Linux has gained a lot of popularity past decades, but its inner working can still remain obscure to many peoples, because it's not primarily based on graphic user interface, and is more often used via a terminal and command line, which can seem daunting to many users.

Basic architecture

As all modern operating system, linux is based on the different layers , which correspond to cpu memory protection implemented on intel cpu since i386, allowing for memory to be associated with diferent level of privilege, called 'rings'.

When a program is loaded in memory, the machine code will be loaded in memory associated with such rings, and most OS are architectured following this model.

• Ring 0 is kernel ring, it's where the code and data of the kernel will reside.
• Ring 1-2 is driver level, where device drivers or subsystem will reside.
• Ring 3 is application level, where user applications and data will reside.

Booting proccess

image source

When the computer boot up, it will scan all the storage device for a bootable code marker, in the so called MBR for master boot record, and if one is found, it will load this code in memory and execute it.

On PC architecture, the amount of memory that this code can take is very limited, mostly limited to 512 bytes with traditional bios, and moreover, the intel cpu is booted in 16 bits so called 'real mode' , which allow for 1Mo of memory to be addressed.

It's why linux use a multi stage booting.

The first stage is loading the boot sector from the MBR. This code will mostly be used to load the second stage loader from the hard drive, or usb stick.

The second stage will most likely display a menu, and load the boot loader configuration, which contain the location of the kernel, the information to locate the root partition, and eventually some other parameters that can be needed to load and boot the kernel.

The second stage boot loader will then load the kernel from the configuration, and boot the system.

The most used bootloader is called grub.

When a new operating system is installed on the machine, grub will write the first stage boot loader in the target drive 'MBR' (master boot reccord), which contain the information needed to load and run the second stage boot loader (grub) as well as the location of the boot loader configuration file, and then it will finally load and boot the kernel from this configuration.

A ram disk image can also be loaded by the boot loader, because the kernel might need some basic files before the root partition is available. This ramdisk is often contained in a file called something like 'initrd.img', and can be passed by the boot loader as a kernel option.

Linux kernel

image source

The kernel is the part of the operating system that deal with hardware, file system, and process. It's run in ring 0, and is the only piece of code that has access to the hardware and the process table.

It will detect the hardware, and load the required drivers, partition the available memory, and then mount the root partition, run the init process located on this root partition which will then initialize the rest of the system, such as network interface, and services, based on the configuration stored on the root partition.

C Library

(from wikipedia)

As the kernel internal structure is generally poorly documented, and subject to frequent update, most application will not use the kernel interface directly, but rather use the C standard library which contain the code to make the actual kernel calls.

The C library will be responsible for initializing the process, and provide standard API to access files, memory, spawn new process, and access system resources.

Filesystems

Root partition

On unix, the 'root partition' is the global file system, and all partitions and other devices are associated to a path in this root file system. There is only one root partition for an instance of the kernel, and all other partitions and devices are accessed via a location into this root partition.

The process of associating a filesystem to a path in the root filesystem is called 'mounting'.

Common directories

Directory	Use
/bin	contain the base system commands
/boot	contain the files for the bootloader, as well as the kernel.
/lib	contain the base system libraries
/usr	contain the user applications. /usr/bin contains users applications executables. /usr/lib contains user libraries.
/etc	contain configurations files. /etc/fstab contain the list of filesystem mounted at boot. /etc/passwd contain a list of all users, with their uid,gid, and home directory. /etc/group contain a list of all groups and their associated gid. /etc/network/interfaces contain configuration for network interfaces.
/var	contain the data for system and services. /var/log contain system and services logs.
/root	home directories for root user
/home	contain the home directories for users
/dev	virtual file system containing kernel device entries
/proc	virtual file system containing kernel variables

Filesystem attribute

Once a file system is mounted, all entries will be associated with an userid 'uid' also called the owner of the file, a group id, and a set of permission that define the access to the file.

The permission flag can grant read, write or execution access, to either :

• the owner of the file.
• users in the group associated with the file entry 'gid'.
• all others users.

It's generally represented by a 3 digit numbers, each number is a bit flags that represents the permission associated with the owner, users in the group, and all other users.

the flag is a 3 bit flag, which mean it can represent a number from 0 to 7, and flags can be combined to form the permission.

The bit flag are

binary	decimal	meaning
001	1	execution
010	2	write
100	4	read

So a read+write access is 4+2 = 6.

Execution flag for directory mean permission to open it and list its content.

To set the permission of a file as read and write for owner, read only for the user in the group and read only for all other users the permission flag yeld 644.

The first numbers is read/write for the owner, the second is read only for users in group, the third read only for all other users.

Root super user

All unix system have what is called a root super user, which is granted all permission by default. It's uid is always 0. When installing a new system, the installer will generally ask to create a new user, and use this user by default instead of the root user, which is considered safer, as all process run from root have all access to everything, this can lead to security flaw or critical mistakes.

Virtual file system

The big moto on linux is 'everything is a file', which mean all interactions with the hardware, process and everything else will be done through operation on a file descriptor.

In order to make this work, linux kernel make use of virtual file system, which are just like regular file system, except they don't correspond to file or directory on a partition, but represent a mapping of kernel ressources.

When the kernel boots, it will mount a certain numbers of these virtual file system, among which

• the device filesystem, 'devfs' will be mounted on /dev, and will contain entries for all the hardware devices known to the kernel. For example '/dev/disk' will contain device entries for harddrives. Device names for harddrive can be pretty cryptic, but generally made of an id identifying the drive, followed by a number indicating the partition index on the drive. All operations to manipulate device will happen through operations on entries of the '/dev' virtual file system.

• the 'procfs' will be mounted on /proc, and will contain entries for kernel variables, such as the process table keeping track of all processes running on the machines, and various infos about the system and hardware.

Those entries can be manipulated just like regular files on a filesystem, but instead of reading the data from a file on an harddrive or usb stick, it will read the data from kernel memory, or from an hardware device through the kernel.

Processes

image source

Process are piece of code that are loaded in memory and allocated a certain amount of cpu ressource by the task manager. This process of allocating cpu ressources to a process is called scheduling.

Processes can also be considered as file, as on linux all processes will be associated with 3 file descriptors, 'stdin', 'stdout' and 'stderr' that will be used to send data to the process (stdin), read data from the process (stdout), monitor errors output (stderr).

Once the kernel boots up, new process can be created by loading an executable in memory, and adding the code entry point and other information into the kernel's process table. The kernel will then schedule its execution along side with the other process or tasks.

Each process contain at least the following information

• An unique identifier, called the 'pid'.
• An 'uid' as user id and 'gid' as group id, which will determine it's access to filesystem.
• The three files descriptors stdin, stdout, and stderr, which will be used to send and received data to/from it.
• Environment variables, which are values associated with a variable name that the process can access.
• A certain number of memory pages in the RAM that it can access .

Eventually if it's spawn from another process, it will also contain the id of the parent process.

As all operations on the system are handled through an access on entry of a filesystem, the uid and gid of the process will determine it's level of access to all ressources.

A process can also spawn another processes, which can inherits those informations from the parent process.

There are basically 3 kind of process that can be run on the systems

• Daemons will be process running in background, such as services.
• Console process such as command line or console applications which will be bound to a terminal with active monitoring of its stdout/stderr.
• Graphic process such as graphic application, which will be bound to a display on a graphic server, and a window manager.

Init process

Once the kernel bootup, it will run the 'init' process, which will scan the files with executable permission present in the directory '/etc/init.d', and execute them.

It generally include system daemons, script to configure network interfaces and bootstrap a terminal, or shell, which will most likely stand by waiting for a login , and then set its uid/gid according to the login informations for user to enter commands.

Terminal or shell

As all other process, it will have an stdin that will be used to read input from the keyboard or network, and stdout,which will be used to display it's output on the screen or send it to the network.

If the user use a local terminal, the commands from the keyboard are sent to the terminal, which will then execute the command according to it's own permission associated with the shell's uid and gid.

There are two kinds of commands that can be executed by the shell, either built in commands who are specific to the shell, or executable files that are located on a mounted filesystem.

Bultin commands are specific to each shells.

Such built in commands commonly include

• cd to change the current working directory.
• pwd print the current working directory.
• export display or set environment variables.
• unset clear an environment variable.
• echo output the specified text or environment variable.
• which used to find the location of an executable file on the filesystems.

A list of all environment variable can be seen by running the command 'export' without any argument.

For example, the content of the PATH variable used to automatically search for executable command is

echo $PATH

The home directory of the current user can be seen with

echo $HOME

Full list there

https://www.gnu.org/software/bash/manual/bashref.html#Shell-Builtin-Commands

Running new processes from the shell

Additionally to built in commands, the shell can be used to spawn new process from executable files.

When a new command is sent to the shell, it will look in a certain number of directories, contained in the environment variable 'PATH', to search for an executable file with execution permission granted to the shell's process uid/gid.

If the command start with a '/', it will try to load and execute the file at the specified path.

If the command start with a '~', it will try to load and execute the file at the specified path relative to user's home directory of the shell's uid.

To run a file in the current working directory, need to use './exe_file'.

Basics commands

Core system commands

command	action
whoami	display the current user
su _user_	spawn a new shell as child process with the uid of the specified user.
sudo _command_	execute the specified command as root.
mount _/dev/disk/XXX_ _/mnt/path_	mount the selected partition to the specified mount point. if run with no argument, show all the file systems currently mounted on the system.
umount _/mnt/path_ or _dev/disk/XXX_	un mount the filesystem.
exit	close the current shell instance, and go back to the parent process.
ls _options_ _directory_	list files in the current working directory or the path given as argument. ls -l _/path_ output all informations from the entries. ls -a _/path_ list also hidden files ( starting with a _._ .) in the directory
mkdir _directory_	create the given directory
rmdir _directory_	remove the given empty directory
rm _file_	remove the specified file from the filesystem. rm -rf _directory_ remove the directory and all its files and subdirectories (use with caution :P)
ln _file1_ _file2_	Create a link to file1 in the path specified as file2. The flag -s can be used to create a symlink
cp _file1_ _file2_	copy file1 to file2. cp -r copy directory and subdirectories.
mv _file1_ _file2_	move file1 to file2
ps	list the running process. ps -aux list all the active processes with more informations.
top	run a console application to list all active processes
chown _user_ _file_	change the owner of the specified file. chmod -R _user_ _/path_ change the owner for all entries in the directory and subdirectory
chgrp _group_ _file_	change the group of the specified file. chgrp -R _/path_ change the group for all entries in the directory and subdirectory
chmod _permission flag_ _file_	change the permission flag of the specified file
cat _file_	output the content of the file given as argument
head _file_	output the first lines of the specified file
tail _file_	output the last lines of the specified file
grep	search for a given string in the input
useradd	a new user to the system
usermod _user_ _options_	change attribute of specified user.
find _directory_ _options_	output a list of file in the given directory
passwd _user_	change the password of specified user
man _command_	display the manual page for the given command
kill _pid_	terminate the process with the specified pid
killall _process name_	terminate all the processes matching the given name
ifconfig _network interface_ up|down	if run without argument, list all the active network interfaces. ifconfig eth0 down deactivate the network interface 'eth0'. ifconfig wlan0 up activate the network interface 'wlan0' using the configuration in /etc/network/interfaces.

All commands can be run with optional switch, by adding them to the command line, that will define some option on the output or affect the way the operation is processed.

Running command with the --help switch generally gives details about the command and the different options.

The default behavior when running an executable from the shell is to display the output on the console, but it can also be 'piped' as the input of another process with the character '|', redirected to a file using the character '>', or append to a file using the characters '>>'.

When the output of a process is piped to the command 'xargs', each line of the output can be used as an argument for another command.

For example, to find a given word in all files from a directory, can use

find /path/to/directory -type f | xargs grep -n 'word'

The switch -type f mean find will only output files, -type d can be used to list only directories.

The switch -n for grep will display the line number where the word is found in the input file.

Command line utilities

The following are not always installed by default, they might need to install specific package

command	description	package
nano _file_	basic text editor. basic commands : ctrl+o to save the opened file ctrl+w to search inside the opened file ctrl+x to quit	nano
unzip _file.zip_	unzip the zip file in the current directory	unzip
zip _file.zip_ _path/*_	add the files from the directory into the zip file. zip -r add all files and subdirectories to the zip	zip
gzip _file_	compress a single file to _file.gz_ gzip -d file.gz decompress the gzip file.	gzip
tar -cf _file.tar_ _/path_	archive all files from path into file.tar without compression. tar -czf then compress the .tar file using gzip. tar -xf _file.tar_ extract the file from the .tar file in current directory. tar -xzf file.tar.gz uncompress the tar file and exctract the files in current direcotry	tar

Shell scripts

Most shell also contains a basic script engine, which can be used to parse environment variable, spawn some processes and do some conditional execution based on process return code or output.

Those shell script generally are in files with the .sh extension, and start with the line #!/bin/bash or #!/bin/sh to indicate the shell program used to execute them.

Daemon and services

Daemon are process that will be run as background tasks.

Unlike commands run from the console they will detach themselves from the shell, change their uid and gid to a specific user set in the daemon configuration, and their output will be redirected to a log file, usually either in /var/log, or in a subdirectory of the user's home directory.

The script to run daemon are usually located in /etc/init.d, and their configuration files is usually somewhere in the /etc directory.

Then are also often associated with a port and can serve network request directed to that port.

Their uid and gid define their level of acess to system resources.

Common daemon are

• Apache, HTTP server
• NGix HTTP server
• mysql database server
• sshd remote terminal server
• pureftp FTP server
• proftp FTP server
• exim SMTP mail server
• bitcoind bitcoin node

Package system

Most linux distribution are built up uppon a package system, which contain all the different files that can be installed, removed or updated on the system.

The package system is made of 3 components

• The package repository, which can be located on the installtion cd/flash drive or on a remote server. It contain the list of all packages that can be installed on the system.
• The local package cache, generally located in /var, contain a summary of the repository, as well as all the package installed on the local system.
• The package themselves, who are essentially like a self installer zip, it contain files and installation script to install the package on the system.

Different linux distributions use different repositories, with different set of packages, and it's generally recommanded to stick to a repository compatible with the distribution being installed.

Distributions can also have different repositories such as 'stable' , 'testing' to store more recent versions of the packages, as well as sub repositories for sources packages, or optional packages that are not integrated by default in the main distribution.

There are two commonly used package system on linux, the debian system, and redhat system.

They both contain command to configure repositories, browse these repositories, and manage locally installed packages, as well as the command to deal with the installed package files themselves.

Debian packages

On debian based system, such as debian or ubuntu, the command to manage repository are apt-get, apt-cache, and others starting with apt-, the command to manipulate package files is dpkg.

The repositories that apt- commands will use are configured via the /etc/apt/sources.list file.

apt-get update will update the local cache with available package.

apt-cache search keywords can be used to list the package in the cache associated with the keywords.

apt-get install package can be used to download and install a package from the repository.

apt-get remove package will uninstall the package.

dpkg -l can be used to list all the package installed on the system.

dpkg -L package can be used to list all the files contained in the package installed on the system.

dpkg -S file can be used to find which package contain the specified file.

Redhat packages

On redhat based system, such as redhat, centos, fedora, the command to manage repository is yum, the command to mannage package files is rpm.

Installation on Mac OS using Virtual Box

The video show how to setup ubuntu server inside of virtual box. Virtual box is a convenient way to quickly install guest operating system, the interface is the same on every operating system.

VirtualBox can be downloaded here https://www.virtualbox.org/

The Ubuntu server iso file can be downloaded there https://www.ubuntu.com/download/server

I added the commands as subtitles in the video.

If it's installed on a physical machine, the procedure is roughly the same, and what is displayed in the virtual box window will be what is displayed on the screen, and you can connect the service using the machine's IP and the default ports.

If you use linux from a VPS or dedicated server, you can skip the first part, and skip to 22:00, you just have to select ubuntu 16 64 bit when setting up the box from the hoster panel, and then remote shell software like putty on windows can be used to connect the box directly using the user and password given by the hoster.

Most FTP and shell client will also support sftp transfer using the shell server port, to transfer files on the machine.

If the VPS or dedicated server has a root access, the root user can be used, the password is given in the hoster panel, and then you can skip the 'sudo' prefix on commands.

If you use a server without root access, it will generally have phpmyadmin already installed, and you can access it through the admin panel of the hoster, and most likely the database are created and configured through the admin panel too.

I will also try to complete with more informations or clarify certain things if they are not clear enough or lacking details.