A Relatively Secure LEMP Server Stack Setup in Ubuntu 18.04 LTS + phpMyAdmin

In this guide, LEMP stands for Linux, Nginx (pronounced as Engine-X), MySQL and PHP (PHP Hypertext Preprocessor). Also, as a bonus, we will also learn to setup phpMyAdmin.

I have gone through many websites in order to learn even just the basics of setting up a LEMP server. Hence I know the hassle. Here I have created a through guide to help someone relatively new to setup a powerful LEMP machine easily and effortlessly. I hope this guide comes to someone’s rescue.

Introduction

The instructions on this guide has been tested to work on a fresh install of Ubuntu 18.04 as the time of this writing (NPT 11/03/2018 10.26AM). Also, the system was fully updated before we started with the LEMP setup procedure.

For any other platform, this guide should still serve as a useful resource. The “mini goals” are well defined in various paragraphs. And one can easily look elsewhere for specific instructions for that platform to achieve same “mini goal”, one at a time.

For a system already running other version of server stacks (example LAMP), some additional steps (like removing those packages or disabling them) might be required. That is beyond the scope of this guide.

Specifications/Target

• Ubuntu v18.04
• Nginx v1.15
• MySQL v8.0
• PHP v7.2
• (Bonus) phpMyAdmin v4.8

But before we start, let’s quickly make sure that we have some basic tools ready. Run the following commands in the terminal.

sudo apt update
sudo apt install wget
sudo apt install software-properties-common

Now let’s start!

Custom Repositories

Before beginning the installation, we want to add some repositories which will give us the latest corresponding packages for our server stack.

Nginx Repository

For Ubuntu, in order to authenticate the Nginx repository signature and to eliminate warnings about missing PGP key during installation of the Nginx package, it is necessary to add the key used to sign the Nginx packages and repository to the apt program keyring. Only after then we will dare to add the repositories.

The above fact is true every time we add a custom repository. If we don’t want to add any custom repository and use the ones provided to us by “vanilla” Ubuntu itself, we can just ignore this section of the guide, entirely. We have to keep in mind that the version numbers used in this guide are according to the default, most recent versions of the respective packages at the time of creation of this guide. So, we might have to be careful in coming sections of the guide where we start installation and setup of the stack. We would want to make sure then, that the version number would match to what we have installed, not what is shown in this guide.

Run the following code one by one in the terminal to add the Nginx mainline repository. We need to accept any prompts, if asked.

wget https://nginx.org/keys/nginx_signing.key
sudo apt-key add nginx_signing.key && rm nginx_signing.key
sudo sed -i '$a deb http://nginx.org/packages/mainline/ubuntu/ bionic nginx' /etc/apt/sources.list
sudo sed -i '$a # deb-src http://nginx.org/packages/mainline/ubuntu/ bionic nginx' /etc/apt/sources.list

MySQL Repository

Just like we did with Nginx, we will add the MySQL repository. Run the following commands in the terminal to do so. We need to accept any prompts, if asked.

During the installation of the package, you will be asked to choose the versions of the MySQL server and other components. Just select Ok and hit the key Enter to complete the setup.

wget https://dev.mysql.com/get/mysql-apt-config_0.8.10-1_all.deb
sudo dpkg -i mysql-apt-config_0.8.10-1_all.deb && rm mysql-apt-config_0.8.10-1_all.deb

PHP Repository

The repository here we are going to install is the PHP PPA by Ondrej. We can update our system with “unsupported” packages from this “untrusted” PPA by adding ppa:ondrej/php to our system’s Software Sources. The following commands will help us to do so. We need to accept any prompts, if asked.

sudo add-apt-repository ppa:ondrej/php

We might feel a little bit confused by the terms “untrusted PPA”, but there is actually no reason to worry. We just need to remember that this is not an official upgrade path. But the PPA is well known, and is relatively safe to use.

(Bonus) phpMyAdmin Repository

Default Ubuntu repository gives us only the 4.6.6 version, whereas the latest version currently is 4.8.3. To tackle this issue, we will use the STABLE branch of phpMyAdmin directly from its official GitHub repository. We will see later how.

The Installation

Let’s finally begin the actual installations processes.

During the installation of any package, when faced with any unsure prompt, just go with the default option/action.

Update APT

First, we want to make sure we have the latest records in our local packages registry. Let’s run the following command in the terminal like so.

sudo apt update

Installing Nginx

First thing we’re going to install is the server called Nginx.

sudo apt install nginx

We can check if Nginx is installed by typing nginx -v in the terminal.

Installing MySQL

Now we want to install the database management system (DBMS). We choose MySQL.

sudo apt install mysql-server mysql-client

We can check if MySQL is installed by executing mysql --version in the terminal.

Installing PHP

Next thing we want to install is PHP. We need to install PHP with a few extensions that are mandatory for modern web applications.

sudo apt install php-bz2 php-cli php-common php-curl php-fpm php-gd \
    php-gettext php-mbstring php-mysql php-pear php-phpseclib php-sqlite3 \
    php-tcpdf php-xdebug php-xml php-zip

We may run php -v in the terminal to check the version of PHP installed.

Configurations

Time to make the installations “talk” to each other.

Configuring Nginx

We don’t need to change anything right now. But if we want to, we can change the main configuration of Nginx as follows:

sudo gedit /etc/nginx/nginx.conf

In the config file, notice the line with user nginx. This means Nginx will run as the user nginx. We should not forget to restart the Nginx service if we made any change to the configuration file.

sudo systemctl restart nginx.service

Configuring PHP to work with Nginx

In order for PHP and Nginx to work together, we need to configure both of them. We need to make sure that PHP-FPM (PHP FastCGI Process Manager) runs as the same user as Nginx. And for that we need to run the following command in the terminal.

sudo gedit /etc/php/7.2/fpm/pool.d/www.conf

And change the relevant lines as:

...
user = nginx
group = nginx
...
listen.owner = nginx
listen.group = nginx
...

Note the command where we used … php/7.2/fpm … . We want to make sure that 7.2 is the version that we actually have installed in our system. Refer this section to go back and see how we installed PHP and PHP-FPM, and how to see the version of PHP installed.

If we made changes to the configuration, we need to run the following in the terminal to load the changes.

sudo systemctl restart php7.2-fpm.service

Configuring Xdebug for PHP

Xdebug can be very helpful during development of php applications. To set it up, open the configuration file /etc/php/7.2/fpm/conf.d/20-xdebug.ini as follows:

sudo gedit /etc/php/7.2/fpm/conf.d/20-xdebug.ini

And replace the contents with this:

zend_extension=xdebug.so
xdebug.remote_enable=1
xdebug.remote_handler=dbgp
xdebug.remote_host=localhost
xdebug.remote_port=9009
xdebug.remote_autostart=1
xdebug.var_display_max_depth=10
xdebug.auto_trace=on
xdebug.show_error_trace=on
xdebug.show_exception_trace=on

Let’s not forget the 9009 port while setting up debugger in our IDE!

Save and restart the php-fpm service.

sudo systemctl restart php7.2-fpm.service

Default Site

Now comes the fun part where we create a default site that supports PHP. In our case, we want ~/www as our directory of all websites. Normally, /var/www is used as the default one. Here we want to change it to a custom directory inside our home directory, as mentioned above.

Please note extra carefully that this might be nor the smartest neither the safest idea to let the web directory to have same ownership as the “human” user! But we are doing this for our ease. Please do remember that “ease” and “security” usually contradict each other!

First, we want to make sure the directory exists. Let’s create a default site directory _default_ with the following command.

mkdir -p ~/www/_default_/public

Note that to add other sites, we can follow a similar pattern. We may create a new folder for each site, which has a public folder in it as the public entry point of the site.

Now to edit the default site configuration, let’s run the following command in the terminal.

sudo cp /etc/nginx/conf.d/default.conf /etc/nginx/conf.d/default.conf.bak
sudo gedit /etc/nginx/conf.d/default.conf

And replace its content with this:

server {
    listen 80 default_server;
    listen [::]:80 default_server;

    root /home/[OUR_USERNAME]/www/_default_/public;

    index index.html index.htm index.php;

    server_name _;

    location / {
        try_files $uri $uri/ =404;
        autoindex on;
    }

    location ~ \.php$ {
        try_files $uri =404;
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
        fastcgi_pass unix:/run/php/php7.2-fpm.sock;
        fastcgi_index index.php;
        fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
        include fastcgi_params;
    }
}

Please note that we need to change [OUR_USERNAME] from above config file to our actual username.

Now let’s run the following to reload our new configuration.

sudo systemctl restart nginx.service

Now we should be able to see on browser that http://localhost actually works, and most probably shows an empty index.

**Ba Dum Tis**

We can put any file in the ~/www/_default_/public directory and it should be showing in the browser after a refresh.

Configuring MySQL

This one is easy. Let’s open our terminal and run the following:

sudo mysql_secure_installation

We just need to carefully follow all of the prompts and we will properly set up MySQL.

(Bonus) Installing phpMyAdmin

Setting Up Host

We want to be able to lunch phpMyAdmin by going to http://phpmyadmin/ in the address bar of the browser.

So, first of all, run:

sudo gedit /etc/hosts

And add entries as follows:

...

127.0.0.1   phpmyadmin
::1         phpmyadmin

...

phpMyAdmin

Since the official repository has older version, we will pull the latest one directly from the GitHub.

But before that, let’s prepare ourselves better. We need to have composer installed.

wget https://raw.githubusercontent.com/composer/getcomposer.org/1b137f8bf6db3e79a38a5bc45324414a6b1f9df2/web/installer -O - -q | php -- --quiet
sudo mv composer.phar /usr/bin/composer
composer config --global repo.packagist composer https://packagist.org

Now, let’s clone the the official repository from GitHub.

The repository is huge (~0.5 GB), so it may take a while for the download to complete and the deltas to be resolved.

git clone https://github.com/phpmyadmin/phpmyadmin.git && cd phpmyadmin
git checkout STABLE
composer update --no-dev --prefer-dist

The phpMyAdmin needs to have some initial configurations to work properly. Run the following in the shell while still being in the phpmyadmin directory.

mkdir tmp && chmod 777 tmp
touch config.inc.php
gedit config.inc.php

And paste the following code in it and save it.

<?php
    // use here a value of your choice at least 32 chars long
    $cfg['blowfish_secret'] = '1{dd0`<Q),5XP_:R9UK%%8\"EEcyH#{o';

    $i=0;
    $i++;
    $cfg['Servers'][$i]['auth_type']     = 'cookie';

But before we go and setup the server-block for phpMyAdmin, let’s be aware that, at the time of this writing, php drivers are not able to connect to MySQL 8 with new authentication method called caching_sha2_password. Hence, we need to change default authentication method to mysql_native_password. In the shell, run:

mysql -u root -p
# enter your mysql root password here

You will be logged in the SQL console. Then write:

ALTER USER 'root'@'localhost' identified with mysql_native_password by 'root';
EXIT;

Notice above that in addition to the authentication method for the user root, the password has also been changed to root. Also change the default from the mysql config.

sudo gedit /etc/mysql/mysql.conf.d/mysqld.cnf

And add default-authentication-plugin=mysql_native_password just below the line that says [mysqld], like so:

...
[mysqld]
default-authentication-plugin=mysql_native_password
...

Restart the MySQL server.

sudo systemctl restart mysql.service

Setting Up Server Block

Now, we will setup an Nginx server block (a.k.a. virtual host in Apache httpd).

Let’s run the following command to create a site (configuration file).

sudo touch /etc/nginx/conf.d/phpmyadmin.conf

Let’s open it with:

sudo gedit /etc/nginx/conf.d/phpmyadmin.conf

And add the contents as follows.

server {
    listen 80;
    listen [::]:80;

    root /home/[username]/phpmyadmin; # make sure to enter the correct location of phpmyadmin here
    index index.php index.html index.htm;

    server_name phpmyadmin; # as defined in the '/etc/hosts'

    location / {
        try_files $uri $uri/ /index.php?$query_string;
    }

    location ~ \.php$ {
        try_files $uri /index.php =404;
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
        fastcgi_pass unix:/run/php/php7.2-fpm.sock;
        fastcgi_index index.php;
        fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
        include fastcgi_params;
    }
}

Activating the server block

Now we have to restart Nginx to activate our new site (config file) by running:

sudo systemctl restart nginx.service

Try hitting http://phpmyadmin/ and it should work! (If you don’t remember the username or password, try entering both of them root.)

Conclusion

There we have it! We should by now have a working and relatively secure LEMP server stack with Nginx running at http://localhost, as well as our phpMyAdmin app running at http://phpmyadmin/

In this guide we didn’t talk anything about firewall. This is because a fresh install of “vanilla” Ubuntu 18.04 should not have one running it automatically. We may research about it later if we wish to. Right now, that would be beyond the scope of this guide.

So, did you find this guide helpful? Feedbacks are precious. Suggestions are highly appreciated.