exec used but not allowed while running my script

Question

I am running a script to import data from csv file to mysql database. But after few seconds i am getting this errors in console

SHTML Wrapper - 500 Server Error [an error occurred while processing this directive]

Actually the thing is that not only the script but also almost every page that load with a query result (which takes more than 40 sec or so) are having the problem. It did not happened in case of shared account. After converting the account dedicated in bluehost, i am facing the problem.

I also checked error logs from my cpanel that says - exec used but not allowed in .../500.shtml, referer: http://..../controller/function_name

Is it a apache conf problem or permission problem?