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I am using the Sun Grid Engine (SGE) to submit embarassingly parallel task arrays. Suppose I have the file job_script:

#!/bin/bash
#$ -cwd -V
#$ -l h_rt=0:01:00
#$ -o logs
#$ -e logs
#$ -N name_of_code
#$ -t 1-1000

count=1
echo "hello $count" > output.${count}
./cpp_code $count

which can be submitted using qsub job_script. What I am stuck on: writing a for loop whereby the variable count is passed into job_script as an argument. For example:

#!/bin/bash
#$ -cwd -V
#$ -l h_rt=0:01:00
#$ -o logs
#$ -e logs
#$ -N name_of_code
#$ -t 1-1000

count=$1
echo "hello $count" > output.${count}
./cpp_code $count

I (incorrectly) thought that count corresponds to the first argument passed from the command line into job_script, but

for count in {1..10..1}
do
  qsub job_script $count
done

does not work. What am I doing wrong and how do I fix it? Thank you for your time.

Kian
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0 Answers0