The Agave Linux Shell: Setup

Preliminary

Before obtaining a shell on the Agave cluster, several items must be in check:

  1. Make sure you have an account on the cluster. If you have not already, please fill out an account request with your faculty sponsor listed (faculty may list themselves as sponsors).
  2. Upon receiving a confirmation email of account activation, you will have the ability to connect to the cluster. However, you may only access the cluster through the “Cisco” Virtual Private Network (Cisco VPN). If you are unfamiliar with the process, please visit sslvpn.asu.edu, which will guide you through the installation process of the necessary software. Once the software is installed and running, it will prompt you for a webaddress, specify sslvpn.asu.edu/2fa and proceed through the steps. Note: if you are accessing the supercomputer from the ASU network you will not explicitly need the VPN.
  3. With an account created and the VPN running, you should now have access to the cluster. From the Windows 10 command prompt or MacOS or Linux terminal you should be able to connect to the cluster with the shell command: ssh <asurite>@agave.asu.edu, where <asurite> is a placeholder for your asurite username. This method is the traditional way of obtaining a shell on the supercomputer!

I have access, now what?

The recommended way to learn how to use the supercomputer and gain access to a cluster shell is through the Open Ondemand webapp. This webapp is maintained by the Ohio Supercomputing Center and is actively funded by the National Science Foundation. The webapp is operating system (OS) independent (the browser Chrome is recommended, followed by Brave or Firefox), and supplants a number of OS-dependent applications that would have been necessary to interact with the supercomputer otherwise. To obtain the shell through the Open OnDemand webapp, find the Clusters tab within the navigation bar at the top of the webpage, and from the submenu, select >_ Agave Shell Access. Those that are feeling more confident may gain a shell on the cluster through other means, such as an ssh session via a terminal, as indicated in step 3 in the previous section.

Workshop Setup

Once on Agave and within a shell, you’ll need to download some files to follow the lesson. Below are instructions that will be covered during the lesson.

  1. Download data-shell.zip and move the file to your Desktop. This can be done using wget.
    Ask: how did I get the link for the required zip?
  2. Unzip/extract the file.
    You should end up with a new folder called data-shell on your Desktop.
$ mkdir ~/Desktop  
$ cd ~/Desktop  
$ wget https://github.com/jyalim/agave-shell-novice/raw/gh-pages/data/data-shell.zip    
$ unzip data-shell.zip

Additional Help

This workshop is supplemental to our official documentation (http://links.asu.edu/docs).

Please note that we have office hours every Tuesday from 1:00-3:30PM over zoom (as well as Wednesday during the regular semester). We are happy to answer any and all questions during these sessions.

We also host a number of workshops over the year, which are listed on our official documentation: http://links.asu.edu/learn.

We also have specific tutorial pages, and a small sampling are featured below:

What does the shell look like on my computer?

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.

For the entirety of this lesson, we’ll be working on the Agave cluster, which is comprised of Linux CentOS 7 systems and provides its own shell interface.

However, many operating systems support the shell we will encounter today. The text below is included from the original Software Carpentries lesson to provide context to those local shells.

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.

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

Linux

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

If your machine is set up to use something other than Bash, you can run it by opening a terminal and typing bash.

macOS

For a Mac computer running macOS Mojave or earlier releases, the default Unix Shell is an older version of Bash.

For a Mac computer running macOS Catalina or later releases, the default Unix Shell is Zsh.

Your default shell is available via the Terminal program within your Utilities folder. Alternative shells are available upon install, such as iterm2.

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.
  • Recommended Use the Mac ‘Spotlight’ computer search function. Search for: Terminal and press Return.

To check if your machine is set up to use something other than Bash, type echo $SHELL in your terminal window.

If your machine is set up to use something other than Bash, you can run it by opening a terminal and typing bash.

While newer versions of MacOS use Zsh as a default, it is recommend to become familiar with a newer version of Bash, if possible, as it is the default across the majority of Linux systems.

Reference

How to Use Terminal on a Mac

Windows

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 Git for Windows, which gives you access to both Bash shell commands and Git. If you are attending a Software Carpentry workshop session, it is likely you have already received instructions on how to install Git for Windows.

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

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.

Reference

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

*Please note that commands in the Windows Subsystem for Linux (WSL) or Cygwin may differ slightly from those shown in the lesson or presented in the workshop.