Alpine Positron

Launch Positron on Alpine, the University of Colorado Boulder's HPC cluster.

Overview

This SLURM batch script allocates a compute node on Alpine and provides SSH connection instructions for remote development with Positron. The script uses a ProxyJump SSH configuration to connect through Alpine's login node to your allocated compute node.

Prerequisites

• Access to Alpine HPC cluster
• Positron installed on your local machine
• SSH key configured for Alpine access

Setup (One-time)

Add your local machine's SSH key to Alpine:

If you haven't already, you need to add your local machine's public SSH key to Alpine's authorized_keys file.

1. On your local machine, copy your public key:

   cat ~/.ssh/id_rsa.pub

   Or if you use a different key:

   cat ~/.ssh/id_ed25519.pub

2. Log into Alpine and add the key to authorized_keys:

   ssh <your-username>@login.rc.colorado.edu

3. On Alpine, add your public key:

   mkdir -p ~/.ssh
   chmod 700 ~/.ssh
   echo "your-public-key-content" >> ~/.ssh/authorized_keys
   chmod 600 ~/.ssh/authorized_keys

   Replace your-public-key-content with the output from step 1.

This allows your local machine to authenticate with Alpine compute nodes via the ProxyJump connection.

Quick Start

1. Submit the job to Alpine:

   sbatch alpine-positron.sh

2. Check job status:

   squeue -u $USER

3. View connection instructions:

   cat logs/positron-<JOB_ID>.out

   Replace <JOB_ID> with your actual job ID from squeue.

4. Add SSH config to your local machine:

   Copy the SSH config block from the log file and add it to your ~/.ssh/config on your local machine. It will look like:

   Host positron-<JOB_ID>
       HostName <compute-node>
       User <your-username>
       ProxyJump <your-username>@login-ci.rc.colorado.edu
   

5. Connect from Positron:

   • Open Positron on your local machine
   • Press Cmd+Shift+P (Mac) or Ctrl+Shift+P (Windows/Linux)
   • Select "Remote-SSH: Connect to Host"
   • Choose positron-<JOB_ID> from the list
   • Positron will install itself on the remote node automatically

6. When finished:

   scancel <JOB_ID>

Configuration

The script allocates resources via SLURM directives in alpine-positron.sh:

• --time=08:00:00 - Maximum job duration (8 hours)
• --mem=20gb - Memory allocation (20 GB)
• --partition=amilan - Alpine partition for general compute
• --qos=normal - Quality of service tier

Adjust these parameters based on your computational requirements. See Alpine documentation for available options.

Troubleshooting

Job won't start:

• Check queue status: squeue -u $USER
• Check available resources: sinfo
• Verify your account has hours: curc-quota

Can't connect via SSH:

• Ensure SSH config was added to your local ~/.ssh/config (not on Alpine)
• Verify job is running: squeue -u $USER
• Check log file for correct hostname and job ID
• Verify your local SSH public key is in Alpine's ~/.ssh/authorized_keys (see Setup section)

Connection drops:

• SSH connection may timeout if idle. The job itself will continue running.
• Reconnect using the same SSH host entry.

Notes

• The compute node allocation will run for the full time requested or until you cancel it
• Always remember to scancel your job when done to free resources
• Log files are stored in the logs/ directory with the pattern positron-<JOB_ID>.out

Resources

• Alpine Documentation
• Positron Documentation
• Positron Remote SSH Documentation
• CU Research Computing Support