Fix indexing of pbs key in config

[SeanBryan51]

Fixes #188

[SeanBryan51]

Integration tests

Specify PBS parameters for ncpus, mem, walltime and storage

#!/bin/bash
bench_example_dir='bench_example_test_pbs_params'
rm -rf $bench_example_dir
git clone git@github.com:CABLE-LSM/bench_example.git $bench_example_dir
cd $bench_example_dir
git reset --hard 6287539e96fc8ef36dc578201fbf9847314147fb
cat > config.yaml << EOL
project: tm70

experiment: AU-Tum

realisations:
  - path: "trunk"

fluxsite:
  pbs:
    ncpus: 20
    mem: 20GB
    walltime: 01:00:00
    storage: [gdata/ct11]

modules: [
  intel-compiler/2021.1.1,
  netcdf/4.7.4,
  openmpi/4.1.0
]
EOL
benchcab fluxsite-submit-job -v
cat benchmark_cable_qsub.sh

The generated PBS job is as follows

#!/bin/bash
#PBS -l wd
#PBS -l ncpus=20
#PBS -l mem=20GB
#PBS -l walltime=01:00:00
#PBS -q normal
#PBS -P tm70
#PBS -j oe
#PBS -m e
#PBS -l storage=gdata/ks32+gdata/hh5+gdata/ct11

set -ex

module purge
module load intel-compiler/2021.1.1
module load netcdf/4.7.4
module load openmpi/4.1.0

/home/189/sb8430/.local/bin/benchcab fluxsite-run-tasks --config=config.yaml -v

/home/189/sb8430/.local/bin/benchcab fluxsite-bitwise-cmp --config=config.yaml -v

[codecov[bot]]

Codecov Report

Merging #189 (f5c5d5a) into main (068e0bb) will not change coverage. Report is 1 commits behind head on main. The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #189   +/-   ##
=======================================
  Coverage   88.37%   88.37%           
=======================================
  Files          25       25           
  Lines        1591     1591           
=======================================
  Hits         1406     1406           
  Misses        185      185           

Files	Coverage Δ
benchcab/benchcab.py	32.96% <ø> (ø)