Connecting to the remote HPC system

Overview

Teaching: 25 min
Exercises: 15 min

Questions

• How do I open a terminal?

• How do I connect to a remote computer?

• What is an SSH key?

Objectives

• Connect to a remote HPC system.

Opening a Terminal

Connecting to an HPC system is most often done through a tool known as “SSH” (Secure SHell) and usually SSH is run through a terminal. So, to begin using an HPC system we need to begin by opening a terminal. Different operating systems have different terminals, none of which are exactly the same in terms of their features and abilities while working on the operating system. When connected to the remote system the experience between terminals will be identical as each will faithfully present the same experience of using that system.

Here is the process for opening a terminal in each operating system.

Linux

There are many different versions (aka “flavours”) of Linux and how to open a terminal window can change between flavours. Fortunately most Linux users already know how to open a terminal window since it is a common part of the workflow for Linux users. If this is something that you do not know how to do then a quick search on the Internet for “how to open a terminal window in” with your particular Linux flavour appended to the end should quickly give you the directions you need.

Mac

Macs have had a terminal built in since the first version of OS X since it is built on a UNIX-like operating system, leveraging many parts from BSD (Berkeley Software Distribution). The terminal can be quickly opened through the use of the Searchlight tool. Hold down the command key and press the spacebar. In the search bar that shows up type “terminal”, choose the terminal app from the list of results (it will look like a tiny, black computer screen) and you will be presented with a terminal window. Alternatively, you can find Terminal under “Utilities” in the Applications menu.

Windows

While Windows does have a command-line interface known as the “Command Prompt” that has its roots in MS-DOS (Microsoft Disk Operating System) it does not have an SSH tool built into it and so one needs to be installed. There are a variety of programs that can be used for this; a few common ones we describe here, as follows:

MobaXterm

MobaXterm is a terminal window emulator for Windows and the home edition can be downloaded for free from mobatek.net. If you follow the link you will note that there are two editions of the home version available: Portable and Installer. The portable edition puts all MobaXterm content in a folder on the desktop (or anywhere else you would like it) so that it is easy to add plug-ins or remove the software. The installer edition adds MobaXterm to your Windows installation and menu as any other program you might install. If you are not sure that you will continue to use MobaXterm in the future, the portable edition is likely the best choice for you.

Download the version that you would like to use and install it as you would any other software on your Windows installation. Once the software is installed you can run it by either opening the folder installed with the portable edition and double-clicking on the executable file named MobaXterm_Personal_11.1 (your version number may vary) or, if the installer edition was used, finding the executable through either the start menu or the Windows search option.

Once the MobaXterm window is open you should see a large button in the middle of that window with the text “Start Local Terminal”. Click this button and you will have a terminal window at your disposal.

Git BASH

Git BASH gives you a terminal like interface in Windows. You can use this to connect to a remote computer via SSH. It can be downloaded for free from here.

Windows Subsystem for Linux

The Windows Subsystem for Linux also allows you to connect to a remote computer via SSH. Instructions on installing it can be found here.

Creating an SSH key

SSH keys are an alternative method for authentication to obtain access to remote computing systems. They can also be used for authentication when transferring files or for accessing version control systems. In this section you will create a pair of SSH keys, a private key which you keep on your own computer and a public key which is placed on the remote HPC system that you will log in to.

Linux, Mac and Windows Subsystem for Linux

Once you have opened a terminal check for existing SSH keys and filenames since existing SSH keys are overwritten,

$ ls ~/.ssh/

then generate a new public-private key pair,

$ ssh-keygen -o -a 100 -t rsa -b 4096 -f ~/.ssh/id_ARCHER2_rsa

• -o (no default): use the OpenSSH key format, rather than PEM.
• -a (default is 16): number of rounds of passphrase derivation; increase to slow down brute force attacks.
• -t (default is rsa): specify the “type” or cryptographic algorithm. ed25519 is faster and shorter than RSA for comparable strength.
• -f (default is /home/user/.ssh/id_algorithm): filename to store your keys. If you already have SSH keys, make sure you specify a different name: ssh-keygen will overwrite the default key if you don’t specify!

The flag -b sets the number of bits in the key. The default is 2048. EdDSA uses a fixed key length, so this flag would have no effect.

When prompted, enter a strong password that you will remember. Cryptography is only as good as the weakest link, and this will be used to connect to a powerful, precious, computational resource.

Take a look in ~/.ssh (use ls ~/.ssh). You should see the two new files: your private key (~/.ssh/key_ARCHER2_rsa) and the public key (~/.ssh/key_ARCHER2_rsa.pub). If a key is requested by the system administrators, the public key is the one to provide.

Private keys are your private identity

A private key that is visible to anyone but you should be considered compromised, and must be destroyed. This includes having improper permissions on the directory it (or a copy) is stored in, traversing any network in the clear, attachment on unencrypted email, and even displaying the key (which is ASCII text) in your terminal window.

Protect this key as if it unlocks your front door. In many ways, it does.

Further information

For more information on SSH security and some of the flags set here, an excellent resource is Secure Secure Shell.

Windows

On Windows you can use

• puttygen, see the Putty documentation
• MobaKeyGen, see the MoabXterm documentation

Logging onto the system

With all of this in mind, let’s connect to a remote HPC system. In this workshop, we will connect to ARCHER2 — an HPC system located at the EPCC, The University of Edinburgh. Although it’s unlikely that every system will be exactly like ARCHER2, it’s a very good example of what you can expect from an HPC installation. To connect to our example computer, we will use SSH (if you are using PuTTY, see above).

SSH allows us to connect to UNIX computers remotely, and use them as if they were our own. The general syntax of the connection command follows the format ssh -i ~/.ssh/key_for_remote_computer yourUsername@remote.computer.address when using SSH keys and ssh yourUsername@some.computer.address if only password access is available. Let’s attempt to connect to the HPC system now:

ssh -i ~/.ssh/key_ARCHER2_ed25519 yourUsername@login.archer2.ac.uk

or

ssh -i ~/.ssh/key_ARCHER2_rsa yourUsername@login.archer2.ac.uk

or if SSH keys have not been enabled

ssh yourUsername@login.archer2.ac.uk

This node is running Cray's Linux Environment version 1.3.2

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Hostname:     uan01
Distribution: SLES 15.1 1
CPUS:         256
Memory:       257.4GB
Configured:   2021-04-27

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If you’ve connected successfully, you should see a prompt like the one below. This prompt is informative, and lets you grasp certain information at a glance. (If you don’t understand what these things are, don’t worry! We will cover things in depth as we explore the system further.)

auser@ln01:~> 

Telling the Difference between the Local Terminal and the Remote Terminal

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 makes it clear 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 reported before the $ 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:

• [local]$ when the command is to be entered on a terminal connected to your local computer
• auser@ln01:~> 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.

Being certain which system your terminal is connected to

If you ever need to be certain which system a terminal you are using is connected to then use the following command: $ hostname.

Keep two terminal windows open

It is strongly recommended that you have two terminals open, one connected to the local system and one connected to the remote system, that you can switch back and forth between. If you only use one terminal window then you will need to reconnect to the remote system using one of the methods above when you see a change from [local]$ to auser@ln01:~> and disconnect when you see the reverse.

Key Points

• To connect to a remote HPC system using SSH and a password, run ssh yourUsername@remote.computer.address.

• To connect to a remote HPC system using SSH and an SSH key, run ssh -i ~/.ssh/key_for_remote_computer yourUsername@remote.computer.address.