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Setting Up Tufts HPC Access in VSCode

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Step 0: Establish a VPN connection​

Whether you are on or off of Tufts campus, you'll will need to be first connected to the Tufts VPN. For instructions, see https://access.tufts.edu/vpn

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Even if you are on-campus, we always recommend that you connect to the Tufts VPN when interfacing with the Tufts High-Performance Computing (HPC).

  • Only connecting to the HPC through the Tufts Secure Wi-Fi network can be problematic due to intermittent connection drops that will make you temporarily lose connection to the HPC and can potentially lead to errors when running this workflow. This problem is especially prevalent when connecting via VSCode.

  • Additionally, you will not need to need to authorize your interactions with the HPC on Duo as frequently, if at all, after you initially connect to the VPN.

Step 1: Download and Install Visual Studio Code (VSCode)​

Visual Studio Code (VSCode) is a free, open-source code editor developed by Microsoft. It's widely used for software development due to its versatility, rich feature set, and extensive extension ecosystem. In the context of interacting with the Tufts High-Performance Computing (HPC) resources, VSCode offers several advantages:

  • Remote Development: VSCode can seamlessly connect to remote servers, allowing you to edit files, run code, and manage projects directly on the HPC without leaving your local environment.
  • Integrated Terminal: Access the HPC terminal within VSCode, enabling efficient command-line operations alongside your coding activities.
  • Extensions and Customization: Enhance your development experience with extensions tailored for specific programming languages, debugging tools, and workflow optimizations.

Download and Install VSCode​

Windows:​

  • Run the downloaded .exe installer.
  • Follow the installation prompts, accepting the license agreement and selecting desired installation options (e.g., adding VSCode to your PATH).

macOS:​

  • Open the downloaded .dmg file.
  • Drag and drop the VSCode application into the Applications folder.

Launch VSCode​

After installation, open VSCode from your application launcher or by running code in your terminal (if added to PATH).

To enhance your experience when working with the Tufts HPC, consider installing the following extensions:

tip

While not all of these extensions are required they are all highly recommended as they will dramatically improve your coding experience when using VSCode in conjunction with this workflow.

🔒 SSH Extensions – 🚨[Required]🚨​

Facilitate secure connections and file transfers:

  • SSH FS
    Mounts SSH remote filesystems locally for easy access and editing.
    Essential for connecting to the Tufts HPC.
note

There are multiple options for SSH extensions in VSCode that can replace the functionality of SSH FS, but this extension is the extension used currently by the creators of this workflow. If you are already familiar with another extension, feel free to use it instead.

🐍 Python Extensions – 🚨[Required]🚨​

Enhance Python development with debugging and language support:

  • Python
    Provides rich support for Python, including IntelliSense, linting, and debugging.

  • Pylance
    Offers fast and feature-rich language support for Python.

  • Python Debugger
    Integrated debugging capabilities for Python applications.

🐍 Snakemake Extensions – 🚨[Required]🚨​

Streamline Snakemake workflows:

  • Snakemake Language
    Adds syntax highlighting and snippets for Snakemake files.

  • Snakefmt
    Formats Snakemake files according to best practices.

🔧 VSCode Quality of Life Extensions​

Improve your coding environment with these quality-of-life extensions:

  • indent-rainbow
    Highlights indentation levels with different colors for better readability.

  • Material Icon Theme
    Provides a set of icons for various file types to enhance the visual appeal of your file explorer.

  • oh-lucy
    Adds aesthetic themes and enhancements to your editor.

  • Prettier
    An opinionated code formatter that supports many languages.

  • Todo Tree
    Displays TODOs, FIXMEs, and other annotations in a tree view.

  • vscode-pdf
    Enables PDF viewing directly within VSCode.

📄 Markdown Extensions​

Improve Markdown editing and linting:

  • Markdown All in One
    Provides comprehensive Markdown support with shortcuts and previews.

  • markdownlint
    Lints Markdown files to enforce consistent style and formatting.

📈 Excel/CSV File Extensions​

Manage Excel and CSV files seamlessly:

  • Rainbow CSV
    Highlights CSV and other delimited files with different colors for each column.

  • Excel Viewer
    Allows viewing Excel files directly within VSCode.

🗂️ Git Extensions​

Optimize your Git workflows:

  • Git Graph
    Visualize Git repositories with a comprehensive graph view.

📊 R Extensions​

Enhance R programming with debugging and documentation:

  • R
    Provides R language support, including syntax highlighting and snippets.

  • R Debugger
    Implements debugging tools for R scripts.

  • Doxygen Documentation Generator
    Assists in generating Doxygen-style documentation from R code.

📌 Additional Notes​

  • Installation:
    To install these extensions, open VSCode, navigate to the Extensions view by clicking on the Extensions icon in the sidebar or pressing Ctrl+Shift+X (Cmd+Shift+X on macOS), and search for each extension by name.

  • Configuration:
    Some extensions require additional configuration. Refer to each extension's documentation for set-up and usage instructions.

  • Sync Settings:

    Ensure that your VSCode settings are optimized for remote work. Consider synchronizing settings across devices if you work from multiple machines. You can accomplish this by signing into VSCode using a GitHub account.

Step 3: Configuring SSH FS to Remotely Connect to the Tufts HPC​

Set-Up SSH Keyless Access to the Tufts HPC​

Please follow the instructions below to setup your SSH keyless access. This will make your life much easier in the long run as you will not need to input your password every time you connect to the cluster using VSCode.

Setting Up SSH FS​

Configuring a Connection​

Using a Configuration​

Step 4: Learning to Connect and Navigate the Tufts HPC in VSCode​

Command Line Access​

Directory / File Management​