If you have an requirement to execute jobs in sequence after the 1st job has completed, only then the 2nd job can launch, you can use the -W command
For example, if you have a running job with a job ID 12345, and you run the next job to run only after job 12345 run.
$ qsub -q clusterqueue -l nodes=1:ppn=8 -W depend=afterany:12345 parallel.sh -v file=mybinaryfile
You will notice that the job will hold until the 1st job executed.
..... ..... 24328 kittycool Hold 2 10:00:00:00 Sat Mar 2 02:20:12