With "several hundreds if not thousands jobs running at any give time"  you 
must be using an automated job scheduler of some sort.  Does your scheduler 
maintain 'average run time' in its database?  Does the scheduler itself, allow 
notification if that average time is exceeded?

If not - you can use MXG,   or other means, to calculate statistics about run 
time.  If you have to get notification in real time,  you're going to need to 
code some stuff in exits.  

One approach (I haven't coded this so bear it in mind):  

Store the average time somewhere (MXG, wherever).  For each job put that time 
into a comment card in the JCL.  Use a fixed, easy to parse format.

In exit IEFUJV,  parse that comment card to make the average run time into a 
binary, add store it into a storage area you GETMAIN for each job (make sure to 
store the pointer into the user area for the job provided by the SMF user exit 
interface).  Mark a flag in that area as 'no msg issued'.

In exit IEFUJI,  get the current time, add the average run time to it, and 
store the result in your job 'control block'

In IEFU83  (shouldn't need IEFU84/85 for regular batch jobs, I wouldn't think?) 
 get the current time, and compare it to what you stored.   If  it is larger 
than what you stored,  issue a message via WTO and mark the flag as 'message 
issued'.  This is to prevent issuing the message more than once for the job.  
IEFU83 gets called a lot since it is called for every SMF record created for a 
job so make sure your routine is coded efficiently.

This is off the top of my head.  I used IEFU83 to provide the ability to notify 
as soon as you exceeded what you expected;  if you don't need to be that 
granular use IEFACTRT for step end, or IEFUSI at step initiation, and check 
between steps.  The 'hard part' is getting the information into the system with 
the job.

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