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.

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24328 kittycool Hold 2 10:00:00:00 Sat Mar 2 02:20:12