Initial setup of WRF-runner

wrf-runner/README.md

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+# WRF Runner
+
+* Run a complete WPS/WRF experiment in one go
+* Make a dedicated directory for each experiment
+* The original WRF source code is untouched
+* Namelists under version control so you can always go back
+
+## How to use
+
+It assumes you have a compiled WRF and WPS with the following folder structure
+
+  * $HOME/wrf-model/WPS  # compiled clone of https://github.com/wrf-model/WRF
+  * $HOME/wrf-model/WRF  # compiled clone of https://github.com/wrf-model/WPS
+  * $HOME/Urban-M4/misc/wrf-runner  # clone of https://github.com/Urban-M4/misc
+  * $HOME/Urban-M4/experiments  # destination for input/output of each experiment
+
+Make sure the paths are set up correctly on your system and match with the paths
+in `wrf_runner.sh`. Modify (and commit) the namelists as seen fit, then call the
+runner:
+
+```bash
+# Run interactive job
+bash wrf_runner.sh
+
+# Or submit as batch job to slurm queue
+sbatch wrf_runner.sh
+```
+
+This will create a new folder in `$HOME/Urban-M4/experiments/<timestamp>` where
+all output and intermediate files are stored, and run all steps for WPS and WRF.
+
+## Notes
+
+[f90nml](https://f90nml.readthedocs.io/en/latest/) is used to format and modify
+namelists from the command line. Beware that:
+
+  * paths must be in "'double quotes'" (see https://github.com/marshallward/f90nml/issues/126)
+  * cannot update in place
+
+
+## To do
+
+* Use MODIS_LCZ landuse with wudapt-to-wrf (checkout [this branch](https://github.com/matthiasdemuzere/w2w/pull/127#issuecomment-2066019831))
+* Use the "standard" heatwave case for amsterdam
+* Use IFS analysis for initial/boundary conditions
+* Use custom WUR landuse from summer in the city (checkout different branch of WRF?)
+* Use custom river temperatures from rijkswaterstaat(?)
+* Enable additional custom landuse for building albedo/emissivity
+* Add some default plots of input/output for quick inspection of results

wrf-runner/namelist.input

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+&time_control
+    run_days = 0
+    run_hours = 12
+    run_minutes = 0
+    run_seconds = 0
+    start_year = 2024, 2024, 2024, 2024
+    start_month = 4, 4, 4, 4
+    start_day = 19, 19, 19, 19
+    start_hour = 0, 0, 0, 0
+    start_minute = 0, 0, 0, 0
+    start_second = 0, 0, 0, 0
+    end_year = 2024, 2024, 2024, 2024
+    end_month = 4, 4, 4, 4
+    end_day = 19, 19, 19, 19
+    end_hour = 12, 12, 12, 12
+    end_minute = 0, 0, 0, 0
+    end_second = 0, 0, 0, 0
+    interval_seconds = 10800
+    input_from_file = .true., .true., .true., .true.
+    history_interval = 60, 60, 60, 60
+    frames_per_outfile = 1000, 1000, 1000, 1000
+    restart = .false.
+    restart_interval = 5000
+    io_form_history = 2
+    io_form_restart = 2
+    io_form_input = 2
+    io_form_boundary = 2
+    debug_level = 1
+/
+&domains
+    time_step = 60
+    time_step_fract_num = 0
+    time_step_fract_den = 1
+    max_dom = 1
+    e_we = 120, 121, 121, 126
+    e_sn = 120, 121, 121, 126
+    num_metgrid_levels = 34
+    num_metgrid_soil_levels = 4
+    dx = 12500.0, 2500.0, 500.0, 100.0
+    dy = 12500.0, 2500.0, 500.0, 100.0
+    grid_id = 1, 2, 3, 4
+    parent_id = 1, 1, 2, 3
+    i_parent_start = 1,  48, 50, 55
+    j_parent_start = 1,  48, 51, 55
+    parent_grid_ratio = 1, 5, 5, 5
+    parent_time_step_ratio = 1, 5, 5, 5
+    feedback = 1
+    smooth_option = 0
+    max_ts_locs = 57
+    ts_buf_size     =         6000
+    p_top_requested = 1000
+    e_vert = 74, 74, 74, 74
+    eta_levels = 1.0,                       0.99421191128831299,  0.98958514826812849,  0.98367625218041377,   0.97655838524794414,
+                      0.96838285571891347,  0.95870112135559438,  0.94744530276601047,  0.93462088213306749,   0.9202339396959881,
+                      0.90428158484924004,  0.88677817094443068,  0.86778769000747558,  0.84739755793670579,   0.82566728133565903,
+                      0.80266872663842503,  0.77850745078494887,  0.75332140543234494,  0.72721046598554695,   0.70028138549713437,
+                      0.67266294542736116,  0.64451821579865431,  0.61596501370545731,  0.58712285073511083,   0.55812618988288065,
+                      0.52913800149514079,  0.50043977074507839,  0.47231557438325439,  0.44503493645651632,   0.41884565163219539,
+                      0.39398016446548717,  0.3704105656615998,   0.34809080488412658,  0.32696187390979314,   0.30696745576875156,
+                      0.28805332668826317,  0.27016755544480436,  0.25326020433590829,  0.23728352853227014,   0.22219187640169447,
+                      0.20794139048093696,  0.19449020682780963,  0.18179805631696985,  0.16982666334413157,   0.15853924744580114,
+                      0.14790092200348867,  0.13787789683528531,  0.12843837528033888,  0.1195517567904311,    0.11118883628208323,
+                      0.10330246698230749,  0.09583304261151257,  0.088729828058808871, 0.081949862945427374,  0.075456366807874403,
+                      0.069218440069773235, 0.063209568901071531, 0.057410715175679049, 0.051829952653874897,  0.046480538250685273,
+                      0.041374134064291058, 0.036519112883129826, 0.031920458509843014, 0.027582357338649388,  0.023507899327186641,
+                      0.019698978320458513, 0.016156491402940443, 0.012879740842262649, 0.0098666334413157249, 0.0071139795664091707,
+                      0.004616596062795914, 0.002368203339147769, 0.00036052828307999075,  0.0
+/
+&physics
+    use_wudapt_lcz = 1
+    mp_physics = 6, 6, 6, 6, 6
+    ra_lw_physics = 4, 4, 4, 4, 4
+    ra_sw_physics = 4, 4, 4, 4, 4
+    radt = 0, 0, 0, 30, 30
+    sf_sfclay_physics = 1, 1, 1, 1, 1
+    sf_surface_physics = 2, 2, 2, 2, 2
+    bl_pbl_physics = 1, 1, 1, 0, 0
+    bldt = 0, 0, 0, 0, 0
+    cu_physics = 3, 3, 0, 0, 0
+    cudt = 5, 5, 5, 5, 5
+    isfflx = 1
+    ifsnow = 1
+    icloud = 1
+    surface_input_source = 1
+    num_soil_layers = 4
+    num_land_cat = 21
+    sf_urban_physics = 1, 1, 1, 1
+
+/
+&fdda
+/
+&dynamics
+    w_damping = 0
+    diff_opt = 1, 1, 1, 2, 2
+    km_opt = 4, 4, 4, 3, 3
+    diff_6th_opt = 0, 0, 0, 0, 0
+    diff_6th_factor = 0.12, 0.12, 0.12, 0.12, 0.12
+    base_temp = 290.0
+    damp_opt = 0
+    zdamp = 5000.0, 5000.0, 5000.0, 5000.0, 5000.0
+    dampcoef = 0.2, 0.2, 0.2, 0.2, 0.2
+    khdif = 0, 0, 0, 0, 0
+    kvdif = 0, 0, 0, 0, 0
+    non_hydrostatic = .true., .true., .true., .true., .true.
+    moist_adv_opt = 1, 1, 1, 1, 1
+    scalar_adv_opt = 1, 1, 1, 1, 1
+/
+&bdy_control
+    spec_bdy_width = 5
+    spec_zone = 1
+    relax_zone = 4
+    specified = .true., .false., .false., .false., .false.
+    nested = .false., .true., .true., .true., .true.
+/
+&grib2
+/
+&namelist_quilt
+    nio_tasks_per_group = 0
+    nio_groups = 1
+/

wrf-runner/namelist.wps

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+&share
+ wrf_core = 'ARW',
+ max_dom = 1,
+ start_date = '2024-04-19_00:00:00','2024-04-19_00:00:00','2024-04-19_00:00:00','2024-04-19_00:00:00',
+ end_date   = '2024-04-19_12:00:00','2024-04-19_12:00:00','2024-04-19_12:00:00','2024-04-19_12:00:00',
+ interval_seconds = 10800
+ io_form_geogrid = 2,
+/
+
+&geogrid
+ parent_id         =   1,   1,  2, 3
+ parent_grid_ratio =   1,   5,  5, 5
+ i_parent_start    =   1,  48, 50, 55
+ j_parent_start    =   1,  48, 51, 55
+ e_we              =   120, 121, 121, 126
+ e_sn              =   120, 121, 121, 126
+ geog_data_res     =   '30s','30s','30s','30s'
+ dx = 12500,
+ dy = 12500,
+ map_proj = 'lambert',
+ ref_lat   =  51.964716,
+ ref_lon   =   5.663308,
+ truelat1  =  30.0,
+ truelat2  =  60.0,
+ stand_lon = 4.55,
+ geog_data_path = '/projects/0/prjs0914/wrf-data/default/static/WPS_GEOG'
+/
+
+&ungrib
+ out_format = 'WPS',
+ prefix = 'FILE',
+/
+
+&metgrid
+ fg_name = 'FILE'
+ io_form_metgrid = 2,
+/
+
+
+

wrf-runner/wrf_runner.sh

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+#!/bin/bash
+#SBATCH --job-name=wrf_experiment     # Job name
+#SBATCH --partition=thin              # Partition or queue name
+#SBATCH --nodes=1                     # Number of nodes
+#SBATCH --ntasks-per-node=4           # Number of tasks per node
+#SBATCH --cpus-per-task=1             # Number of CPU cores per task
+#SBATCH --time=1:00:00                # Maximum runtime (D-HH:MM:SS)
+
+# Security; fail on first error; explicit vars only
+set -euxo pipefail
+
+# Load dependencies
+module load 2023
+module load netCDF-Fortran/4.6.1-gompi-2023a  # also loads gcc and gompi
+module load Python/3.11.3-GCCcore-12.3.0
+
+# For modifying namelists programmatically
+pip install --user f90nml
+
+# Set some paths
+export NETCDF=/sw/arch/RHEL8/EB_production/2023/software/netCDF-Fortran/4.6.1-gompi-2023a
+export WPS_HOME=$HOME/wrf-model/WPS
+export WRF_HOME=$HOME/wrf-model/WRF
+export WRF_RUNNER=$HOME/Urban-M4/misc/wrf-runner
+export OUTPUT_DIR=$HOME/Urban-M4/experiments
+export DATA_HOME=/projects/0/prjs0914/wrf-data/default
+
+# Make new run directory
+export RUNDIR=$OUTPUT_DIR/$(date +"%Y-%m-%d_%H-%M-%S")
+mkdir -p $RUNDIR
+cd $RUNDIR
+echo $PWD
+f90nml $WRF_RUNNER/namelist.wps namelist.wps
+
+# Run WPS
+f90nml -g geogrid -v opt_geogrid_tbl_path="'$WPS_HOME/geogrid/'" namelist.wps patched_nml && mv patched_nml namelist.wps
+f90nml -g metgrid -v opt_metgrid_tbl_path="'$WPS_HOME/metgrid'" namelist.wps patched_nml && mv patched_nml namelist.wps
+ln -s $WPS_HOME/ungrib/Variable_Tables/Vtable.GFS Vtable
+$WPS_HOME/link_grib.csh "${DATA_HOME}/real-time/gfs-data/*"
+$WPS_HOME/geogrid.exe
+$WPS_HOME/ungrib.exe
+$WPS_HOME/metgrid.exe
+
+# Run WRF
+f90nml $WRF_RUNNER/namelist.input namelist.input
+$WRF_HOME/run/real.exe
+$WRF_HOME/run/wrf.exe
+
+# Report status
+status=$? && [ $status -eq 0 ] && echo "Run successful"