Positron over Remote SSH

Launch Positron on Alpine (CU Boulder) or amc-bodhi (CU Anschutz) HPC clusters.

Overview

This script allocates a compute node on your HPC cluster and provides SSH connection instructions for remote development with Positron. It uses a ProxyJump SSH configuration to connect through the login node to your allocated compute node.

• Alpine (CU Boulder): Uses SLURM job scheduler
• amc-bodhi (CU Anschutz): Uses SLURM job scheduler

Prerequisites

• Access to Alpine or amc-bodhi HPC cluster
• Positron installed on your local machine
• SSH key configured for cluster access
• amc-bodhi only: Connected to AMC VPN

Setup (One-time)

Run the setup command from your local machine:

# For Alpine:
./positron-remote.sh setup alpine

# For amc-bodhi:
./positron-remote.sh setup bodhi

This will:

1. Copy your local SSH public key to the cluster (via ssh-copy-id)
2. Create a Positron Server symlink on scratch storage (Alpine only — $HOME has limited space, /scratch/alpine has more room)
3. Print recommended Positron settings

Important notes (Alpine):

• /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 re-run ./positron-remote.sh setup alpine to recreate the symlink
• For more details on how Positron Remote-SSH works, see: https://positron.posit.co/remote-ssh.html#how-it-works-troubleshooting

Recommended Positron Settings

By default, R and Python sessions terminate when Positron disconnects. On HPC, brief network interruptions are common and you don't want to lose your session within a running SLURM allocation. Add this to your Positron settings.json (local machine):

{
    "kernelSupervisor.shutdownTimeout": "never"
}

This keeps R/Python sessions alive on the remote host so you can reconnect without losing your work.

Quick Start (Alpine)

1. Submit the job to Alpine

./positron-remote.sh alpine

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-alpine-<JOB_ID>
      HostName <compute-node>
      User <your-username>
      ProxyJump <your-username>@login-ci.rc.colorado.edu
      ForwardAgent yes
      ServerAliveInterval 60
      ServerAliveCountMax 3
  

• Select "Remote-SSH: Connect to Host"

• Choose positron-alpine-<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>

Quick Start (amc-bodhi)

Important: You must be connected to the AMC VPN before proceeding.

1. Submit the job to amc-bodhi

./positron-remote.sh bodhi

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-bodhi-<JOB_ID>
      HostName <compute-node>
      User <your-username>
      ProxyJump <your-username>@amc-bodhi.ucdenver.pvt
      ForwardAgent yes
      ServerAliveInterval 60
      ServerAliveCountMax 3
  

• Select "Remote-SSH: Connect to Host"

• Choose positron-bodhi-<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

Resources are configured via SLURM directives in positron-remote.sh. Default values per cluster:

Setting	Alpine	amc-bodhi
--time	8 hours	8 hours
--mem	24 GB	20 GB
--partition	amilan	normal
--qos	normal	normal

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 on the cluster (re-run ./positron-remote.sh setup alpine)

Connection drops

• SSH connection may timeout if idle. The job itself will continue running.
• Reconnect using the same SSH host entry.
• The SSH config generated by the script includes ServerAliveInterval and ServerAliveCountMax to reduce idle timeouts.

Connection fails after updating Positron

• The Positron client and server must be exactly the same version. If you update Positron on your local machine, the remote ~/.positron-server may have an old version.
• Delete the remote server and reconnect:

  # On Alpine:
  rm -rf /scratch/alpine/${USER}/.positron-server
  # Or if not using the scratch symlink:
  rm -rf ~/.positron-server

• Positron will automatically reinstall the correct server version on reconnect.

Extensions missing in remote session

• Extensions installed on your local machine are not automatically available on the remote host.
• After connecting to a remote session, install any needed extensions from the Extensions panel — they will be installed on the remote server.

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