This limit is controlled by the variable open_files_limit. You can read this in phpMyAdmin (or the MySQL command line utility) with the statement:
To set this variable to a higher number, edit the /etc/my.cnf file and add the lines:
[mysqld] open_files_limit = 5000Then be sure to restart mysql with: sudo /etc/init.d/mysql restart
Remember to use the server administrative account and sudo when you edit the file. The choice of editor is up to you.
Now, showing the variable should show the number you choose.
Note that 5000 shown above is an example. A good rule of thumb is to take the current number of files and add 1000 to it. If this doesn't help, add some more. This number affects tha amount of memory that MySQL uses, so setting it to a very high number is not a good idea.
If you are not comfortable at the command line, ProHosterz Support will be happy to adjust this variable for you.