Linux
Table of Contents
0.1. Goals and Objectives
Scientific computing moves in advance of consumer adoption. To be able to take full advantage of your computer as a research tool you may need to install software or applications that require new tools or techniques or that are not user friendly. In fact, the main consumer operating systems: Windows and OSX may not meet your needs out-of-the-box. By installing and using Linux you will learn and practice installing software that should prepare you for the day when you need some program or some computational tool that is not available through an app store. Or when you need to figure out how to do something completely novel with your machine.
0.2. Installing Linux to Your Own Computer
There are a few different methods for getting Linux to run on your computer. All of them pose challenges. Any of the are acceptable, but I will recommend using a virtual machine 1. The other methods are summarized here, and you are welcome to try them if you wish. They will work just fine. But they are also methods that require a bit more patience, benfit from some experience, or involve a greater risk of data loss.
I will summarize the different approaches for installing the Linux operating system (OS) to your computer below, and then follow with more specific instructions.
0.2.1. Linux Only
When you do this you will irrevocably erase everything on your computer's hard disk and you will only have linux. This is the easiest method if you have a laptop accessible that you do not need for another purpose. With all the computers we have all bought over the years this is not so far fetched. Even a ten year old laptop will probably be just fine. One of the computers I used to develop this course dates from 2011 (Lenovo X220T).
0.2.2. Dual Boot
With this set up you have more than one operating system. You can use your usual Windows or Mac operating system, but you can also opt to use the Linux system you installed. If you have a Windows laptop this is not particularly hard to get working, but there is some risk when you partition your hard drive. You will need be pay close attention to that step.
If you have an older Mac with the Intel chip this is also not too hard. The same cautions apply and you will need to follow slightly different directions.
If you have a Mac with an M1 or M2 chip this is not advised at this time (Spring 2023). There is active work porting the Linux operating system to the newer Mac hardware, but is it still a bit early for the novice user in my opinion. You can track progress of the Asahi Linux project if you are interested in this.
Contact me if you want to try this method and I will point you to some example instructions.
0.2.3. Run from a USB (or SD card or external hard drive) DEPRECATED
This is the method that does the least to your laptop and so there is the least risk of data loss. It is also the hardest, most technically demanding, and has the highest concentration of black magic (where you will be typing incantations you don't understand just to make things work). Thus I call this method "deprecated." If you are adventurous, have some spare time, or just curious feel free to give it a go, but for most of you I think the Virtual Machine method will be just as safe and technically easier.
Most of the Linux distributions have a "live" version that can be run from a USB, but those live versions do not allow persistent data. That means anything you write or download will be lost when you power down. It is fine therefore to try out a new distribution of linux to see if you like the look and feel, but not ideal if you want to do work. Also, since USB and SD cards were not made with the intention of being used daily as the host of the operating system they are more prone to catastrophic failure where the card gets corrupted and you lose all your saved files. Your computer will be fine, but not the data that you have saved only to the USB or SD card.
If you want to try this method you will want a new USB, and you should ask me to point you to directions. I have them in an older branch of this course, but they are not linked here to decrease the risk of someone accidentally trying an old or outdated method or using the Mac method when the need the Windows version or vice versa.
0.2.4. Install Linux As A Virtual Machine
This is the method I prefer as of Spring 2023. There are a number of videos for Mac and Windows users on how to do this on the Internet. Pay careful attention to the dates. Things are changing rapidly in this space and what worked even just last year may not work well now. Note the rules are different depending on whether you are using an M1/M2 mac or an Intel mac or a Window machine. Don't know which you have? Well, find out. A good workman knows their tools.
IMPORTANT For all these methods and regardless of your machine make sure you have fully update Windows or OSX to the latest available version. This means Windows 11 where possible and Ventura (13) on Macs. You also need free disk space. I recommend 64gb, but 32gb is a minimum. Check the free space on your computer's hard disk before starting (not how much one-drive or icloud space you have). If you do not have enough space, then you will need to make some by uninstalling old programs you never use, and deleting those video and music files you have backed-up elsewhere and never listen to.
- Windows
In order to use a virtual machine on Windows you need to make sure that the BIOS permits virtualization. Your BIOS is the basic input output system that starts up even before your operating system starts to tell your computer where to find essential start up files and to make sure that the hardware is set up to correctly use and communicate with the available software. Getting to the BIOS is generally unique to your laptop's make and model and you will have to look up how to enter the BIOS for your laptop yourself. Sometimes the default settings for Windows machines can obstruct your ability to do this. You may need to turn of Smart Boot and Quick Boot features. But try first without fiddling with those settings.
Once you can do that the following video will show you the virtualization settings you need to enable.
Cag: Getting to the BIOS on windows (i2c4p) from Britt Anderson on Vimeo.
/The tool that you need to run a virtual machine on Windows (and you can run VMs for operating systems other than Linux) requires a tool called hypervisor. This may not be on by default. The next video shows you how to make sure you have hypervisor enabled.
After that you should install Ubuntu (or Xubuntu). These are two different versions of Linux which have a slightly different look and feel. Ubuntu is the more resource intensive of all the 'buntu flavors, but it is also the one with greatest user base so it is often the one with the best support and the most available information for troubleshooting problems. If you get Ubuntu working you could always create a new virtual machine for a different version of Linux later.
Cai : Installing Ubuntu as a VM on Windows 11 (i2c4p) from Britt Anderson on Vimeo.
- MAC OSX (INTEL)
For Macintosh computer/laptops with intel based chips we can use a virtual machine software called virtual box. It is like the hypervisor described above for Windows. It is free and open and is a good choice.
Caa: Intel Mac Get Virtual Box (i2c4p) from Britt Anderson on Vimeo.
After you have installed the software (and you really want to make sure that you have updated your machine to the latest version of the OSX operating system and that you have a reasonable amout of hard disk space available (at least 32 gigs and ideally closer to 64) you will need to create the virtual machine. It is the virtual machine that we will install Linux to.
Cab: intel macs make a virtual machine with virtual box (i2c4p) from Britt Anderson on Vimeo.
And as your final step you will install either Xubuntu or Ubuntu, and that will require getting and downloading a copy.
Cac: you are going to need a xubuntu iso (i2c4p) from Britt Anderson on Vimeo.
And as our final step in the process will install our linux operating system to the VM.
Cad: intel mac - install Xubuntu to your VM (i2c4p) from Britt Anderson on Vimeo.
- MAC OSX (ARM, ie M1 or M2)
In some ways the newer macs make things harder, in others easier. You will have many less options to get a VM going and fewer choices, at this time, for linux versions, but the method for getting a Ubuntu VM installed is quite slick, and simpler than the Intel mac.
M1 Mac VM instructions (2022) from Britt Anderson on Vimeo.
installM2VMUbuntu.mp4 from Britt Anderson on Vimeo.
Installing a Ubuntu Virtual Machine on an M2 Mac Using UTM (2023)
0.3. Xubuntu Walkthrough
When you start up your Linux desktop for the first time you may wonder what to do to get started. In the following video I show you a basic walkthrough of a first boot and I demo this on Xubuntu. The steps are similar for Ubuntu. In addition, you will hear me mention starting from a USB. This video was made when I was using that method, but you can just ignore the USB talk. It will be basically the same once you have started U(Xu)buntu on your VM.
A couple of steps that I demonstrate is how to turn off the power management features so that your computer does not go to sleep during updates. You can always turn them back on later.
Next I illustrate updating all the software to the latest and greatest using terminal commands. We will see more about the terminal later, but you will basically type what you see in the video to get started.
0.4. Package Management
Any particular program that you want to run in modern times probably requires several other pieces of software to be available on your computer. Thus, to install a program you usually have to install a package, which is that collection of pieces of code and their dependencies: the things they depend on to work. Of course, those dependencies are software too and they may also have dependencies. Some software you download and run will require downloading many pieces of software. A package manager is a convenient tool to make this job easier. Different Linux distributions use different package managers. The terminal based package manager that we will be using in this course is apt. The course also makes extensive use of a text processing program called emacs and so we will download emacs as our first package. The steps for doing that are demonstrated in the following video.
1. Assessments
1.1. Installing Linux
Demonstrate that you have installed Ubuntu to your computer. If you are one of my uwaterloo students you will do this by uploading a screen shot of your Ubuntu desktop to the Learn Dropbox. Have something open where you can type in your name and student id so that I can verify who is who.
1.1.1. Comments
There are screen capture tools available for your Ubuntu installation.
1.2. Install Emacs Package
1.2.1. Task
Demonstrate that you have a functioning Linux installation and that you can use the package management system.
Installing Emacs on Ubuntu 2023 from Britt Anderson on Vimeo.
A short demo of installing emacs on a Ubuntu virtual machine (running on an M2 Mac Air)
1.2.2. Details
- Open up a terminal. In Xubuntu go to the upper left of your desktop and click the icon. Type terminal in the search bar and select the top option.
- When the terminal opens type
sudo apt updateto update your list of currently available packages. This package manager works for Xubuntu, but will not be found on all Linux distributions. - Type
sudo apt install emacs - Follow the on screen instructions. When installation is complete type, in the same terminal window,
emacs &. - Emacs will open. Use the
Filemenu to create a new file with a sensible name in the file itself type in your name and student id and save the file as type.org. Make a note of where you save it, because you will need to … - Log on to learn and submit the file.
1.2.3. Comments
If you want to try something fun open the file back up in emacs after doing the above. Then type C-c C-e h h. C-c means typing the "Ctrl" key and the lower case "c" key simultaneously. The spaces between those instructions mean you have a sequence of four key chords to enter. If all goes well you have just created a web page of that file. You should be able to open it in your browser. To test, use the file browser in Xubuntu to navigate to the file with the name you used above, but now ending in .html and not the .org one. Double click and your web browser should open with that file displayed.
To get ahead of things and learn more about the org-mode utilities you just used you can search for emacs and orgmode online. Or type C-h i to open the information functionality and navigate to the orgmode chapter.
And if you get stressed you can always consult Emacs' built in therapist with M-x doctor.
Footnotes:
This presents problems for us when it comes to the Psychopy session. If you are using a virtual machine as recommended you will need to take a different approach to handling the psychopy assignment. If you are dual booting Linux or using a laptop running over Linux then there should be no problems.