Statistical software

This documentation page provides a comprehensive guide on how to use the software installed on our Kristiania-HPC. It also includes instructions for accessing the software on a Kristiania-HPC cluster via SSH.

1. Accessing Stata on HPC

SSH login

Log in to the HPC cluster via SSH:

ssh username@hpc_server_ip

Launch Stata

To run Stata in interactive mode:

stata

To run Stata in batch mode, create a .do file and execute it:

stata -b do script.do

This will execute the commands in script.do and save the output to script.log.

Forward GUI for Stata (Optional)

If you want to use Stata’s graphical interface, enable X11 forwarding:

  1. Install an X server on your local machine:

    • For macOS: Install XQuartz.

    • For Windows: Use an SSH client with X11 support, such as MobaXterm or Xming.

    • For Linux: Ensure xauth and an X server (e.g., xorg) are installed.

  2. Connect to the HPC with X11 forwarding:

    ssh -X username@hpc_server_ip

  3. Launch Stata GUI:

    xstata

2. Accessing RStudio on HPC

Set Up SSH Tunnel for RStudio

To securely access RStudio Server, create an SSH tunnel:

ssh -L 8787:localhost:8787 username@hpc_server_ip

  • Replace username with your HPC username.

  • Replace hpc_server_ip with the HPC cluster’s IP address.

This forwards the HPC’s RStudio port (8787) to your local machine.

Access RStudio in Your Browser

  1. Open a web browser on your local machine.

  2. Navigate to:

    http://localhost:8787

  3. Log in using your HPC credentials.

3. [Optional] Mounting HPC Storage to Your Local System

You can mount HPC storage to your local system for easy file access.

macOS

  1. Install macFUSE:

    • Download and install from macFUSE.

  2. Use sshfs to mount the HPC storage:

    brew install sshfs
mkdir ~/hpc_mount
sshfs username@hpc_server_ip:/path/to/hpc/storage ~/hpc_mount

Windows

  1. Install WinFsp and SSHFS-Win:

  2. Mount the HPC storage using File Explorer:

    • Open This PC, click Map Network Drive, and use the address:

      \sshfs\username@hpc_server_ip\path\to\hpc\storage

Linux

  1. Ensure sshfs is installed:

    sudo apt install sshfs

  2. Mount the HPC storage:

    mkdir ~/hpc_mount
sshfs username@hpc_server_ip:/path/to/hpc/storage ~/hpc_mount

4. [Alternative to 3] Accessing Remote Folders Using VS Code

You can use Visual Studio Code’s Remote - SSH extension to access HPC remote folders seamlessly.

Steps to Configure

  1. Install VS Code:

  2. Install the Remote - SSH Extension:

    • Open VS Code.

    • Go to the Extensions view (Ctrl+Shift+X or Cmd+Shift+X on macOS).

    • Search for “Remote - SSH” and install the extension.

  3. Configure SSH in VS Code:

    • Open the Command Palette (Ctrl+Shift+P or Cmd+Shift+P on macOS).

    • Type “Remote-SSH: Add New SSH Host” and select it.

    • Enter the SSH command to connect to the HPC, e.g.:

      ssh username@hpc_server_ip

    • Choose the SSH configuration file where this should be saved (usually ~/.ssh/config).

  4. Connect to the HPC:

    • Open the Command Palette.

    • Type “Remote-SSH: Connect to Host” and select your HPC entry.

    • A new VS Code window will open, connected to the HPC.

  5. Access Remote Folders:

    • In the new window, use the File Explorer to browse and edit remote files.

For assistance, contact your HPC system administrator.