Ubuntu server for Ruby and PHP apps

Published Wednesday, Dec 16 2015

There are several guides on the Internet on setting up Ubuntu server, but I thought I’d add here some notes on how to set up Ubuntu server for Ruby and PHP apps at the same time. Ubuntu’s latest Long Term Support (LTS) release is 14.04, so this guide will be based on that release.

I will assume you already have a a server with the basic Ubuntu Server Edition installed – be it a dedicated server or a VPS from your provider of choice – with just SSH access enabled and nothing else. We’ll be bootstrapping the basic system and install all the dependencies required for running Ruby and PHP apps; I usually use Nginx as web server, so we’ll be also using Phusion Passenger as application server for Ruby and fastcgi for PHP to make things easier.

Configure Ubuntu server for Ruby and PHP apps

Before anything else, it’s a good idea to update the system with the latest updates available. So SSH into the new server with the IP and credentials you’ve been given and -recommended- start a screen session with

screen -S <session-name>

Now change the root password with

passwd

then open /root/.ssh/authorized_keys with and editor and ensure no SSH keys have already been added other than yours; if you see any keys, I recommend you comment them out and uncomment them only if you ever need to ask your provider for support.

Done that, as usual run:

apt-get update
apt-get upgrade -y

to update the system.

Next, edit /etc/hostname with vi or any other editor and change the hostname with the hostname you will be using to connect to this server; also edit /etc/hosts and add the correct hostname in there as well. Reboot:

reboot now

SSH access

It’s a good idea to use a port other than the default one for SSH access, and a user other than root. In this guide, we’ll be:

using the example port 17239
disabling the root access and enabling access for the user deploy (only) instead
switching from password authentication to public key authentication for good measure.

Of course you can choose whichever port and username you wish.

For convenience, on your client computer (that is, the computer you will be connecting to the server from) edit ~/.ssh.config and add the following content:

Host my-server (or whichever name you prefer)
  Hostname <the ip address of the server>
  Port 22
  User root

So you can more easily SSH into the new server with just

ssh my-server

As you can see for now we are still using the default port and user until the SSH configuration is updated.

Unless your public key has already been added to /root/.ssh/authorized_keys during the provisioning of the new server, still on the client machine run

ssh-copy-id <hostname or ip of the server>

to copy your public key over. You should now be able to SSH into your server without password.

Back on the server, it’s time to setup the user which you will be using to SSH into the server instead of root:

adduser deploy

Edit /etc/sudoers and add:

deploy ALL=(ALL:ALL) ALL

On the client, ensure you can SSH into the server as deploy using your key:

ssh-copy-id deploy@my-server

You should now be able to login as deploy without password.

Now edit /etc/ssh/sshd_config and change settings as follows:

Port 17239
PermitRootLogin no
PasswordAuthentication no
UseDNS no
AllowUsers deploy

This will:

change the port
disable root login
disable password authentication so we are forced to use public key authentication
disable DNS lookups so to speed up logins
only allow the user deploy to SSH into the system

Restart SSH server with:

service ssh restart

Keep the current session open just in case for now. On the client, open again ~/.ssh/config and update the configuration of the server with the new port and user:

Host my-server (or whichever name you prefer)
  Hostname <the ip address of the server>
  Port 17239
  User deploy

Now if you run

ssh my-server

you should be in as deploy without password. You should no longer be able to login as root though; to test run:

ssh root@my-server date

you should see an error:

Permission denied (publickey).

Firewall

Now that SSH access is sorted, it’s time to configure the firewall to lock down the server so that only the services we want (such as ssh, http/https and mail) are allowed. Edit the file /etc/iptables.rules and paste the following:

# Generated by iptables-save v1.4.4 on Sat Oct 16 00:10:15 2010
*filter
:INPUT ACCEPT
:FORWARD ACCEPT
:OUTPUT ACCEPT
-A INPUT -i lo -j ACCEPT
-A INPUT -d 127.0.0.0/8 ! -i lo -j DROP
-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -p tcp -m tcp --dport 80 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 443 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 587 -j ACCEPT
-A INPUT -p tcp -m state --state NEW -m tcp --dport 17239 -j ACCEPT
-A INPUT -m limit --limit 5/min -j LOG --log-prefix "iptables [Positive[False?]: " --log-level 7
-A INPUT -p icmp -m icmp --icmp-type 8 -j ACCEPT
-A INPUT -j LOG
-A INPUT -j REJECT --reject-with icmp-port-unreachable
-A OUTPUT -j ACCEPT
COMMIT
# Completed on Sat Oct 16 00:10:15 2010
# Generated by iptables-save v1.4.4 on Sat Jun 12 23:55:23 2010
*mangle
:PREROUTING ACCEPT
:INPUT ACCEPT
:FORWARD ACCEPT
:OUTPUT ACCEPT
:POSTROUTING ACCEPT
COMMIT
# Completed on Sat Jun 12 23:55:23 2010
# Generated by iptables-save v1.4.4 on Sat Jun 12 23:55:23 2010
*nat
:PREROUTING ACCEPT
-A PREROUTING -p tcp --dport 25 -j REDIRECT --to-port 587
:POSTROUTING ACCEPT
:OUTPUT ACCEPT
COMMIT
# Completed on Sat Jun 12 23:55:23 2010

It’s a basic configuration I have been using for some years. It locks all incoming traffic apart from SSH access, web traffic (since we’ll be hosting Ruby and PHP apps) and mail. Of course, make sure you specify the SSH port you’ve chosen here if other than 17239 as in the example.

To apply the setting now, run:

iptables-restore < /etc/iptables.rules

and verify with

iptables -L

You should see the following output:

Chain INPUT (policy ACCEPT)
target prot opt source destination
ACCEPT all -- anywhere anywhere
DROP all -- anywhere loopback/8
ACCEPT all -- anywhere anywhere state RELATED,ESTABLISHED
ACCEPT tcp -- anywhere anywhere tcp dpt:http
ACCEPT tcp -- anywhere anywhere tcp dpt:https
ACCEPT tcp -- anywhere anywhere tcp dpt:submission
ACCEPT tcp -- anywhere anywhere state NEW tcp dpt:17239
LOG all -- anywhere anywhere limit: avg 5/min burst 5 LOG level debug prefix "iptables [Positive[False?]: "
ACCEPT icmp -- anywhere anywhere icmp echo-request
LOG all -- anywhere anywhere LOG level warning
REJECT all -- anywhere anywhere reject-with icmp-port-unreachable

Chain FORWARD (policy ACCEPT)
target prot opt source destination

Chain OUTPUT (policy ACCEPT)
target prot opt source destination
ACCEPT all -- anywhere anywhere

Now if you reboot the server, these settings will be lost, so you need to persist them in either of two ways:

1) open /etc/network/interfaces and add, in the eth0 section, the following line:

post-up iptables-restore < /etc/iptables.rules

So the file should now look similar to the following:

auto eth0
iface eth0 inet static
address ...
netmask ...
gateway ...
up ip addr add 10.16.0.5/16 dev eth0
dns-nameservers 8.8.8.8 8.8.4.4
post-up iptables-restore < /etc/iptables.rules

OR,

2) Run

apt-get install iptables-persistent

Either way, reboot now and verify again with iptables -L that the settings are persisted.

ZSH shell, editor (optional)

If you like me prefer ZSH over BASH and use VIM as editor, first install ZSH with:

apt-get install zsh git-core
curl -L https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh | sh
ln -s ~/dot-files/excid3.zsh-theme ~/.oh-my-zsh/themes

Then you may want to use my VIM configuration so to have a nicer editor environment:

cd; git clone https://github.com/vitobotta/dot-files.git
cd dot-files; ./setup.sh

I’d repeat the above commands for both the deploy user and root (as usual you can use sudo -i for example to login as root). Under deploy, you’ll need to additionally run:

chsh

and specify /usr/bin/zsh as your shell.

Dependencies for Ruby apps

You’ll need to install the various dependencies required to compile Ruby and install various gems:

apt-get install build-essential curl wget openssl libssl-dev libreadline-dev libmysqlclient-dev ruby-dev mysql-client ruby-mysql xvfb firefox libsqlite3-dev sqlite3 libxslt1-dev libxml2-dev

You’ll also need to install nodejs for the assets compilation (Rails apps):

apt-get install software-properties-common
add-apt-repository ppa:chris-lea/node.js
apt-get update
apt-get install nodejs

Next, as deploy:

install rbenv (ref. https://github.com/rbenv/rbenv#basic-github-checkout); important: see note about ZSH on that page
install ruby-build as plugin (ref. https://github.com/sstephenson/ruby-build)
open a new shell session to load rbenv
see list of available Ruby versions with rbenv install –list
install the desired version of Ruby, e.g. rbenv install 2.2.4
set the new Ruby as default with rbenv global 2.2.4

Ensure the following lines are present in the shell rc files (.zshrc and .zprofile) and reload the shell so the new Ruby can be “found”:

export PATH="$HOME/.rbenv/bin:$HOME/.rbenv/shims:$PATH"
eval "$(rbenv init -)"

ruby -v should now output the expected version number, 2.2.4 in the example.

Optionally, you may want to install the rbenv-vars plugin for environment variables support with rbenv:

git clone https://github.com/sstephenson/rbenv-vars.git ~/.rbenv/plugins/rbenv-vars
chmod +x ~/.rbenv/plugins/rbenv-vars/bin/rbenv-vars

Dependencies for PHP apps

Install the various packages required for PHP-FPM:

apt-get install php5-fpm php5-mysql php5-curl php5-gd php5-intl php-pear php5-imagick php5-mcrypt php5-memcache php5-memcached php5-ming php5-ps php5-pspell php5-recode php5-snmp php5-sqlite php5-tidy php5-xmlrpc php5-xsl php5-geoip php5-mcrypt php-apc php5-imap

MySQL

I am assuming here you will be using MySQL – I usually use the Percona distribution. If you plan on using some other database system, skip this section.

First, install the dependencies:

apt-get install curl build-essential flex bison automake autoconf bzr libtool cmake libaio-dev libncurses-dev zlib1g-dev libdbi-perl libnet-daemon-perl libplrpc-perl libaio1
gpg --keyserver hkp://keys.gnupg.net --recv-keys 1C4CBDCDCD2EFD2A
gpg -a --export CD2EFD2A | sudo apt-key add -

Next edit /etc/apt/sources.list and add the following lines:

deb http://repo.percona.com/apt trusty main
deb-src http://repo.percona.com/apt trusty main

Install Percona server:

apt-get update
apt-get install percona-xtradb-cluster-server-5.5 percona-xtradb-cluster-client-5.5 percona-xtradb-cluster-galera-2.x

Test that MySQL is running:

mysql -uroot -p

Getting web apps up and running

First install Nginx with Passenger for Ruby support:

apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 561F9B9CAC40B2F7
apt-get install apt-transport-https ca-certificates

Edit /etc/apt/sources.list.d/passenger.list and add the following:

deb https://oss-binaries.phusionpassenger.com/apt/passenger trusty main

Update sources:

chown root: /etc/apt/sources.list.d/passenger.list
chmod 600 /etc/apt/sources.list.d/passenger.list
apt-get update

Then install Phusion Passenger for Nginx:

apt-get install nginx-extras passenger

Edit /etc/nginx/nginx.conf and uncomment the passenger_root and passenger_ruby lines, making sure the latter points to the version of Ruby installed with rbenv, otherwise it will point to the default Ruby version in the system. Make the following changes:

user deploy;
worker_processes auto;
pid /run/nginx.pid;

events {
  use epoll;
  worker_connections 2048;
  multi_accept on;
}

http {
  sendfile on;
  tcp_nopush on;
  tcp_nodelay on;
  keepalive_timeout 65;
  types_hash_max_size 2048;
  server_tokens off;
  …
  passenger_root /usr/lib/ruby/vendor_ruby/phusion_passenger/locations.ini;
  passenger_ruby /home/deploy/.rbenv/shims/ruby;
  passenger_show_version_in_header off;
}

Restart nginx with

service nginx restart

Test that nginx works by opening http://the_ip_or_hostname in your browser.

For PHP apps, we will be using fastcgi with unix sockets. Create for each app a profile in /etc/php5/fpm/pool.d/, e.g. /etc/php5/fpm/pool.d/myapp. Use the following template:

[<app name>]
listen = /tmp/<app name>.php.socket
listen.backlog = -1
listen.owner = deploy
listen.group = deploy

; Unix user/group of processes
user = deploy
group = deploy

; Choose how the process manager will control the number of child processes.
pm = dynamic
pm.max_children = 75
pm.start_servers = 10
pm.min_spare_servers = 5
pm.max_spare_servers = 20
pm.max_requests = 500

; Pass environment variables
env[HOSTNAME] = $HOSTNAME
env[PATH] = /usr/local/bin:/usr/bin:/bin
env[TMP] = /tmp
env[TMPDIR] = /tmp
env[TEMP] = /tmp

; host-specific php ini settings here
; php_admin_value[open_basedir] = /var/www/DOMAINNAME/htdocs:/tmp

To allow communication between Nginx and PHP-FPM via fastcgi, ensure each PHP app’s virtual host includes some configuration like the following:

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

location ~ \.php$ {
  fastcgi_split_path_info ^(.+\.php)(/.+)$;
  fastcgi_pass unix:/tmp/<app name>.php.socket;
  fastcgi_index index.php;
  include fastcgi_params;
  fastcgi_param SCRIPT_FILENAME $document_root/$fastcgi_script_name;
}

Edit /etc/php5/fpm/php.ini and set cgi.fix_pathinfo to 0. Restart both FPM and Nginx:

service php5-fpm restart
service nginx restart

Congrats, you should now be able to run both Ruby and PHP apps.

Backups

There are so many ways to backup a server…. what I usually use on my personal servers is a combination of xtrabackup for MySQL databases and duplicity for file backups.

As root, clone my admin scripts:

cd ~
git clone https://github.com/vitobotta/admin-scripts.git
apt-key adv --keyserver keys.gnupg.net --recv-keys 1C4CBDCDCD2EFD2A

Edit /etc/apt/sources.list and add:

deb http://repo.percona.com/apt trusty main
deb-src http://repo.percona.com/apt trusty main

Proceed with the installation of the packages:

apt-get update
apt-get install duplicity xtrabackup

Next refer to this previous post for the configuration.

Schedule the backups with crontab -e by adding the following lines:

MAILTO = <your email address>

00 02 * * sun /root/admin-scripts/backup/duplicity.sh full
00 02 * * mon-sat /root/admin-scripts/backup/duplicity.sh incr
00 13 * * * /root/admin-scripts/backup/xtrabackup.sh incr

Mailing

install postfix and dovecot with

apt-get install postfix dovecot-common mailutils

run dpkg-reconfigure postfix and set the following:

General type of mail configuration -> Internet Site
System mail name -> same as the server’s hostname
Root and postmaster email recipient -> your email address
Force synchronous updates on mail queue -> no
Local networks -> leave default
Mailbox size limit (bytes) -> set 10485760 (10MB) or so, to prevent the default mailbox from growing with no limits
Internet protocols to use -> all
SMTP authentication: run

postconf -e 'home_mailbox = Maildir/'
postconf -e 'smtpd_sasl_type = dovecot'
postconf -e 'smtpd_sasl_path = private/auth'
postconf -e 'smtpd_sasl_local_domain ='
postconf -e 'smtpd_sasl_security_options = noanonymous'
postconf -e 'broken_sasl_auth_clients = yes'
postconf -e 'smtpd_sasl_auth_enable = yes'
postconf -e 'smtpd_recipient_restrictions = permit_sasl_authenticated,permit_mynetworks,reject_unauth_destination'

TLS encryption: run

mkdir /etc/postfix/certificate && cd /etc/postfix/certificate
openssl genrsa -des3 -out server.key 2048
openssl rsa -in server.key -out server.key.insecure
mv server.key server.key.secure
mv server.key.insecure server.key
openssl req -new -key server.key -out server.csr
openssl x509 -req -days 365 -in server.csr -signkey server.key -out server.crt

postconf -e 'smtp_tls_security_level = may'
postconf -e 'smtpd_tls_security_level = may'
postconf -e 'smtp_tls_note_starttls_offer = yes'
postconf -e 'smtpd_tls_key_file = /etc/postfix/certificate/server.key'
postconf -e 'smtpd_tls_cert_file = /etc/postfix/certificate/server.crt'
postconf -e 'smtpd_tls_loglevel = 1'
postconf -e 'smtpd_tls_received_header = yes'
postconf -e 'myhostname = <hostname>'

SASL: edit /etc/dovecot/conf.d/10-master.conf, and uncomment the following lines so that they look as follows (first line is a comment so leave it…commented out):

  unix_listener /var/spool/postfix/private/auth {
  mode = 0666
}

Postfix smtp-auth

edit /etc/dovecot/conf.d/10-auth.conf and change the setting auth_mechanisms to “plain login”
edit /etc/postfix/master.cf and a) comment out smtp, b) uncomment submission
restart postfix: service postfix restart
restart dovecot: service dovecot restart
verify that all looks good

root@nl:/etc/postfix/certificate# telnet localhost 587
Trying 127.0.0.1...
Connected to localhost.
Escape character is '^]'.
220 <hostname> ESMTP Postfix (Ubuntu)
ehlo <hostname>
250-<hostname>
250-PIPELINING
250-SIZE 10240000
250-VRFY
250-ETRN
250-STARTTLS
250-AUTH PLAIN LOGIN
250-AUTH=PLAIN LOGIN
250-ENHANCEDSTATUSCODES
250-8BITMIME
250 DSN

Test email sending:

echo "" | mail -s "test" <your email address>

There’s a lot more that could be done, but this should get you started. Let me know in the comments if you run into any issues.

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