Reference

VS Code Keyboard Shortcuts

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Essential Shortcuts for Remote Development

Action	Windows/Linux	macOS
Command Palette	Ctrl+Shift+P	Cmd+Shift+P
Quick Open (find file)	Ctrl+P	Cmd+P
Save file	Ctrl+S	Cmd+S
Toggle Sidebar	Ctrl+B	Cmd+B
Toggle Terminal	Ctrl+| Cmd+
Open terminal	Ctrl+Shift+| Cmd+Shift+
Split editor	Ctrl+\	Cmd+\
New terminal	Ctrl+Shift+| Cmd+Shift+
Go to line	Ctrl+G	Ctrl+G
Find	Ctrl+F	Cmd+F
Find in files	Ctrl+Shift+F	Cmd+Shift+F
Find and replace	Ctrl+H	Cmd+H

Remote-SSH Configuration

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SSH Config Syntax

Located at ~/.ssh/config on your local machine:

Host sagehen
    HostName sagehen.hpc.pomona.edu
    User your_username
    IdentityFile ~/.ssh/id_sagehen
    ServerAliveInterval 300
    ServerAliveCountMax 2

Key options: - Host - Alias you use in VS Code - HostName - Full cluster domain - User - Your Pomona username - IdentityFile - Path to your SSH private key - ServerAliveInterval - Keep connection alive (300 = 5 minutes) - ServerAliveCountMax - Max missed pings before disconnect (2)

Connecting to Sagehen HPC from VS Code

1. Click the Remote Explorer icon (left sidebar)
2. Select “SSH Targets” from dropdown (if not already selected)
3. Find “sagehen” in the list
4. Click the connect icon (or right-click → Connect to Host)
5. When prompted, choose “Linux” as the platform
6. Wait for VS Code to initialize remote connection
7. A new window opens connected to Sagehen

Tips for SSH Connection

• First connection takes longer - VS Code installs server components
• DUO authentication - Watch terminal for prompts, approve on phone
• Connection drops - VS Code reconnects automatically
• Multiple windows - Open many VS Code windows, each connected

VS Code Extensions for HPC Work

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Recommended Extensions

Extension	Publisher	Purpose
Remote - SSH	Microsoft	Connect to remote servers
Python	Microsoft	Python development, debugging, linting
Pylance	Microsoft	Advanced Python intelligence
Git Graph	mhutchie	Visualize Git history
Better Comments	Aaron Bond	Color-code comments
Trailing Spaces	Sharla Grayson	Highlight trailing whitespace
SLURM Helper	(if available)	SLURM syntax highlighting

Installing Extensions

On remote system: 1. Open Remote Explorer (Ctrl+Shift+P → “Remote Explorer”) 2. Click Extensions icon in left sidebar 3. Search for extension name 4. Install directly - it installs on Sagehen automatically

On local system: - Same process, but extensions install locally (for local use)

Recommended Settings for HPC

Edit settings (Ctrl+, or Code → Settings):

JSON

{
    "editor.fontSize": 13,
    "editor.formatOnSave": false,
    "editor.autoSave": "afterDelay",
    "editor.autoSaveDelay": 2000,
    "editor.rulers": [79, 120],
    "files.trimTrailingWhitespace": true,
    "files.insertFinalNewline": true,
    "terminal.integrated.fontSize": 12,
    "terminal.integrated.scrollback": 5000,
    "[python]": {
        "editor.defaultFormatter": "ms-python.python",
        "editor.formatOnSave": true
    },
    "remote.SSH.showLoginTerminal": true,
    "remote.SSH.useLocalServer": false
}

Key settings for HPC: - autoSave - Save regularly without asking - rulers - Vertical guides at 79/120 chars (PEP8 standards) - terminal.scrollback - Keep more terminal history - showLoginTerminal - Show authentication prompts (critical!)

Common VS Code Remote-SSH Tasks

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Opening a Folder on Sagehen HPC

1. Click File → Open Folder (Remote)
2. Type the path: /rhome/<myusername>/myproject
3. Click “OK”
4. VS Code opens the folder

Editing Files on Sagehen HPC

Once connected: - File Explorer (Ctrl+Shift+E) shows remote file tree - Click files to open and edit them - Changes sync in real-time - File icons show status (white = unsaved)

Running Code in Terminal

Open the integrated terminal (Ctrl+`) and run commands:

BASH

# Load modules
module load miniconda3

# Run Python script
python my_script.py

# Run Python interactively
python

# Check cluster status
sinfo
squeue -u $USER

Working with Git

VS Code has excellent Git integration even on remote systems:

1. Open Source Control (Ctrl+Shift+G)
2. Initialize repo: “Initialize Repository”
3. Stage files, write commit messages, push/pull

Or from terminal:

BASH

git clone https://github.com/user/repo.git
cd repo
# Edit files...
git add .
git commit -m "message"
git push

Sagehen-Specific Information

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File Paths on Sagehen HPC

BASH

/rhome/<myusername>       # Your home directory (100GB, backed up)
/bigdata/lab/<labname>       # Lab storage (1TB shared, backed up)
/scratch/your_username     # Fast temporary (SSD, not backed up)
/tmpfs                     # RAM-based temp (ultra-fast, not backed up)

For this workshop, edit files in /rhome/<myusername>.

Module System (Lmod)

Load software tools in terminal:

BASH

# View available modules
module avail
module avail python
module avail gcc

# Load modules
module load miniconda3
# gcc is available system-wide on Sagehen -- no module load needed
module load openmpi

# See what's loaded
module list

# Unload
module unload gcc
module purge              # Remove all

# Save/restore environments
module save myenv
module restore myenv

SLURM Job Submission

From the VS Code terminal, submit jobs:

BASH

# Simple job
sbatch my_script.sbatch

# Check queue
squeue -u $USER

# Job details
scontrol show job JOB_ID

# Cancel job
scancel JOB_ID

# View completed jobs
sacct -u $USER --format=jobid,jobname,state,elapsed

Sample SBATCH Script

Create a file my_job.sbatch:

BASH

#!/bin/bash
#SBATCH --job-name=analysis
#SBATCH --output=logs/job_%j.log
#SBATCH --time=01:00:00
#SBATCH --cpus-per-task=4
#SBATCH --mem=8G
#SBATCH --partition=amd

module load miniconda3
python my_analysis.py --input data.csv

Submit with: sbatch my_job.sbatch

Troubleshooting Connection Issues

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General Troubleshooting Steps

1. Verify local SSH works first:

   BASH

   ssh sagehen
   # (type exit to disconnect)

2. Check VS Code output:

   • View → Output
   • Select “Remote-SSH” from dropdown
   • Look for error messages

3. Try reconnecting:

   • Click Remote indicator (bottom-left)
   • Select “Close Remote Connection”
   • Reconnect

4. Restart VS Code:

   • File → Exit
   • Reopen VS Code
   • Reconnect

Common Issues and Solutions

Issue	Cause	Solution
“Could not establish connection”	SSH config or network issue	Verify ssh sagehen works in terminal
“Authentication failed”	Wrong password or expired DUO code	Check caps lock, try new DUO code
“Permission denied (publickey)”	SSH key problem	Try password-only auth, check key permissions
“Operation timed out”	Network/firewall blocking	Check WiFi, try USB tether, contact IT
“VS Code hangs at login”	Remote-SSH not showing terminal	Enable remote.SSH.showLoginTerminal in settings
“Terminal commands not found”	Modules not loaded	Run module load miniconda3 in terminal

Debug Information to Collect

If contacting HPC support:

1. Error message - Copy the exact text from VS Code Output panel
2. Your setup - OS, VS Code version, Remote-SSH version
3. What works - Can you ssh sagehen from terminal?
4. Steps taken - What have you already tried?

Contact: its-hpc@pomona.edu

File Transfer Between Local and Sagehen HPC

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Using SCP from Terminal

BASH

# Copy local file to Sagehen home
scp myfile.txt sagehen:~/

# Copy from Sagehen to local
scp sagehen:~/myfile.txt ./

# Copy entire directory
scp -r sagehen:~/myproject ./myproject_copy

# Copy with progress
scp -v sagehen:~/largefile.tar.gz ./

Using VS Code File Explorer

1. Open folder on Sagehen (File → Open Folder Remote)
2. Right-click a file → “Download…” to get it locally

Or drag-and-drop files between VS Code window and file explorer.

Python Development on Sagehen HPC

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Selecting Python Interpreter

1. Open Command Palette (Ctrl+Shift+P)
2. Type “Python: Select Interpreter”
3. Choose from available environments
4. Or choose “Enter interpreter path…” for custom

Running Python Code

Interactive terminal:

BASH

python
>>> import numpy as np
>>> np.array([1, 2, 3])

Run script:

BASH

python my_script.py

Debug (set breakpoints): 1. Click left of line number to set breakpoint (red dot) 2. Press F5 (or click Run) 3. VS Code stops at breakpoint 4. Use Debug Console to inspect variables

Virtual Environments

Create and use Python venvs:

BASH

# Create venv
python -m venv myenv

# Activate
source myenv/bin/activate

# Install packages
pip install numpy pandas scipy

# Deactivate
deactivate

VS Code’s interpreter picker finds and uses venvs automatically.

Resources and Support

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Documentation

• VS Code Remote-SSH: https://code.visualstudio.com/docs/remote/ssh
• VS Code Settings: https://code.visualstudio.com/docs/getstarted/settings
• SLURM Manual: https://slurm.schedmd.com/sbatch.html
• Sagehen Cluster: https://pomona-college.github.io/

Getting Help

• Email: its-hpc@pomona.edu
• Instructor: Andrew Wilson
• OnDemand: https://ondemand.hpc.pomona.edu/ (web interface alternative)

Useful Commands

BASH

# Check cluster status
sinfo

# Your account info
sacctmgr show user $USER

# Disk usage
du -sh /rhome/$USER
du -sh /scratch/$USER

# Check modules
module avail

# View recent jobs
sacct -u $USER --format=jobid,jobname,state,elapsed --units=M

Tips for Productive HPC Workflow

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1. Use terminal in VS Code - Stays in your project folder
2. Keep files on Sagehen - Avoid syncing large files locally
3. Test scripts locally first - Easier debugging on your machine
4. Use SLURM for real work - Terminal is for testing
5. Monitor jobs frequently - Catch errors early with squeue
6. Save logs - Use #SBATCH --output to capture job output
7. Backup important files - Use /rhome (backed up) not /scratch