timeout in CI

[eluser]ben.IT[/eluser]
Hi,
My CI application is used to manage data files on a data server.

The app launches shell scripts which can run for several hours, I wonder how can I prevent timeout in CI ?
(I need to wait the end of the script execution to perform database operations)

I saw previous topics where guys talked out the php function set_time_limit() :

Code:

set_time_limit(0) ;

But I my case, I am still having this time limit problem ?

How can I fix it ?
thanks,
ben