Databases are backed up daily out of the box (are put into /home/backup on my system)... backup of the whole server is way out of the scope of iRedMail project.

You have a lot of options:
1) use some backup solution like bacula,
2) create a simple batch and run it daily from cron (tar, gzip, rsync, ssh are your friends)
3) if you run iRedMail in virtual environment, you can backup the whole virtual machine from your host easily.

etc.

I am just asking for the back up of the whole iredmail setup noting else on the server and how do I do the cron job to do this back up for /var/vmail?

thanks camel1cz for that information.

It's done automatically / look in /var/vmail/backup/

Does it work if you execute this script manually? For example:

# bash /var/vmail/backup/backup_mysql.sh

Check whether you have cron job to execute this script daily, it's added automatically during iRedMail installation:

# crontab -l -u root

About backup:

*) iRedMail adds cron job to backup mail accounts daily. Backup script and backed up SQL/LDIF files are placed under /var/vmail/backup by default.

*) iRedMail doesn't backup mailboxes. Mailboxes takes large disk space, it doesn't make sense to backup them on the same server which causes double disk I/O and (slightly) slow down the server. And of course we cannot know you have a mounted spare disk for backup. So we leave it to system admin.

*) You don't need to backup config files if you didn't modify it. You know you can get a same, working config file with a new iRedMail installation (with correct SQL/LDAP usernames/passwords). If you did some modification, of course you should write it down somewhere to help you reproduce the same config on a new iRedMail server. This is one of iRedMail benefits: you can always get a working server with (almost) same settings as your old one.