System Management and Installation

Overview

Teaching: 5 min
Exercises: 5 min

Questions

• How do I manage a Virtual Machine

• How I can I install missing software on a Linux Virtual Machine

Objectives

• Know the difference between a regular user and a super user

• Understand the concept of a package manager

• Search for some packages with apt search

Super Users and the sudo command

If you use Mac OS or Windows, you may have noticed that sometimes when you install software or change something on your computer, you have to confirm that you want to do so with an additional security prompt (on Mac OS you have to type in your password). The sudo command is the same idea. If you are trying to make some changes to your system and get the error that your account does not have enough privileges, you should try rerunning the command with sudo in front of it to run it with administrator privileges.

It is a very bad idea to work with administrator privileges by default: if you make a mistake, such as typing in an incorrect rm or mv command, you may break the system entirely. It is therefore a good idea to only use the administrator privileges when you really need them. Furthermore, if you create files as an administrator, you may not be able to access them as a regular user without change the ownership and/or permissions on that file, which can be cumbersome.

Installing packages

Even as a regular user, you can use the package manager to search for packages that you may want to install. For example, suppose you are interested in using Octave, which is an Open Source package that is very similar to MATLAB and even able to run many basic MATLAB scripts.

If we try to type

$ octave

We will get something like the following error:

Command 'octave' not found, but can be installed with:

sudo apt install octave

As we can see, Ubuntu recognized that there is a package that would provide the octave software, but that it is currently not installed. It suggest to do so with the apt install command, preceded by sudo as installing software requires elevated system permissions.

The command apt is a package manager for Debian and Ubuntu based Linux distributions. A package manager is a somewhat similar to an app store application you may know from you smart phone. It allows you to easily install software you want.

Even if you do not have administrator rights on a system, you can still use apt to search which packages are there. Let’s try and search for the octave package:

$ apt search octave

Since this shows a lot of packages that all contain the word octave, you can consider running it with less to be able to browser the output easier:

$ apt search octave | less

You can close the less tool by pressing the Q button.

As you can see, the main package for Octave is called octave. If you would have super-user rights on the virtual machine, which you do not have during the workshop, but would have if you create your own Debian or Ubuntu virtual machine, you could install the package by running

$ sudo apt install octave

Sometimes the software you want is not available in the standard package repository, or the software in the standard repository is too old for your needs. In some cases, the developers of software have additional repositories available which you can use. This is for example the case for R. To be able to install it, you can first tell the apt package manager to add an additional repository and corresponding security certificate (this is not possible during the workshop):

$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
$ sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" 

After that, you should be able to install a (modern) version of R using the package manger

$ sudo apt install r-base

The general advice is too look on the website of the programming environment you want to use, to see how it can be installed in a Linux context. Often multiple options are given, but the option that works with a package manager is often easier than alternatives, such as compiling and installing the software from source code.

Commercial packages and Binary Software

In case you want to use commercial software, such as MATLAB or CPLEX this is typically not available via the package manager. First, this software must be support Linux, and then you should obtain a specific installer for Linux. For shared libraries, you also need a different type of library: a Windows dll file does not work on Linux, as the binary format is different. Look at the documentation of the software you want to use. Note that this typically only holds true for binary applications. Interpreted scripts (such as Python and R use), as well as bytecode based software (Java or C#) generally should be easier to run on different operating systems, but some care is needed if they make use of binary/compiled software.

Key Points

• Have a general idea how additional software can be installed on a Linux machine