The Perfect Server - Ubuntu 16.10 (Yakkety Yak) with Apache, PHP, MySQL, PureFTPD, BIND, Postfix, Dovecot and ISPConfig 3.1

This tutorial shows the installation of an Ubuntu 16.10 (Yakkety Yak) web hosting server with Apache2, Postfix, Dovecot, Bind and PureFTPD to prepare it for the installation of ISPConfig 3.1. The resulting system will provide a Web, Mail, Mailinglist, DNS and FTP Server.

ISPConfig 3 is a web hosting control panel that allows you to configure the following services through a web browser: Apache or nginx web server, Postfix mail server, Courier or Dovecot IMAP/POP3 server, MySQL, BIND or MyDNS nameserver, PureFTPd, SpamAssassin, ClamAV, and many more. This setup covers the installation of Apache (instead of Nginx), BIND (instead of MyDNS), and Dovecot (instead of Courier).

This tutorial is about Ubuntu 16.10, a non-LTS (Long Time Support) version. Most users prefer an LTS version which gets updates and security patches for a much longer time. The latest LTS release is Ubuntu 16.04, this tutorial exists in a Ubuntu 16.04 version as well. Consider carefully if you need latest packages (and don't have a problem with a short support period), then continue with this tutorial. If you need longtime support, then please use the Ubuntu 16.04 Perfect Server Tutorial instead.

1. Preliminary Note

In this tutorial, I use the hostname with the IP address and the gateway . These settings might differ for you, so you have to replace them where appropriate.  Before proceeding further you need to have a basic minimal installation of Ubuntu 16.10 as explained in the tutorial.

2. Edit /etc/apt/sources.list And Update Your Linux Installation

Edit /etc/apt/sources.list. Comment out or remove the installation CD from the file and make sure that the universe and multiverse repositories are enabled. It should look like this afterwards:

nano /etc/apt/sources.list


# deb cdrom:[Ubuntu-Server 16.10 _Yakkety Yak_ - Release amd64 (20161012.1)]/ yakkety main restricted

#deb cdrom:[Ubuntu-Server 16.10 _Yakkety Yak_ - Release amd64 (20161012.1)]/ yakkety main restricted

# See for how to upgrade to
# newer versions of the distribution.
deb yakkety main restricted
# deb-src yakkety main restricted

## Major bug fix updates produced after the final release of the
## distribution.
deb yakkety-updates main restricted
# deb-src yakkety-updates main restricted

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb yakkety universe
# deb-src yakkety universe
deb yakkety-updates universe
# deb-src yakkety-updates universe

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb yakkety multiverse
# deb-src yakkety multiverse
deb yakkety-updates multiverse
# deb-src yakkety-updates multiverse

## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb yakkety-backports main restricted universe multiverse
# deb-src yakkety-backports main restricted universe multiverse

## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb yakkety partner
# deb-src yakkety partner

deb yakkety-security main restricted
# deb-src yakkety-security main restricted
deb yakkety-security universe
# deb-src yakkety-security universe
deb yakkety-security multiverse
# deb-src yakkety-security multiverse

Then run

apt-get update

to update the apt package database and

apt-get upgrade

to install the latest updates (if there are any). If you see that a new kernel gets installed as part of the updates, you should reboot the system afterwards:



3. Change the Default Shell

/bin/sh is a symlink to /bin/dash, however we need /bin/bash, not /bin/dash. Therefore, we do this:

dpkg-reconfigure dash

Use dash as the default system shell (/bin/sh)? <-- No

If you don't do this, the ISPConfig installation will fail.


4. Disable AppArmor

AppArmor is a security extension (similar to SELinux) that should provide extended security. In my opinion, you don't need it to configure a secure system, and it usually causes more problems than advantages (think of it after you have done a week of trouble-shooting because some service wasn't working as expected, and then you find out that everything was ok, only AppArmor was causing the problem). Therefore, I disable it (this is a must if you want to install ISPConfig later on).

We can disable it like this:

service apparmor stop
update-rc.d -f apparmor remove
apt-get remove apparmor apparmor-utils


5. Synchronize the System Clock

It is a good idea to synchronize the system clock with an NTP (network time protocol) server over the Internet when you run a physical server. In case you run a virtual server then you should skip this step. Just run

apt-get -y install ntp ntpdate

and your system time will always be in sync.


6. Install Postfix, Dovecot, MariaDB, rkhunter and binutils

For installing postfix, we need to ensure that sendmail is not installed and running. To stop and remove sendmail run this command:

service sendmail stop; update-rc.d -f sendmail remove

The error message:

Failed to stop sendmail.service: Unit sendmail.service not loaded.

Is ok, it just means that sendmail was not installed, so there was nothing to be removed.

Now we can install Postfix, Dovecot, MariaDB (as MySQL replacement), rkhunter, and binutils with a single command:

apt-get -y install postfix postfix-mysql postfix-doc mariadb-client mariadb-server openssl getmail4 rkhunter binutils dovecot-imapd dovecot-pop3d dovecot-mysql dovecot-sieve dovecot-lmtpd sudo

You will be asked the following questions:

General type of mail configuration: <-- Internet Site
System mail name: <--

It is important that you use a subdomain as "system mail name" like or and not a domain that you want to use as email domain (e.g. yourdomain.tld) later.

Next, open the TLS/SSL and submission ports in Postfix:

nano /etc/postfix/

Uncomment the submission and smtps sections as follows - add the line -o smtpd_client_restrictions=permit_sasl_authenticated,reject to both sections and leave everything thereafter commented:

submission inet n       -       -       -       -       smtpd
  -o syslog_name=postfix/submission
  -o smtpd_tls_security_level=encrypt
  -o smtpd_sasl_auth_enable=yes
  -o smtpd_client_restrictions=permit_sasl_authenticated,reject
#  -o smtpd_reject_unlisted_recipient=no
#  -o smtpd_client_restrictions=$mua_client_restrictions
#  -o smtpd_helo_restrictions=$mua_helo_restrictions
#  -o smtpd_sender_restrictions=$mua_sender_restrictions
#  -o smtpd_recipient_restrictions=permit_sasl_authenticated,reject
#  -o milter_macro_daemon_name=ORIGINATING
smtps     inet  n       -       -       -       -       smtpd
  -o syslog_name=postfix/smtps
  -o smtpd_tls_wrappermode=yes
  -o smtpd_sasl_auth_enable=yes
  -o smtpd_client_restrictions=permit_sasl_authenticated,reject
#  -o smtpd_reject_unlisted_recipient=no
#  -o smtpd_client_restrictions=$mua_client_restrictions
#  -o smtpd_helo_restrictions=$mua_helo_restrictions
#  -o smtpd_sender_restrictions=$mua_sender_restrictions
#  -o smtpd_recipient_restrictions=permit_sasl_authenticated,reject
#  -o milter_macro_daemon_name=ORIGINATING

NOTE: The whitespaces in front of the "-o .... " lines are important!

Restart Postfix afterward:

service postfix restart

We want MySQL to listen on all interfaces, not just localhost. Therefore, we edit /etc/mysql/mariadb.conf.d/50-server.cnf and comment out the line bind-address =

nano /etc/mysql/mariadb.conf.d/50-server.cnf

# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
#bind-address           =

Now we set a root password in MariaDB. Run:


You will be asked these questions:

Enter current password for root (enter for none): <-- press enter
Set root password? [Y/n] <-- y
New password: <-- Enter the new MariaDB root password here
Re-enter new password: <-- Repeat the password
Remove anonymous users? [Y/n] <-- y
Disallow root login remotely? [Y/n] <-- y
Reload privilege tables now? [Y/n] <-- y

Set the password authentication method in MariaDB to native so we can use PHPMyAdmin later to connect as root user:

echo "update mysql.user set plugin = 'mysql_native_password' where user='root';" | mysql -u root

Edit the file /etc/mysql/debian.cnf and set the MYSQL / MariaDB root password there twice in the rows that start with password.

nano /etc/mysql/debian.cnf

The MySQL root password that needs to be added is shown in read, in this example the password is "howtoforge".

# Automatically generated for Debian scripts. DO NOT TOUCH!
host = localhost
user = root
password = howtoforge
socket = /var/run/mysqld/mysqld.sock
host = localhost
user = root
password = howtoforge
socket = /var/run/mysqld/mysqld.sock
basedir = /usr

Then we restart MariaDB:

service mysql restart

Now check that networking is enabled. Run

netstat -tap | grep mysql

The output should look like this:

[email protected]:~# netstat -tap | grep mysql
tcp6 0 0 [::]:mysql [::]:* LISTEN 23476/mysqld
[email protected]:~# 

7. Install Amavisd-new, SpamAssassin, and Clamav

To install amavisd-new, SpamAssassin, and ClamAV, we run

apt-get -y install amavisd-new spamassassin clamav clamav-daemon zoo unzip bzip2 arj nomarch lzop cabextract apt-listchanges libnet-ldap-perl libauthen-sasl-perl clamav-docs daemon libio-string-perl libio-socket-ssl-perl libnet-ident-perl zip libnet-dns-perl postgrey

The ISPConfig 3 setup uses amavisd which loads the SpamAssassin filter library internally, so we can stop SpamAssassin to free up some RAM:

service spamassassin stop
update-rc.d -f spamassassin remove

To start ClamAV use:

service clamav-daemon start

The following error can be ignored on the first run of freshclam.

ERROR: /var/log/clamav/freshclam.log is locked by another process
ERROR: Problem with internal logger (UpdateLogFile = /var/log/clamav/freshclam.log).

7.1 Install Metronome XMPP Server (optional)

The Metronome XMPP Server provides an XMPP chat server. This step is optional, if you do not need a chat server, then you can skip this step. No other ISPConfig functions depend on this software.

Install the following packages with apt.

apt-get -y install git lua5.1 liblua5.1-0-dev lua-filesystem libidn11-dev libssl-dev lua-zlib lua-expat lua-event lua-bitop lua-socket lua-sec luarocks luarocks

luarocks install lpc

Add a shell user for Metronome.

adduser --no-create-home --disabled-login --gecos 'Metronome' metronome

Download Metronome to the /opt directory and compile it.

cd /opt; git clone metronome
cd ./metronome; ./configure --ostype=debian --prefix=/usr
make install

Metronome has now be installed to /opt/metronome.

Share this page:

Suggested articles

19 Comment(s)

Add comment


From: Alexandros Ioannides

Great guide as always. What about a guide for Ubuntu 16.04 with nginx, PHP7-FPM, Roundcube, MariaDB?


Thank you.

From: Radu Costin

apt-get -y install certbot looks like an instruction for debian 8 jessie, not working for me in ubuntu 16

From: till

The instruction is for Ubuntu 16.10. Maybe you use the wrong version of this tutorial? The above tutorial is for Ubuntu 16.10 and not 16.04, the certbot package exists in the Ubuntu repo for 16.10 but not 16.04. If you use Ubuntu 16.04, then please use this tutorial which contains different installation instructions for certbot and other packages.

From: Bradley Hamilton

I used this guide and migrated all my domains to it and could not be more PLEASED! 

From: Ando

Hi. Firstly, this is a VERY nice tutorial. Got my system up in no time :) There are a couple questions, and I am not sure if I missed something. Wehn I log into my ISPconfig panel (and any clients for that fact) there is a certificate error. Also when people try to connect to mail, via POP3 with a m,ail program a certificate error occurs too. What can I do? How do I fix this ? I tried turning on Let's Encrypt to no effect. I tried creating certificate in SSL settings in sites, to no effect. What am I doing wrong ?


Thanks in advance. Ando

From: Tuumke

[email protected]:~# apt-get -y install certbotReading package lists... DoneBuilding dependency treeReading state information... DoneE: Unable to locate package certbot

From: till

You use the wrong Ubuntu version. That's explained already above, see comment from Radu Costin and my answer.

From: carlos campano

Hi, please give the root password please! howtoforge dosen't work

From: till

The password is howtoforge, see last chapter of the tutorial. But on Ubuntu, you login as administrator first, then use sudo to beome root.

From: Mike

Great guide, but why use ntp/ntpdate when I have already a timeserver installed?

"In recent Ubuntu releases timedatectl replaces ntpdate. By default timedatectl syncs the time once on boot and later on uses socket activation to recheck once network connections become active.

If ntpdate / ntp is installed timedatectl steps back to let you keep your old setup. That shall ensure that no two time syncing services are fighting and also to retain any kind of old behaviour/config that you had through an upgrade. But it also implies that on an upgrade from a former release ntp/ntpdate might still be installed and therefore renders the new systemd based services disabled."

Regards Mike

From: wjk940

I don't see amavis on port 10024. All the conf is set up for 10024; however, `netstat -lp` has no `localhost:10024` entry. I'm seeing this issue when cron sends email to `root`, which is expanded to [email protected]`. I get `Undelivered Mail Returned to Sender` with `<[email protected]> (expanded from <root>): connect to[]:10024: Connection refused`.

From: wjk940

`systemctl status amavis.service` will help debug this.

From: wjk940



I think the spamassassin section needs additional steps to enable rule updating.


`vim /etc/default/spamassassin` - change value of cron to 1 `CRON=1`


For some reason, spamassassin installation sets the owner:group to root:root, so the rule update fails. A fix is `sudo chown -R debian-spamd:debian-spamd /var/lib/spamassassin/3.004001`


If you want to get notified of rule updates as a result of the cron job, `vim /etc/init/cron.conf` and change the exec line to `exec cron -L 7`.


There is a bug in `/etc/spamassassin/sa-update-hooks.d/amavisd-new`, which can be fixed by passing $1 to the function (`check_status $1 || exit`).


`/etc/cron.daily/spamassassin` is designed for systems that runs the spamassassin deamon; however, ISPConfig 3 setup uses amavisd which loads the SpamAssassin filter library internally, so the reload function needs to be changed.


```reload() {

    # Reload

    if which invoke-rc.d >/dev/null 2>&1; then

        invoke-rc.d spamassassin reload > /dev/null


        /etc/init.d/spamassassin reload > /dev/null


    if [ -d /etc/spamassassin/sa-update-hooks.d ]; then

        run-parts --lsbsysinit --verbose --arg '-v' /etc/spamassassin/sa-update-hooks.d




Also, you will want to add a `-v` to the update e.g. `--exec /usr/bin/sa-update -- -v \`


From: Islander

I have followed this guide word by word, including the installation of a minimal ubuntu 16.10 server and it ended in a disaster.

I was able to set up most everything without an issue but the ISPConfig does not work at all. It is impossible to have browsers work with the generated SSL certificate but beyond that, I get an INTERNAL SERVER ERROR at ISPConfig port when configured without SSL.

Apache Log says mod_fcgid: error reading data from FastCGI server

Considering that this is a virgin setup, everything being installed as instructed on a minimal server, I can not help but conclude that the ISPConfig package configures everything else correctly but itself!

From: Jonathan

You must have missed something from the guide, I did this setup yesterday and ISPConfig works without issues.

From: till

The generated SSL cert is a so called self-signed SSL cert and it works in all browser, you just have to accept the warning that you get in the browser. When a port is configured with SSL, then you can not use it without SSL, so trying to access it with http makes not much sense. Please post your issue in the ISPConfig forum so we can help you to find out why your setup fails.

From: Latvian

If you get "not supported in kernel" upon runnig "quotaon -avug", do:

check kernel version with:

uname -r

Then do, replacing version number of the package:

apt-get install linux-image-extra-4.4.0-63-generic modprobe quota_v2 modprobe quota_v1

From: Daniel

I think 

apt-get -y install certbot

is changed to

apt-get install letsencrypt

From: Yenco

I have followed these instructions to the letter and I keep getting stuck at:

"echo "update mysql.user set plugin = 'mysql_native_password' where user='root';" | mysql -u root"

where I get:

"ERROR 1698 (28000): Access denied for user 'root'@'localhost'"

I am using sudo where needed!

Does it make a difference that I am using SSL to access?

Any help would be appreciated!

Thank you