In the current version, 3.0, when using the Call Graph collector to collect data on an application that is started by a script, you need to make sure the application and the directory it resides in are writable by the user executing the VTune analyzer. This means, for example,you cannot call graph an application that is installed on a shared, non-writable NFS drive.
Second,you musthave the environment configured as it will be when the application runs in the script, before you start the analyzer. Yes, this is a known limitation. :-( One way to deal with this is to replace the application invocation in the script with the invocation of the analyzer that would then launch the application. This change is required so that any changes that may effect which libraries are loaded by the application can be taken into account by the analyzer when it instruments the application and referenced libraries.
Another limitation of using a script to launch your application is that the analyzer will only collect call graph data for the first invocation of the application. So, if your script launches the application several times, you will only see data for the first time.
We are hoping to address many of these in a future release.