Connecting to a remote HPC system

Overview

Teaching: 10 min
Exercises: 5 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 user interface, 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 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.

Connect to the Cluster

After getting your account, please navigate to ondemand.boisestate.edu, choose your university as the identity provider, and log in with your university credentials.

From here you can acccess the shell, interactive apps like Jupyter and Rstudio, and transfer files.

Logging in with a Terminal Application

The Lesson Setup provides instructions for installing a shell application with SSH. If you have not done so already, please open that shell application with a Unix-like command line interface to your system.

To log in to Borah via ssh, we’ll need to set up ssh keys according to the follwing documentation: Logging in Documentation

You may have noticed that the prompt changed when you logged into the remote system using the 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
• [yourUsername@borah-login ~]$ 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!)

[yourUsername@borah-login ~]$ hostname

borah-login

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

[yourUsername@borah-login ~]$ pwd

/bsuhome/yourUsername

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

[yourUsername@borah-login ~]$ ls

scratch

The system administrators have configured your home directory with a link (a shortcut) to a scratch space reserved for you. You can also include hidden files in your directory listing:

[yourUsername@borah-login ~]$ ls -a

  .            .bashrc           scratch
  ..           .ssh

In the first column, . is a reference to the current directory and .. a reference to its parent (/bsuhome). 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.