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Copy pathideal-coag-wrf-partmc-run.sh
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ideal-coag-wrf-partmc-run.sh
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#!/bin/bash
#SBATCH --job-name=wrf-partmc-les
#SBATCH --nodes=2
#SBATCH -n 96
#SBATCH --partition=sesempi
#SBATCH --time=36:00:00
#SBATCH --mem-per-cpu=5000
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH [email protected]
# Emission rates for aerosols, gases
EMISS_PATH=/data/keeling/a/sf20/b/wrf-partmc-spatial-het/WRFV3/test/em_les/emissions
gas_emiss_data_path=$EMISS_PATH/urbanplume_gas_emiss.csv
aero_emiss_data_path=$EMISS_PATH/urbanplume_aero_emiss.csv
# Initial Conditions for aerosols, gases
IC_PATH=/data/keeling/a/sf20/b/wrf-partmc-spatial-het/WRFV3/test/em_les/initial-conditions
aero_ic_data_path=$IC_PATH/urbanplume_aero_ics.json
gas_ic_data_path=$IC_PATH/urbanplume_gas_ics.csv
# Path to WRF simulation
SIM_PATH=/data/keeling/a/sf20/b/wrf-partmc-spatial-het/WRFV3/test/em_les
cd $SIM_PATH
ARCHIVE_PATH=/data/nriemer/a/sf20/wrf-partmc-ideal-coagulation
OUTPUT_PATH=$ARCHIVE_PATH/slurm-$SLURM_JOB_ID
mkdir $OUTPUT_PATH
mkdir $OUTPUT_PATH/aero_emit_dists
mkdir $OUTPUT_PATH/ics
mkdir $OUTPUT_PATH/out2
cp $SIM_PATH/partmc-files/aero_data.dat $OUTPUT_PATH/aero_data.dat
cp $SIM_PATH/partmc-files/gas_data.dat $OUTPUT_PATH/gas_data.dat
cp $SIM_PATH/partmc-files/gas_params.csv $OUTPUT_PATH/gas_params.csv
cp $SIM_PATH/ideal.exe $OUTPUT_PATH/ideal.exe
cp $SIM_PATH/input_sounding $OUTPUT_PATH/input_sounding
cp $SIM_PATH/LANDUSE.TBL $OUTPUT_PATH/LANDUSE.TBL
cp $SIM_PATH/namelist.input $OUTPUT_PATH/namelist.input
cp $SIM_PATH/wrf.exe $OUTPUT_PATH/wrf.exe
cd $OUTPUT_PATH
timestamp=$(date '+%Y-%m-%d %H:%M:%S')
echo "Start : $timestamp"
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
export MKL_DEBUG_CPU_TYPE=5
export MKL_CBWR=COMPATIBLE
# Initial condition and emission profile parameters
#scenario='uniform-basecase'
#scenario='fx2fy2'
#scenario='fx1fy0'
scenario='road-10x'
#scenario='point-source-10x10'
#scenario='point-source-1x1'
# Get simulation configuration (chemical mechanism, domain dimensions)
file_path="namelist.input"
# Loop through each line in the file
while IFS= read -r line; do
#echo $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"
fi
if [[ $line == *"s_we "* ]]; then
line=$(echo "$line" | cut -d ',' -f 1) # only look at domain 1
S_WE=$(echo "$line" | sed 's/[^0-9]*//g') # remove non-integer values
fi
if [[ $line == *"e_we "* ]]; then
line=$(echo "$line" | cut -d ',' -f 1) # only look at domain 1
E_WE=$(echo "$line" | sed 's/[^0-9]*//g') # remove non-integer values
fi
if [[ $line == *"s_sn "* ]]; then
line=$(echo "$line" | cut -d ',' -f 1) # only look at domain 1
S_SN=$(echo "$line" | sed 's/[^0-9]*//g') # remove non-integer values
fi
if [[ $line == *"e_sn "* ]]; then
line=$(echo "$line" | cut -d ',' -f 1) # only look at domain 1
E_SN=$(echo "$line" | sed 's/[^0-9]*//g') # remove non-integer values
fi
if [[ $line == *"s_vert "* ]]; then
line=$(echo "$line" | cut -d ',' -f 1) # only look at domain 1
S_VERT=$(echo "$line" | sed 's/[^0-9]*//g') # remove non-integer values
fi
if [[ $line == *"e_vert "* ]]; then
line=$(echo "$line" | cut -d ',' -f 1) # only look at domain 1
E_VERT=$(echo "$line" | sed 's/[^0-9]*//g') # remove non-integer values
fi
done < "$file_path"
S_WE=$(expr $S_WE)
E_WE=$(expr $E_WE)
S_SN=$(expr $S_SN)
E_SN=$(expr $E_SN)
S_VERT=$(expr $S_VERT)
E_VERT=$(expr $E_VERT)
extent_we=$(expr $E_WE - $S_WE)
extent_sn=$(expr $E_SN - $S_SN)
extent_vert=$(expr $E_VERT - $S_VERT)
echo "Number of grid cells in west-east: $extent_we"
echo "Number of grid cells in south-north: $extent_sn"
echo "Number of grid cells in vertical: $extent_vert"
# set emissions (gases and aerosols)
python $SIM_PATH/create_aero_emit_dists.py $OUTPUT_PATH $scenario $extent_we $extent_sn $extent_vert $gas_emiss_data_path $aero_emiss_data_path
# set intial conditions (IC specified by scenario)
python $SIM_PATH/create_aero_ics.py $OUTPUT_PATH $scenario $extent_we $extent_sn $extent_vert $aero_ic_data_path
echo
time mpirun -np 8 ./ideal.exe
# set gas initial conditions
#python $SIM_PATH/write_gas_ic_json.py $OUTPUT_PATH $CHEM_OPT $scenario $gas_ic_data_path
#python $SIM_PATH/edit_wrfinput_initcond.py $OUTPUT_PATH $CHEM_OPT $extent_we $extent_sn $extent_vert $scenario
echo
time mpirun -np $SLURM_NPROCS ./wrf.exe
echo
timestamp=$(date '+%Y-%m-%d %H:%M:%S')
echo "End : $timestamp"
cp $SIM_PATH/slurm-$SLURM_JOB_ID.out $OUTPUT_PATH/slurm-$SLURM_JOB_ID.out
rm $SIM_PATH/slurm-$SLURM_JOB_ID.out