wrf_run.sh

#!/bin/bash
#SBATCH --job-name=wrf44-les
#SBATCH --nodes=2
#SBATCH -n 64
#SBATCH --partition=sesempi
#SBATCH --time=9:00:00
#SBATCH --mem-per-cpu=2000
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --mail-user=sf20@illinois.edu

now=$(date +"%T")
echo "Start time : $now"
echo ${run}
source ~/.bashrc
#free the system to have unlimited memory requests
ulimit -s -S unlimited
#make permissions group readable on output files
umask 022
#load libraries that you compiled with
module purge
module load gnu/hdf5-1.10.6-gnu-9.3.0
module load gnu/netcdf4-4.7.4-gnu-9.3.0
module load gnu/openmpi-3.1.6-gnu-9.3.0
#path to WRF simulation
cd /data/keeling/a/sf20/b/WRF4_4/WRF/test/em_les

# Make sure there is a copy of makekeelingloads.csh in your em_les directory
source makekeelingloads.csh
export MKL_DEBUG_CPU_TYPE=5
export MKL_CBWR=COMPATIBLE

time mpirun -np 16 ./ideal.exe 

# Get value of chemical mechanism selection
line=$(sed -n '36p' namelist.output)
# Check if "CHEM_OPT" is present in the line
if [[ $line == *"CHEM_OPT"* ]]; then
    line=$(echo "$line" | cut -d ',' -f 1) # only look at chem_opt for domain 1
    CHEM_OPT=$(echo "$line" | sed 's/[^0-9]*//g') # remove non-integer values
    echo "Using chemical mechanism: $CHEM_OPT"
else
    # Raise an error message
    echo "Error: 'CHEM_OPT' not found in line 36 of namelist.output"
    exit 1  # Exit the script with an error status
fi

# modify initial conditions and chemical emissions profiles
python json_io.py $CHEM_OPT
python edit_wrfinput_initcond.py $CHEM_OPT
python edit_wrfchemi_emissions.py $CHEM_OPT

time mpirun -np 64 ./wrf.exe
python reduce_wrfout_size.py
data_path=$(python create_move_output_files.py)
echo "Data files are located at: $data_path"

now=$(date +"%T") echo "End time : $now"