How to use variables on qsub? - bash

Question

I'm new to qsub and I'm trying to figure out how to use the task queue optimally. I have this script that works well:
#!bin/bash
##PBS -V # Export all environment variables from the qsub command environment to the batch job.
#PBS -N run
#PBS -q normal.q
#PBS -e archivo.err
#PBS -o archivo.out
#PBS -pe mpirun 8
#PBS -d ~/ # Working directory (PBS_O_WORKDIR)
#PBS -l nodes=1:ppn=8
~/brinicle/step-2/onephase_3/./main.x --mesh ~/brinicle/step-2/onephase_3/results/mesh.msh -Rmin 0 -Rmax 10 -Zmin 0 -Zmax 10 -o 2 -r 2 -T_f -10 -a_l 7.8 -a_s 70.8 -dt 0.01 -t_f 1 -v_s 10 -ode 12 -reltol 0.00001 -abstol 0.00001
The problem, as you can see, is that the command line is huge and hard to edit from the command shell. I would want to separate it into variables such as
#MESH="--mesh ~/brinicle/step-2/onephase_3/results/mesh.msh"
#EXE="~/brinicle/step-2/onephase_3/./main.x"
.
.
.
$EXE $MESH $PARAMETERS
And for the other parameters too.
But when I do this the program doesn't run and says that there's an illegal variable or that the variable is undefined. Also, is very important to me to change easily the parameters -o, -r, -ode and send multiple jobs at once. For example 5 equal jobs with -o 1 then 5 with -0 2 and so on. I want to be also able to modify in this way -r and -ode. The problem is that without using the variables I really don't know how to do that.
Please, if someone can tell me how to automate the script in this way would be a huge help.

Answer 1

Use bash arrays.
exe=(~/brinicle/step-2/onephase_3/./main.x)
mesh=(--mesh ~/brinicle/step-2/onephase_3/results/mesh.msh)
parms=(
-Rmin 0
-Rmax 10
-Zmin 0
-Zmax 10
. etc.
)
"${exe[#]}" "${mesh[#]}" "${parms[#]}"
Research bash arrays and how to use then and quoting in shell. Prefer to use lower case variables. Research order of expansions in shell.

Answer 2

One alternative if you have a lot of static parameters and a lot of dynamic ones is to refactor into a function where you hard-code what doesn't change, and interpolate the parts which do change.
qrunmesh () {
qsub <<:
#!bin/bash
##PBS -V # Export all environment variables from the qsub command environment to the batch job.
#PBS -N run
#PBS -q normal.q
#PBS -e archivo.err
#PBS -o archivo.out
#PBS -pe mpirun 8
#PBS -d ~/ # Working directory (PBS_O_WORKDIR)
#PBS -l nodes=1:ppn=8
"$1" --mesh "$2" -Rmin 0 -Rmax 10 -Zmin 0 -Zmax 10 \
-o "$3" -r "$4" -T_f -10 -a_l 7.8 -a_s 70.8 \
-dt 0.01 -t_f 1 -v_s 10 -ode "$5" \
-reltol 0.00001 -abstol 0.00001
:
}
for o in 1 2 3; do
for r in 5 10 15; do
for x in onephase_3 onephase_2 twophase_3; do
for ode in 12 13 15; do
for mesh in onephase_3 otherphase_2; do
qrunmesh "$x" "$mesh" "$o" "$r" "$ode"
done
done
done
done
done
(I'm not very familiar with qsub; I assume it accepts the script on standard input if you don't pass in a script name. If not, maybe you have to store the here document in a temporary file, submit it, and remove the temporary file.)