It seems your mySql server is shut down.
Or possibly port has been closed.

The serveur is actually UP and this port is open. I'm already using my mysql server with other databases and I don't have this "server gone" error. My server is running properly at the moment.

I've seen on the web for this 2006 mysql error a possible solution: grow "max_allowed_packet" valor.
I did it but it still doesn't work. 🙁

Here are few tries to test in my.ini (Windows) or my.cnf (Linux) :

max_allowed_packet=256M 
innodb_buffer_pool_size=256M
max_connections=500
wait_timeout = 600

and restart MySQL

Done.
Still doesn't work.

I have checked my mysql logs and I see when My Projectorria server is connecting on the DB.

 336 Connect   projectorriauser@******* as anonymous on projectorria
                  336 Query     desc audit
                  336 Query     select * from audit where audit.sessionId='s6j9f7ilqhatlb1dd3kvjah9e5'
                  336 Query     select * from audit where id=2
140311 14:26:36   336 Query     select * from audit where id=2
                  336 Query     update audit set lastAccess='2014-03-11 14:26:35' , duration='02:49:18'  where id=2
                  336 Query     desc mailable
                  336 Query     select * from mailable where mailable.name='Audit'
                  336 Query     select id as id, name as name from indicatorable where (idle=0 ) order by indicatorable.name
                  336 Query     desc parameter
                  336 Query     select * from parameter where parameter.idUser is null and parameter.idProject is null and parameter.parameterCode='dbVersion'
                  336 Query     select * from profile where id=1
                  336 Query     select * from parameter where  (idUser is null and idProject is null)


140311 14:27:43     2 Query     COMMIT
                  403 Connect   projectorriauser@******* as anonymous on projectorria
                  403 Query     desc audit
                  403 Query     select * from audit where audit.sessionId='s6j9f7ilqhatlb1dd3kvjah9e5'
                  403 Query     select * from audit where id=2
                  403 Query     select * from audit where id=2
                  403 Query     select id as id, name as name from indicatorable where (idle=0 ) order by indicatorable.name
                  403 Quit
                  404 Connect   projectorriauser@******* as anonymous on projectorria
                  404 Query     desc audit
                  404 Query     select * from audit where audit.sessionId='s6j9f7ilqhatlb1dd3kvjah9e5'
                  404 Query     select * from audit where id=2
                  404 Query     select * from audit where id=2
                  404 Query     select id as id, name as name from indicatorable where (idle=0 ) order by indicatorable.name
                  404 Quit
                  405 Connect   projectorriauser@******* as anonymous on projectorria
                  405 Query     desc audit
                  405 Query     select * from audit where audit.sessionId='s6j9f7ilqhatlb1dd3kvjah9e5'
                  405 Query     select * from audit where id=2
                  405 Query     select * from audit where id=2
                  405 Query     select id as id, name as name from indicatorable where (idle=0 ) order by indicatorable.name
                  405 Query     desc alert
                  405 Query     select * from alert where alert.idUser=1 and alert.readFlag=0 and alert.idle=0 order by id asc
                  405 Quit

******* = my server's hostname
projectorriauser has got ALL mysql rights. And i can connect with it from multiple machines + localhost

These logs show that connection to MySql works. These are single request to track connection.
So your connection parameters are good. No issue ion this side.

There must be an issue in preserving connection : projeqtor uses same Connection during the whole script execution, whatever the number of requests.
So maybe you're facing some connection droping.

You can try to extend wait_timeout, as decribed in http://linux.overshoot.tv/wiki/mysql_server_has_gone_away

wait_timeout=432000

default value is 28800 and should be enough, but maybe you configured it too small.

You can also try and force reconnection.
First method is to change in my.cnf :

 mysqli.reconnect = On

Second method is to update code in /model/persistence/Sql.php, line 221 :

  private static function getConnection() {
    if (self::$connexion != NULL) {
    	if (!mysql_ping($this->conn)) $this->reconnect();
      return self::$connexion;
    }

I've done the changes and restarted apache service + mysql service. Still doesn't work. I continue to investigate.

I discovered a behavior change of the website: on the login interface, when I enter admin/admin credentials, I see the loading wheel and it loads infinitely.
It doesn't show the empty interface of projectorria website anymore.

Which log files should I check to find more clues/news ?

Hi,

If you left defaut configuration, log file is in /files/log directory. One file per day.