A quick notes on PBS job arrays (as implemented on our cluster), b/c i could not find the documentation easily:

qsub has an option for creating job arrays (-J). Given a range, for example 1-2, this results in 2 jobs being created as part of a job array. Each job will be called with $PBS_ARRAY_INDEX being set to the corresponding number. For example let’s take this highly sophisticated analysis script batch script

#! /bin/bash
echo "Greetings from job $PBS_ARRAY_INDEX in $PBS_JOBID run on $(hostname)"

Calling qsub with this qsub call

qsub -m n -J 1-2 -l nodes=1:c2 batch.sh

then results in this output

Greetings from job 1 in 5915539[1].biobos run on p298
Greetings from job 2 in 5915539[2].biobos run on p303

So $PBS_ARRAY_INDEX can be used to feed in different input files, for example.