Send array to pbs script

Question

I have a bash script that calls qsub with several variables:

group=group_1
normals=$(IFS=,; echo *.txt)

qsub -v VAR1=$group,VAR2=${normals[@]} [...] run_script.pbs

---

run_script.pbs

#PBS -l nodes=1:ppn=16  
#PBS -l walltime=2:00:00  
#PBS -l mem=10GB

group=$VAR1
normals=$VAR2

echo ${normals[@]}

In this case, the array normals contains multiple file names, but when I try to access these in the .pbs script only the first one is printed.

What is the correct way to pass and access an array in a .pbs script?

Answer 1

You are not storing the file list in an array at all. You are just doing command-substitution syntax $(..) and storing the output in a variable's context and trying to access it as an array.

The right way to get the list of files (don't need $(..)) and store it in an array would be,

shopt -s nullglob
fileList=(*.txt)

oldIFS="$IFS"
IFS=,
printf -v var_list "%s" "${fileList[*]}"
IFS="$oldIFS"
shopt -u nullglob

The nullglob option is needed to handle the case when the *.txt didn't return any files on the current folder. Not including will spit some errors on the console. We unset it with -u when we no longer need the option set.

With the -v option that printf supports, you can store the array output with comma separated format directly into the variable var_list

Now you can pass the $var_list containing the list of files in comma separated format to the command you want.

qsub -v VAR1=$group,VAR2="${var_list}"