By using Linux on your own computer you can more quickly incorporate what you learn into your own research. Before the first class, please ensure you have done the following…

1. Selected a computer to use in the class
2. Learned how to open the Linux terminal on your computer
3. Downloaded a text editor
4. Requested a Summit user account

You will need to have either a MAC laptop or a laptop running Windows 10 (Anniversary Update or higher) or a Linux laptop. We will no longer be supporting PC laptops running Windows versions less than 10. If you don't have a MAC, Windows10, or Linux laptop, please obtain one. There are laptops available for rental through the Morgan Library. Your graduate program or your lab may have laptops to borrow.

The computer should be a laptop. A tablet-only or iPad is not going to cut it.

What is a linux terminal? It should look something like this:

Here are the options for accessing a a linux terminal on different systems. Again, please verify you can access your terminal before class:

Lucky you! Your MAC runs on a Linux-like operating system. All you need to get running is to familiarize yourself with the Terminal application.

1. Go to Finder
2. Go to Applications
3. Go to Utilities
4. Click on Terminal to open the application
5. For faster access, you can drag and drop Terminal into your Dock.

To bump your Mac into power user mode, you'll need Xcode. To obtain Xcode…

• Go to App Store
• Search for Xcode
• Download and install Xcode. This will take a while to download and install. It may be a good idea to do this overnight.

Your PC needs to be running 64-bit Windows 10 with the Windows 10 Fall Creator Update (October 2017). To check your version check updates here. If your computer is up to date, you can install Linux on top of the Windows operating system. Please read Install the Linux Subsystem on Windows 10 to install the system. Opt for UBUNTU distribution (not LTS) if/when you have a choice.

When complete, you'll be asked for a username and password specific to your Ubuntu installation. These don't need to be the same as your Windows 10 credentials. With this step complete, you'll find yourself at the Ubuntu bash command line.

Tips for installation

• Don't forget your username and password for ubuntu! Write it down. You'll need it for the class!!!
• Having trouble getting the `Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux` line to execute? Make sure you are in a PowerShell with Administrator privileges (aka, an elevated powershell). To open one, search PowerShell in the windowsStart search bar, then RIGHT click on powershell, then select “Run as Administrator”

If you have a laptop that is running a Linux distro natively, you are all set to go. To access the terminal, search the DASH for Terminal. Click on the Terminal icon to open the application.

If you can't access a Linux terminal, please contact Erin Nishimura prior to class. I will be available the week of August 17 - August 21 to help you troubleshoot.

Everyone will need to install a text editor for writing and modifying plain text files.

• Mac: we recommend BBEdit . Click Download under the BBEdit software. You don't need to buy it. The free version does everything you need.

• Windows 10: we recommend Notepad++
• We do not recommend TextEdit, Wordpad, Notebook, EMACS, or Microsoft Word.
• If you already have a text editor you like that is not listed, you are free to use it provided it saves files in true flat .txt and not rich text format.

We will be using the RMACC Summit Supercomputer for the last week of the course. Please request access to Summit by starting on Step 3 under HPC Summit: Get Started.

To do Step 3 you will need a DUO app on your phone. Many CSU students already have this, but in case you don't, go here for instructions to download: DUO

Also, make sure you do this:

Be sure to check the box next to “I would like to run high-performance compute jobs on the RMACC Summit Cluster”.

Otherwise, you will not be added to csu-general. This general use allocation is available to all CSU users and allows you to test your workflow on the system before applying for allocation for your project.

If you are having trouble with this, we can do it together once the class begins.