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)

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

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.

2. Configure Positron Server location on Alpine

By default, Positron installs its server components to ~/.positron-server, but $HOME on Alpine has limited space. To avoid filling up your home directory, set up Positron Server on /scratch/alpine:

On Alpine (login or compute node):

# Create directory on scratch (larger allocation)
mkdir -p /scratch/alpine/${USER}/.positron-server

# Create symlink from home to scratch
ln -s /scratch/alpine/${USER}/.positron-server ~/.positron-server

Important notes:

• /scratch/alpine is purged every 90 days of files not accessed
• If the directory is purged, Positron will automatically reinstall the server when you next connect
• You may need to recreate the symlink if it's removed: ln -s /scratch/alpine/${USER}/.positron-server ~/.positron-server
• For more details on how Positron Remote-SSH works, see: https://positron.posit.co/remote-ssh.html#how-it-works-troubleshooting

Quick Start

1. Submit the job to Alpine

sbatch alpine-positron.sh

2. Check job status

squeue -u $USER

Wait until your job is in the "R" (running) state.

3. View connection instructions

cat logs/positron-<JOB_ID>.out

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

4. Connect from Positron

• Open Positron on your local machine

  • Press Cmd+Shift+P (Mac) or Ctrl+Shift+P (Windows/Linux)
  • Select "Remote-SSH: Open SSH Configuration File"

• Paste in your SSH config (from the log file) and save:

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

• Select "Remote-SSH: Connect to Host"

• Choose positron-<JOB_ID> from the list

• Positron will install its server components on the remote node automatically

5. When finished

Always cancel your job to free resources:

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.

R interpreter not discovered

R interpreter discovery can be unreliable on remote systems. If you don't see R under "Start Session" (even though Python interpreters appear):

If you find you are able to use R versions available in the modules system, please let me know.

1. Install R through mamba/conda on the remote system:

   mamba install -c conda-forge r-base

2. Enable conda discovery in Positron settings (on your local machine):

   • Press Cmd+, (Mac) or Ctrl+, (Windows/Linux) to open Settings
   • Search for "Positron R Interpreters Conda Discovery"
   • Enable the checkbox, or add to your settings.json:

     {
         "positron.r.interpreters.condaDiscovery": true
     }

3. Manually trigger interpreter discovery:

   • Press Cmd+Shift+P (Mac) or Ctrl+Shift+P (Windows/Linux)
   • Select "Interpreter: Discover all interpreters"

After these steps, R should appear in the interpreter dropdown and start successfully.

Note: There are multiple discussions in the Positron repository about interpreter discovery issues, though solutions may vary by system configuration.

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