It seems set_time_limit function call has no effect when php is running with mod_fcgid (the default in webmin). Can someone tell me how to make it work?
Make sure you're editing
/etc/php5/cgi/php.ini and that after editing it, you restart php-cgi. The command for that should be
sudo /etc/init.d/php-fastcgi restart
To increase timelimit, you'll need to find
max_execution_time in your php.ini. Default value is 30 seconds. This is required if PHP is running in safe mode.
To disable safe mode, search for
safe_mode in php.ini and set it to off.
See PHP Runtime Configuration page for more info on that.