Introduction

You will encounter a variety of operating systems (e.g., Windows, Mac, Linux) in research labs. Each has pros and cons. In this lesson, I tell you about what operating systems do, compare and contrast the main choices, and describe how you can have multiple operating systems at one time using virtual machines!

The operating system (OS) interacts with hardware, allocates hardware resources, regulates the software you can install, and provides an interface to access files and folders (directories).

Operating systems interact with hardware through device drivers. The device driver is software that allows the OS to properly use a particular piece of hardware. Most OSs have a selection of common device drivers. In addition, the hardware manufacturer may make a device driver available for download. If an OS does not recognize the new hardware, it may fail completely to use that hardware OR it may use a default device driver that does not take full advantage of the new hardware's capabilities.

In addition to interacting with hardware, the OS also allocates hardware resources (e.g., CPU, RAM, devices) to applications (programs). An important issue to be aware of is that ill-behaved applications might not return memory resources to the OS after they are finished using them! This can result in a memory leak that reduces performance and even causes thrashing. Memory leaks result from bugs in the application.

The OS also regulates what programs you can run:

For example, Microsoft Office is designed for Windows operating systems. There is a different (and less capable) version of Microsoft Office available for the Mac, but there is not a version for Linux. Instead, Linux users need an alternative like Libre Office. Libre Office is free and available for Linux, Mac and Windows!
Many neuroimaging applications (e.g., AFNI, FSL, Freesurfer) are designed for Linux. They typically also run on Mac, but not always Windows. This is because Mac and Linux are related (they are both Unix operating systems), but Windows is completely different.

WSL2

Windows allows you to install a Unix subsystem called "Windows Subsystem for Linux". This continues to evolve and improve as the years go by, making it possible to work with a Bash terminal window, or install Docker, but it is not guaranteed to solve all problems related to running unix-based applications.

Finally, the operating system provides an interface for you to interact with it. The two common interfaces are the GUI (Graphical User Interface) and the CLI (Command-Line Interface). You will learn more about how to use a CLI, especially the Unix command line, in coming lessons. The command line turns out to be very important for scientific applications.

Goals This lesson will make you aware of the differences between operating systems so that you can choose the OS that best serves your needs. It also prepares you to understand the role of the Unix operating systems in scientific computing.

I've found that a lot of scientific software is designed for Unix-based operating systems, and being familiar with Unix makes it easier to work on supercomputers, which are Unix-based. So, for me, Mac and Linux are my preference, though I do sometimes find software that only works on Windows (e.g., Microsoft Access), or that has fewer problems on Windows (SPM12 for neuroimaging). Since Apple moved to RISC instead of CISC CPUs, I sometimes find software is incompatible with the Mac, but does work on a CISC-Linux machine. So, there are always tradeoffs and interactions, and all of that changes with the passage of time.

Learning Objectives This lesson contributes to the objective to "Explain the relationship between file systems and operating systems" by "comparing operating systems (e.g. Windows, Mac, Linux)".

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Operating Systems (5 pts)