Connecting to Sagehen HPC

Last updated on 2026-08-27 | Edit this page

Overview

Questions

  • How do I connect to Sagehen using VS Code Remote-SSH?
  • How do I handle DUO authentication in VS Code?
  • What should I do if I get disconnected?

Objectives

  • Connect to Sagehen HPC cluster using Remote-SSH
  • Authenticate with DUO MFA through VS Code
  • Open a remote folder and browse files
  • Handle disconnections and reconnect

Your First Connection

Step 1: Open the Remote Explorer

The VS Code Remote Explorer panel open from the activity bar. Under Remotes and an SSH group, a host named sagehen appears with a green connected badge.
The Remote Explorer sidebar with the sagehen host from your SSH config, shown here already connected.

Click the Remote Explorer icon in the left sidebar. You should see “sagehen” listed from your ~/.ssh/config. If not, click the “+” icon to add a new SSH target and enter sagehen.hpc.pomona.edu.

Step 2: Connect

  1. Hover over “sagehen” in the Remote Explorer
  2. Click the connect icon (arrow pointing to a folder)
  3. A new VS Code window opens
  4. Select Linux when prompted for platform
  5. Click Yes, I trust the authors if a trust dialog appears

Step 3: DUO Authentication

A VS Code window mid-connection. The integrated terminal notes this shell runs on the local machine, prints OpenSSH warnings that the connection is not using a post-quantum key exchange algorithm, and shows a password prompt for the user at sagehen.hpc.pomona.edu. A notification reads Setting up SSH Host sagehen, Initializing VS Code Server.
Mid-connection: the login terminal asks for your Pomona password while VS Code Server is set up on Sagehen. The OpenSSH “post-quantum key exchange” warning above the prompt is expected — it’s informational, not an error.
Callout

Completing DUO Authentication in VS Code

A terminal window appears at the bottom of VS Code:

  1. Enter your Pomona password at the password prompt
  2. At the DUO prompt, type a 6-digit code from your DUO app, or type “call”
  3. Complete the authentication

After success, the terminal closes and VS Code shows “SSH: sagehen” in the bottom-left status bar.

Opening Your Remote Folder

  1. Click File > Open Folder (or Ctrl+K Ctrl+O / Cmd+K Cmd+O)
  2. Navigate to /rhome/<myusername> (your home directory)
  3. Click Open

The Explorer sidebar now shows your remote files on Sagehen.

Connection States and Reconnection

State Indicator Action
Connected Green “SSH: sagehen” Working normally
Connecting Blue/spinning Wait 5-10 seconds
Reconnecting Blue VS Code auto-reconnects (~5 min)
Offline Red/disconnected Fix network, click Reconnect

If automatic reconnection fails:

  1. Click the SSH status button (bottom-left)
  2. Select “Close Remote Connection”
  3. Wait a few seconds, then reconnect from Remote Explorer

For extended disconnections, close VS Code entirely, reopen, and reconnect through Remote Explorer. You will need to re-authenticate with DUO.

Disconnecting When Done

  1. Click the “SSH: sagehen” button (bottom-left)
  2. Select “Close Remote Connection”

Your files on Sagehen remain unchanged.

Challenge

Challenge: Connect, Explore, and Reconnect

  1. Connect to Sagehen from Remote Explorer
  2. Open your home folder (/rhome/<myusername>)
  3. Browse some folders in the Explorer sidebar
  4. Disconnect (SSH button > Close Remote Connection)
  5. Reconnect and verify “SSH: sagehen” reappears

Success indicators:

  • Bottom-left shows green “SSH: sagehen” button
  • Explorer sidebar shows your home directory contents (.bashrc, project folders)
  • Opening a terminal (Ctrl+`) shows [<myusername>@sagehen-login-1 ~]$
  • After reconnecting, the green indicator returns (faster than first connection since VS Code Server is already installed)

If no DUO prompt appears, verify remote.SSH.showLoginTerminal is enabled.

Key Points
  • Use Remote Explorer to connect to Sagehen and select Linux as the platform
  • remote.SSH.showLoginTerminal must be enabled for DUO prompts to appear
  • After connecting, open /rhome/<myusername> to browse your remote files
  • VS Code automatically attempts reconnection after network interruptions
  • Disconnect via the SSH status button when finished