2. Accessing the HPC environment

Questions:

• "How do I log on to the HPC resources?"

Objectives:

• "Learn to access the HPC environment from your OS"

Keypoints

• "Remote shells, EI’s HPC hostname"

The High Performance Computing (HPC) system offers versatile remote access options, whether you're on-site or off-site, utilizing a secure VPN connection. Upon gaining remote access, users are allocated a 'session' or 'shell' on a 'login' node, also known as 'submission' or 'head' nodes. Once connected, users can directly submit commands to HPC nodes or queue larger jobs through the integrated job scheduling system, SLURM.

To initiate a session on the HPC, the process varies depending on your operating system. Assuming that you’re on the campus network:

Accessing NBI HPC (Mac):

• Open a terminal (cmd+SPACE, then type 'terminal').

• Enter the command: ssh USERID@slurm.nbi.ac.uk or simply ssh hpc to log in to the main submission node.

Accessing NBI HPC (Windows):

• Windows does not have a native terminal system (unless you have installed the Linux subsystem for windows) so instead we’ll be using Putty, a free terminal emulator, serial console, and network file transfer application. Putty is widely used on Windows platforms for connecting to remote servers, routers, and other network devices to perform command-line tasks and configuration.

• Open the Putty application

• Enter the command: ssh USERID@slurm.nbi.ac.uk or ssh hpc to log in to the main submission node.

Accessing NBI HPC (Linux):

• Open a terminal (Ubuntu shortcut: Ctrl+Alt+t).

• Use the command: ssh USERID@slurm.nbi.ac.uk or ssh hpc to log in to the main submission node.

Additionally, access can be facilitated via VPN (covered separately) or through a browser service:

• Browser access: Visit https://ood.hpc.nbi.ac.uk/ to utilize services such as running GUI applications (e.g., RStudio) and easily uploading/downloading small files to HPC storage.

After establishing a connection, users can perform various actions. For instance:

• Verify your current directory location using the command pwd; you will be in your home directory (/hpc-home/ also accessible as '~/'), a directory that only you have read or write access to with a capacity of approximately 300GB.