First of all, get the Simple Job Manager developed by Will Roethel for BaBar. You can download it from here:

sjm was designed to run many instances of an executable with different inputfiles, i.e. it expects your jobs to look like <executable> <input1>
<executable> <input2>
<executable> <input3>

if you want to set up your jobs to deviate from this format, you may need to perform non-trivial modifications to the following example.

SJM operates in two modes:
a) Using an executable to split your input files into pieces
b) Manually splitting your input

either way, sjm expects the input to be of the format <Name>-i.tcl, where <Name> is the name of the sjm project, and i is the number of the input file, starting with 1.