In the directory /scratch/jeppesen/test-run there are the following files: 
-rw-r--r--   1 jeppesen user          347 Jul 16 12:58 PHADIA.INI
-rwxr-xr-x   1 jeppesen user       164567 Jul 16 12:58 a.out
-rw-r--r--   1 jeppesen user           75 Jul 16 12:58 job
The files are a.out (the executable), PHADIA.INI (some input file for the executable), and job - the job file to be submitted to the queuing system. In this case the job file is as simple as: 
###############################################################################
# First we have some directives to the queueing system. Must be in the first
# block of comment lines.
#
# We want to receive an e-mail when the job starts (b) and ends (e).
#
PBS -m be
#
# Make sure that we are in the same subdirectory as where the qsub command
# is issued.
#
cd $PBS_O_WORKDIR

#
# Just for fun: which node did we end up on ?
#
/bin/hostname

#
# Run the executable. *DO NOT PUT* a '&' at the end - it will not work.
#
time ./a.out

#
# End of script-file.
#
###############################################################################
The job can be submitted from /scratch/jeppesen/test-run as follows: 
<434 beofront../test-run> qsub job
185.beofront.mrl.ucsb.edu
Note: you get a recipt from the qsub command - the job-id. In this case it's 185. The job could now be terminated using the qdel command: qdel 185. The qstat command can be used to monitor the job: 
<437 beofront../test-run> qstat
Job id           Name             User             Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
185.beofront     job              jeppesen         00:00:30 R dque
A more usefull command for managing your jobs is the X-windows command xpbs.

When a job finishes the queuing system saves standard out and error in two files job-file-name.ejob-id and job-file-name.ojob-id respectively. In this example: 

-rw-------   1 jeppesen user            0 Jul 16 13:06 job.e185
-rw-------   1 jeppesen user          186 Jul 16 13:06 job.o185
There were no errors so job.e185 is empty - but job.o185 has the following content (output from hostname and time included): 
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
node5.beowulf
 FREQ          800
 FREQ          800
159.690u 0.010s 2:39.85 99.9%   0+0k 0+0io 134pf+0w