are checked, you’re ready to start the workshop!