Start here · RCC ClusterDocs

Use VS Code with RCC

VS Code with Microsoft's Remote - SSH extension is the recommended day-to-day interface for most RCC users. It gives you an editor, terminal, Git tools, and a small remote file view in one window.

VS Code is the interface. It does not create a compute allocation. Use it to prepare and inspect work on the shell host; submit computation through Slurm.

Before installing VS Code

Make terminal SSH work first:

ssh shellhost

Follow the macOS or Windows 11 checklist if this does not work. VS Code uses the same SSH key, configuration, jump host, and shell host. The editor cannot repair an incorrect SSH setup.

1. Install the editor and one extension

1. Install the current stable Visual Studio Code from Microsoft's official distribution for macOS or Windows.
2. Open the Extensions view.
3. Install Microsoft's Remote - SSH extension.
4. Do not install a large extension collection at first. Add only what the project needs after reviewing its publisher and permissions.

On a managed workstation, use the institution's approved software route when one is provided. Do not disable Gatekeeper, SmartScreen, antivirus, or other endpoint controls to install the editor.

2. Connect to the shell host

1. Open the Command Palette with F1 or Shift-Command-P on macOS, or F1 or Ctrl-Shift-P on Windows.
2. Choose Remote-SSH: Connect to Host….
3. Select shellhost.
4. Confirm only the expected, independently verified RCC host identity.
5. Wait for the lower-left connection indicator to show the remote target.

Do not select the jump-host alias. ProxyJump crosses that forwarding gateway automatically and opens VS Code on the shell host.

3. Open one useful directory

Open the smallest project subdirectory that contains the code you need, for example:

/projects/<project>/workflows/<workflow>/

Do not open /projects, /groups, /homes, an entire large project, a raw data tree, or a workflow cache as the VS Code workspace. Broad file watching, Git discovery, search, and language indexing can turn a convenient editor into a large shared-storage workload.

4. Exclude data and generated trees

Add project-specific exclusions to .vscode/settings.json only after review. A useful starting shape is:

{
  "files.watcherExclude": {
    "**/.git/objects/**": true,
    "**/.snakemake/**": true,
    "**/.nextflow/**": true,
    "**/work/**": true,
    "**/results/**": true,
    "**/data/**": true,
    "**/envs/**": true
  },
  "search.exclude": {
    "**/.snakemake": true,
    "**/.nextflow": true,
    "**/work": true,
    "**/results": true,
    "**/data": true,
    "**/envs": true
  }
}

Adjust this list to the repository. Do not exclude workflow definitions, configuration, tests, logs needed for diagnosis, or other source that the team expects to review.

5. Use the integrated terminal correctly

Good shell-host activities in the VS Code terminal include:

• editing and testing small pieces of code;
• using Git;
• running a Snakemake dry run;
• starting the managed Snakemake or rcc-nextflow controller;
• submitting a batch job with sbatch;
• checking squeue, sacct, and small text logs; and
• opening a documented interactive allocation.

Do not run sustained Python, R, genomics, model, GPU, large-memory, or high-I/O analysis directly in the VS Code terminal on the shell host. Do not assume a Python or Jupyter extension has allocated compute resources.

6. Treat the remote workspace as executable

VS Code extensions, repository tasks, debug configurations, notebook kernels, and workspace settings can execute commands with your RCC account. Before granting Workspace Trust to an unfamiliar repository:

• inspect .vscode/, task definitions, launch configurations, and notebooks;
• review extension recommendations;
• remove secrets and protected identifiers from settings and logs; and
• confirm that tasks submit sustained work through Slurm.

Never enable SSH agent forwarding, paste a private key into VS Code, or bypass a changed host-key warning to make Remote - SSH connect.

7. Edit a repeatable workflow

A useful project window normally contains small, reviewable files such as:

README.md
config/
workflow/ or main.nf
scripts/
envs/
tests/

Use the script-to-workflow guide when the starting point is shell history or a command collection. Keep large inputs, outputs, installed Conda environments, container caches, and workflow work directories outside Git and outside editor-wide search.

Common failures

You are ready when

• terminal SSH and Remote - SSH reach the same configured target;
• VS Code opens only the relevant project or repository directory;
• data and generated trees are excluded from watching and search;
• the integrated terminal submits computation through Slurm; and
• you can explain that the jump host forwards, the shell host controls, and a Slurm worker computes.

For screenshots and deeper settings, continue with the complete SSH and VS Code reference.