How to properly pass on an environment variable to Sun Grid Engine?
What I've been always doing is the following:
##send.shexport a=10qsub ./run.shand the script run.sh:
##run.sh#$ -Vecho $awhen I call send.sh, the .o has an output of 10.
Assuming that your variable is just an incrementing counter: You can use Array Jobs to achieve this. This will set an $SGE_TASK_ID environment variable to the count which you can then copy to $i or use directly.
If the variable is anything else, then I think you'll have to generate multiple job scripts and submit each; that's the "solution" I use when I have loads of jobs with differing parameters.
I'm not certain you can pass variables by their name through qsub. I've had success with passing values (you should probably write a front-end script for this instead of doing it interactively):
$ export ii=19$ qsub -N "test_env" -cwd -v i=$ii run.sh