Summary and Setup

Prerequisite

To begin this lesson you must have completed the following

  • Register for the course
  • Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they can download and run MobaXterm on. Alternatively, they should have a few specific software packages installed (listed in the Setup section below). They are also required to abide by the ARCHER2 Training Code of Conduct.
  • Attendees should be familiar with using the bash shell. This is covered in the introduction to the shell HPC course.
  • Complete the software/system setup including the connection to Archer2 via SSH.

Registration

Please use the ARCHER2 course registration form to sign up for the workshop.

General Information

This lesson is an introduction to using high-performance computing systems effectively. We obviously can’t cover every case or give an exhaustive course on parallel programming in just one lesson of teaching time. Instead, this lesson is intended to give students a good introduction and overview of the tools available and how to use them effectively.

By the end of this lesson, students will know how to:

Checklist

  • Identify problems an HPC system can help solve
  • Use the UNIX shell (also known as terminal or command line) to operate a computer, connect to an HPC system, and write simple shell scripts.
  • Submit and manage jobs on an HPC system using a scheduler, transfer files, and use software through environment modules.

Setup

There are several pieces of software you will wish to install before the workshop. Though installation help will be provided at the workshop, we recommend that these tools are installed (or at least downloaded) beforehand.

Bash and SSH

This lesson requires a terminal application (bash, zsh, or others) with the ability to securely connect to a remote machine (ssh).

Where to type commands: How to open a new shell

The shell is a program that enables us to send commands to the computer and receive output. It is also referred to as the terminal or command line.

Some computers include a default Unix Shell program. The steps below describe some methods for identifying and opening a Unix Shell program if you already have one installed. There are also options for identifying and downloading a Unix Shell program, a Linux/UNIX emulator, or a program to access a Unix Shell on a server.

Shell Setup

Details

Setup for different systems can be presented in dropdown menus via a solution tag. They will join to this discussion block, so you can give a general overview of the software used in this lesson here and fill out the individual operating systems (and potentially add more, e.g. online setup) in the solutions blocks.

Computers with Windows operating systems do not automatically have a Unix Shell program installed. In this lesson, we encourage you to use an emulator included in MobaXterm for Windows, which gives you access to both Bash shell commands and SSH.

Once installed, you can open a terminal by running the program MobaXterm from the Windows start menu.

Reference

Alternatives to MobaXterm and Git for Windows

Other solutions are available for running Bash commands on Windows. There is now a Bash shell command-line tool available for Windows 10. Additionally, you can run Bash commands on a remote computer or server that already has a Unix Shell, from your Windows machine. This can usually be done through a Secure Shell (SSH) client. One such client available for free for Windows computers is PuTTY. See the reference below for information on installing and using PuTTY, using the Windows 10 command-line tool, or installing and using a Unix/Linux emulator.

For advanced users, you may choose one of the following alternatives:

On macOS, the default Unix Shell is accessible by running the Terminal program from the /Application/Utilities folder in Finder.

To open Terminal, try one or both of the following:

  • In Finder, select the Go menu, then select Utilities. Locate Terminal in the Utilities folder and open it.
  • Use the Mac ‘Spotlight’ computer search function. Search for: Terminal and press Return.

Reference

How to Use Terminal on a Mac

On most versions of Linux, the default Unix Shell is accessible by running the (Gnome) Terminal or (KDE) Konsole or xterm, which can be found via the applications menu or the search bar.

Special cases

If none of the options above address your circumstances, try an online search for: Unix shell [your operating system].

This setup takes you through getting ready for the course by ensuring you have an SSH client installed and registering for an ARCHER2 account (you can also use an existing ARCHER2 account if you are already a user).

Setup an SSH client

Details

All attendees should have an SSH client installed. SSH is a tool that allows us to connect to and use a remote computer as our own. Please follow the directions below to install an SSH client for your system if you do not already have one.

Modern versions of Windows have SSH available in Powershell. You can test if it is available by typing ssh --help in Powershell. If it is installed, you should see some useful output. If it is not installed, you will get an error. If SSH is not available in Powershell, then you should install MobaXterm as described below.

An alternative is to install MobaXterm from https://mobaxterm.mobatek.net. You will want to get the Home edition (Installer edition). However, if Powershell works, you do not need this.

macOS comes with SSH pre-installed, so you should not need to install anything. Use your “Terminal” app.

Linux users do not need to install anything, you should be set! Use your terminal application.

Connect to ARCHER2

Details

Note: If you already have an ARCHER2 account you can use that for this course. Please see see the notes at the end of this page rather than requesting a new account. Of course, if you prefer to sign up for another ARCHER2 account specifically for this course, you are welcome to do this instead!

Please sign up for your account on our HPC machine, ARCHER2, which will be available to you for the duration of the course and for a few days afterwards, to allow you to complete the practical exercises and put some of what you have learned into practice.

Sign up for a SAFE account

To sign up, you must first register for an account on SAFE (our service administration web application):

If you are already registered on the SAFE you do not need to re-register. Please proceed to the next step.

  1. Go to the SAFE New User Signup Form
  2. Fill in your personal details. You can come back later and change them if you wish. Note: you should register using your institutional or company email address - email domains such as gmail.com, outlook.com, etc. are not allowed to be used for access to ARCHER2
  3. Click “Submit”
  4. You are now registered. A single use login link will be emailed to the email address you provided. You can use this link to login and set your password.

Sign up for an account on ARCHER2 through SAFE

  1. Login to SAFE
  2. Go to the Menu “Login accounts” and select “Request login account”
  3. Choose the ta133 project “Choose Project for Machine Account” box and click “Next”
  4. On the next page, the ARCHER2 system should be selected. Click “Next”
  5. Enter the username you would prefer to use on ARCHER2. Every username must be unique, so if your chosen name is taken, you will need to choose another

Now you have to wait for the course organiser to accept your request to register. When this has happened, your account will be created on ARCHER2. Once this has been done, you should be sent an email. If you have not received an email but believe that your account should have been activated, check your account status in SAFE which will also show when the account has been activated. You can then pick up your one shot initial password for ARCHER2 from your SAFE account.

Generate an SSH key pair and upload it to SAFE

In addition to your password, you will need an SSH key pair to access ARCHER2. There is useful guidance on how to generate SSH key pairs in the ARCHER2 documentation.

Once you have generated your key pair, you need to add the public part to your ARCHER2 account in SAFE:

  1. Login to SAFE
  2. Go to the Menu “Login accounts” and select the ARCHER2 account you want to add the SSH key to
  3. On the subsequent Login account details page click the “Add Credential” button
  4. Select “SSH public key” as the Credential Type and click “Next”
  5. Either copy and paste the public part of your SSH key into the “SSH Public key” box or use the button to select the public key file on your computer.
  6. Click “Add” to associate the public SSH key part with your account

The public SSH key part will now be added to your login account on the ARCHER2 system.

Log into ARCHER2

You should now be able to log into ARCHER2 by following the login instructions in the ARCHER2 documentation.

Using an existing ARCHER2 account

If you wish to use an existing ARCHER2 account for the course, that is perfectly fine. The only differences from the specific course account are that you will not have access to the the node reservations for the course or the course account code. Instead, you can use your existing account code (the cost of the jobs is negligible as they are very short and small) and the ARCHER2 short QoS . When the course talks about setting the following options:

BASH 

--qos=short --reservation=

you should replace them with:

BASH 

--qos=short --reservation=short

Similarly, when you are writing job submission scripts, you should replace:

BASH 

#SBATCH --qos=standard
#SBATCH --reservation=

with

BASH 

#SBATCH --qos=short
#SBATCH --reservation=short