WRF

WRF (Weather Research and Forecasting Model) is a widely used mesoscale numerical weather prediction system developed by NCAR and NOAA. It supports both idealized simulations and real-data forecasts, and is used for research and operational weather prediction.

Keywords: weather, climate, numerical weather prediction, atmospheric science, mesoscale

Available modules

Midway2Midway3

-------------------- /software/modulefiles2 --------------------
wrf/4.1.5(default)  wrf/4.7.1

-------------------- /software/modulefiles ---------------------
wrf/4.1.5  wrf/4.7.1(default)

To see what a module sets up:

module show wrf/4.7.1

Executables

Loading a WRF module adds the following executables to your PATH:

Executable	Description
`wrf.exe`	Main WRF model (MPI)
`real.exe`	Real-data initialization — reads WPS `met_em` files (MPI)
`ndown.exe`	One-way nesting / downscaling (MPI)
`tc.exe`	Tropical cyclone bogussing (MPI)
`geogrid.exe`	WPS — geographical data processing (MPI)
`ungrib.exe`	WPS — GRIB file decoding (serial)
`metgrid.exe`	WPS — meteorological field interpolation (MPI)

ideal.exe — per-case compilation required

ideal.exe is not included in the pre-built conda WRF binaries. To compile it for a specific idealized case:

module load wrf/4.7.1
cd $WRF_DIR
./compile em_quarter_ss   # replace with your test case name
# result: $WRF_DIR/main/ideal.exe

Available idealized cases: em_quarter_ss, em_b_wave, em_tropical_cyclone, and others under $WRF_DIR/test/.

Idealized run (quick start)

The following runs the em_quarter_ss squall line case with WRF 4.7.1:

module load wrf/4.7.1

# Compile ideal.exe for this case (one-time)
cd $WRF_DIR && ./compile em_quarter_ss

# Set up run directory
mkdir -p /scratch/$USER/wrf_ideal && cd /scratch/$USER/wrf_ideal
ln -sf $WRF_DIR/run/* .
cp --remove-destination $WRF_DIR/test/em_quarter_ss/namelist.input .
cp --remove-destination $WRF_DIR/main/ideal.exe .

# Submit
sbatch run_ideal.sh

Example job script for Midway3 (run_ideal.sh):

#!/bin/bash
#SBATCH --job-name=wrf-ideal
#SBATCH --account=pi-[cnetid]
#SBATCH --partition=caslake
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=00:30:00
#SBATCH --exclusive

module load wrf/4.7.1

export OMPI_MCA_pml=ob1
export OMPI_MCA_btl=sm,self

cd /scratch/$USER/wrf_ideal
mpirun -np 8 ./ideal.exe
mpirun -np 8 ./wrf.exe

For Midway2, the module built-in help is self-contained and includes the full workflow and ready-to-run example commands — run:

module help wrf/4.7.1
module help wrf/4.1.5

em_tropical_cyclone — single MPI task only

The tropical cyclone idealized case (em_tropical_cyclone) has a 201×201 domain that does not decompose cleanly across multiple MPI tasks. Run it with mpirun -np 1 for both ideal.exe and wrf.exe.

Real-data run (WPS → WRF chain)

Real-data WRF runs require WPS preprocessing before running real.exe and wrf.exe. The full chain is:

geogrid.exe → ungrib.exe → metgrid.exe → real.exe → wrf.exe

Always use wrf/4.1.5 for the metgrid step

The metgrid.exe shipped with wrf/4.7.1 (WPS V4.6.0) has a known NetCDF4 write bug that silently produces empty met_em files. Always use wrf/4.1.5's metgrid.exe for the WPS step regardless of which WRF version you intend to run.

Step 1 — geogrid (geographical preprocessing)

module load wrf/4.7.1   # or wrf/4.1.5

mkdir -p /scratch/$USER/wps_run && cd /scratch/$USER/wps_run

# WPS table files must be in subdirectories (not flat)
mkdir -p geogrid metgrid
ln -sf $WPS_DIR/geogrid/GEOGRID.TBL geogrid/GEOGRID.TBL
ln -sf $WPS_DIR/metgrid/METGRID.TBL metgrid/METGRID.TBL

cp $WPS_DIR/namelist.wps .
# Edit namelist.wps: set geog_data_path, start/end dates, domain config
mpirun -np 4 geogrid.exe

Geographic data resolution

Use geog_data_res = 'lowres' in namelist.wps if working with the low-resolution GEOG dataset (WPS_GEOG_LOW_RES). The default 'default' key expects 30-arc-second data which may not be present.

Step 2 — ungrib (GRIB decoding)

module load wrf/4.1.5   # switch to 4.1.5 for ungrib + metgrid

ln -sf $WPS_DIR/ungrib/Variable_Tables/Vtable.GFS Vtable
$WPS_DIR/link_grib.csh /path/to/grib/files/gfs.*
ungrib.exe

Step 3 — metgrid (meteorological interpolation)

# Still with wrf/4.1.5 loaded
mpirun -np 4 metgrid.exe
# Verify output: met_em.d01.YYYY-MM-DD_HH:MM:SS.nc files should be ~2–3 MB each
ls -lh met_em.*

Step 4 — real.exe and wrf.exe

module load wrf/4.7.1   # switch back to desired WRF version

mkdir -p /scratch/$USER/wrf_real && cd /scratch/$USER/wrf_real
ln -sf $WRF_DIR/run/* .
ln -sf /scratch/$USER/wps_run/met_em.* .

# Edit namelist.input: start/end dates, domain, physics options
sbatch run_real_wrf.sh

Example job script for Midway3 (run_real_wrf.sh):

#!/bin/bash
#SBATCH --job-name=wrf-real
#SBATCH --account=pi-[cnetid]
#SBATCH --partition=caslake
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --time=02:00:00
#SBATCH --exclusive

module load wrf/4.7.1

export OMPI_MCA_pml=ob1
export OMPI_MCA_btl=sm,self

cd /scratch/$USER/wrf_real
mpirun -np 4 real.exe
mpirun -np 4 wrf.exe

Check for successful completion:

grep "SUCCESS" rsl.error.0000
# Expected: wrf: SUCCESS COMPLETE WRF

Notes

OMPI_MCA bypass: RCC clusters require OMPI_MCA_pml=ob1 and OMPI_MCA_btl=sm,self (single-node) or sm,tcp,self (multi-node) in all WRF SLURM scripts. This is a known OpenMPI/UCX memory-pinning limitation on these nodes.
WPS table subdirectories: geogrid.exe and metgrid.exe look for their table files in ./geogrid/GEOGRID.TBL and ./metgrid/METGRID.TBL respectively — not in the current directory directly.
ideal.exe symlink trap: Avoid using symlinks to ideal.exe across multiple run directories. If you recompile for a different case, all symlinked directories will silently pick up the wrong binary. Use cp --remove-destination instead.
num_land_cat: When using WPS_GEOG_LOW_RES, set num_land_cat = 24 in namelist.input and avoid physics suites that expect 20 or 21 land categories (e.g., the CONUS physics suite).
Lustre stat cache: On /scratch (Lustre), add sync && sleep 2 between geogrid.exe and metgrid.exe to avoid race conditions where metgrid cannot immediately see the geo_em file.