Connecting to a remote HPC system

Overview

Teaching: 25 min
Exercises: 10 min

Questions

• How do I log in to a remote HPC system?

Objectives

• Configure secure access to a remote HPC system.

• Connect to a remote HPC system.

Secure Connections

The first step in using a cluster is to establish a connection from our laptop to the cluster. When we are sitting at a computer, we have come to expect a visual display with icons, widgets, and perhaps some windows or applications: a graphical userinterface, or GUI. Since computer clusters are remote resources that we connect to over slow or intermittent interfaces (WiFi and VPNs especially), it is more practical to use a command-line interface, or CLI, to send commands as plain-text. If a command returns output, it is printed as plain text as well. The commands we run today will not open a window to show graphical results.

If you have ever opened the Windows Command Prompt or macOS Terminal, you have seen a CLI. If you have already taken The Carpentries’ courses on the UNIX Shell or Version Control, you have used the CLI on your local machine extensively. The only leap to be made here is to open a CLI on a remote machine, while taking some precautions so that other folks on the network can’t see (or change) the commands you’re running or the results the remote machine sends back. We will use the Secure SHell protocol (or SSH) to open an encrypted network connection between two machines, allowing you to send & receive text and data without having to worry about prying eyes.

SSH clients are usually command-line tools, where you provide the remote machine address as the only required argument. If your username on the remote system differs from what you use locally, you must provide that as well. If your SSH client has a graphical front-end, such as PuTTY or MobaXterm, you will set these arguments before clicking “connect.” From the terminal, you’ll write something like ssh userName@hostname, where the argument is just like an email address: the “@” symbol is used to separate the personal ID from the address of the remote machine.

When logging in to a laptop, tablet, or other personal device, a username, password, or pattern are normally required to prevent unauthorized access. In addition to your Stanford password, you will be required to use Duo Two-Factor Authentication.

Log In to the Cluster

Go ahead and open your terminal or graphical SSH client, then log in to the cluster. Replace SUNetID with your username or the one supplied by the instructors.

[you@laptop:~]$ ssh SUNetID@login.farmshare.stanford.edu

You may be asked for your password. Watch out: the characters you type after the password prompt are not displayed on the screen. Normal output will resume once you press Enter.

You may have noticed that the prompt changed when you logged into the remote system using the terminal (if you logged in using PuTTY this will not apply because it does not offer a local terminal). This change is important because it can help you distinguish on which system the commands you type will be run when you pass them into the terminal. This change is also a small complication that we will need to navigate throughout the workshop. Exactly what is displayed as the prompt (which conventionally ends in $) in the terminal when it is connected to the local system and the remote system will typically be different for every user. We still need to indicate which system we are entering commands on though so we will adopt the following convention:

• [you@laptop:~]$ when the command is to be entered on a terminal connected to your local computer
• [SUNetID@rice-02:~]$ when the command is to be entered on a terminal connected to the remote system
• $ when it really doesn’t matter which system the terminal is connected to.

Looking Around Your Remote Home

Very often, many users are tempted to think of a high-performance computing installation as one giant, magical machine. Sometimes, people will assume that the computer they’ve logged onto is the entire computing cluster. So what’s really happening? What computer have we logged on to? The name of the current computer we are logged onto can be checked with the hostname command. (You may also notice that the current hostname is also part of our prompt!)

[SUNetID@rice-02:~]$ hostname

rice-02

So, we’re definitely on the remote machine. Next, let’s find out where we are by running pwd to print the working directory.

[SUNetID@rice-02:~]$ pwd

/home//SUNetID

Great, we know where we are! Let’s see what’s in our current directory:

[SUNetID@rice-02:~]$ ls

  afs-home    go

The system administrators may have configured your home directory with some helpful files, folders, and links (shortcuts) to space reserved for you on other filesystems. If they did not, your home directory may appear empty. To double-check, include hidden files in your directory listing:

[SUNetID@rice-02:~]$ ls -a

  .            .bashrc           afs-home
  ..           .ssh              go

In the first column, . is a reference to the current directory and .. a reference to its parent (/home/). You may or may not see the other files, or files like them: .bashrc is a shell configuration file, which you can edit with your preferences; and .ssh is a directory storing SSH keys and a record of authorized connections.

Key Points

• An HPC system is a set of networked machines.

• HPC systems typically provide login nodes and a set of worker nodes.

• The resources found on independent (worker) nodes can vary in volume and type (amount of RAM, processor architecture, availability of network mounted filesystems, etc.).

• Files saved on one node are available on all nodes.