WRF-SFIRE End-to-End Workflow

Complete workflow for generating a WRF-SFIRE wildfire simulation run over a 10 km × 10 km domain: dx=dy=1000 m, 3-day forecast window, WRF history output every 30 minutes (145 timestamps), single SFIRE ignition centered in the domain.

Note: Replace placeholder values like <TAG>, <PATH>, <DATE>, <group>, <user> with your actual run values. All commands assume you are inside the correct run directory for that stage.

0. Quick Glossary

WPS outputs

WRF/WRF-SFIRE outputs

1. Environment Setup (ORCA runtime)

module purge
module load gcc
module load openmpi

1.2 — NetCDF and compression libraries (Jasper / PNG / Zlib)

export LD_LIBRARY_PATH=$HOME/libs/netcdf/lib:$HOME/libs/jasper/lib64:$LD_LIBRARY_PATH
export PATH=$HOME/libs/netcdf/bin:$PATH   # makes ncdump available

1.3 — Define code locations (WPS and WRF)

export WPS_DIR=$HOME/wrf_sfire/WPS_clean/WPS-4.6.0
export WRF_DIR=$HOME/wrf_sfire/WRF

2. Example Directory Layout

$HOME/wrf_sfire/
  WPS_clean/WPS-4.6.0/     # built WPS
  WRF/                     # built WRF-SFIRE
  libs/netcdf/             # NetCDF libraries
  libs/jasper/             # Jasper (+ png/zlib) libraries

/scratch/<group>/<user>/
  WPS_RUN_<TAG>/           # WPS run dir  (geo_em, FILE:, met_em)
  WRF_RUN_<TAG>/           # WRF run dir  (wrfinput, wrfbdy, wrfout)

3. WPS Preprocessing

3.0 Create and enter your WPS run directory

mkdir -p /scratch/<group>/<user>/WPS_RUN_<TAG>
cd /scratch/<group>/<user>/WPS_RUN_<TAG>

# Copy your namelist
cp -p <PATH_TO_YOUR_NAMELIST>/namelist.wps .

# Symlink executables
ln -sf $WPS_DIR/geogrid/src/geogrid.exe .
ln -sf $WPS_DIR/ungrib/src/ungrib.exe .
ln -sf $WPS_DIR/metgrid/src/metgrid.exe .
ln -sf $WPS_DIR/link_grib.csh .

# Verify
ls -l geogrid.exe ungrib.exe metgrid.exe link_grib.csh namelist.wps

3.1 geogrid.exe

What it does: Reads namelist.wps and the GEOG dataset and creates geo_em.d01.nc (terrain height, landuse, soil type, etc.).

Verify key namelist settings:

grep -nE "max_dom|dx|dy|e_we|e_sn|map_proj|ref_lat|ref_lon|truelat1|truelat2|stand_lon|geog_data_path|start_date|end_date" namelist.wps

Run:

rm -f geo_em.d0*.nc geogrid.log
./geogrid.exe |& tee geogrid.log

Validate:

ls -lh geo_em.d0*.nc
tail -n 60 geogrid.log

Expected: log ends with a success message and geo_em.d0*.nc files are present.

Common failures:

3.2 ungrib.exe

What it does: Converts GRIB meteorology (e.g., GFS) into WPS intermediate files (FILE:YYYY-MM-DD_HH), later consumed by metgrid.

Choose and link the correct Vtable:

# For GFS:
ln -sf $WPS_DIR/ungrib/Variable_Tables/Vtable.GFS Vtable

Link GRIB files:

# Adjust pattern to your GRIB naming
./link_grib.csh /path/to/grib/files/gfs*.f*

# Check GRIBFILE links
ls -1 GRIBFILE.* | head -n 20

Run:

./ungrib.exe |& tee ungrib.log

Validate:

ls -1 FILE:* | head -n 20
tail -n 80 ungrib.log

Common failures:

A) Missing runtime libraries (Jasper/PNG)

error while loading shared libraries: libjasper.so...

Fix: export LD_LIBRARY_PATH=$HOME/libs/jasper/lib64:$LD_LIBRARY_PATH

B) w3 / g2 link errors during WPS build

If ungrib fails to link w3/g2, create symlinks so ungrib finds the libraries:

cd $WPS_DIR/ungrib/src/ngl
ln -sf w3/libw3.a   libw3.a
ln -sf g2/libg2_4.a libg2_4.a

Then rebuild WPS.

C) Wrong Vtable for your GRIB source — ungrib runs but produces incomplete or empty outputs. Pick the correct Vtable.* for your dataset (GFS vs ERA5 vs NAM, etc.).

3.3 metgrid.exe

What it does: Combines geo_em.d0*.nc (from geogrid) + FILE:* (from ungrib) → met_em.d0*.<timestamp>.nc, which real.exe consumes.

Ensure METGRID.TBL is present:

ln -sf $WPS_DIR/metgrid/METGRID.TBL METGRID.TBL
ls -l METGRID.TBL

Run:

rm -f met_em.d0*.nc metgrid.log
./metgrid.exe |& tee metgrid.log

Validate:

ls -lh met_em.d0*.nc | head
tail -n 80 metgrid.log

You should see met_em.d01.<YYYY-MM-DD_HH:MM:SS>.nc files spanning your forecast window.

3.4 WPS Completion Checklist

Before moving on to WRF, confirm all of these exist:

ls -1 geo_em.d0*.nc          # geogrid outputs
ls -1 FILE:* | head           # ungrib outputs
ls -1 met_em.d0*.nc | head   # metgrid outputs
ls -1 geogrid.log ungrib.log metgrid.log  # logs

Do not proceed to WRF until all files are present.

4. WRF / WRF-SFIRE Setup

4.1 Create and enter the WRF run directory

mkdir -p /scratch/<group>/<user>/WRF_RUN_<TAG>
cd /scratch/<group>/<user>/WRF_RUN_<TAG>

Expected structure inside WRF_RUN_<TAG>/:

namelist.input
met_em.d01.*.nc        (symlinked from WPS run)
real.exe               (symlink)
wrf.exe                (symlink)
logs/
rsl.out.0000, rsl.error.0000, ...
wrfinput_d01
wrfbdy_d01
wrfout_d01_YYYY-MM-DD_HH:MM:SS

4.2 Load modules and set exports

module purge
module load gcc
module load openmpi

export LD_LIBRARY_PATH=$HOME/libs/netcdf/lib:$HOME/libs/jasper/lib64:$LD_LIBRARY_PATH
export PATH=$HOME/libs/netcdf/bin:$PATH
export WRF_DIR=$HOME/wrf_sfire/WRF

4.3 Link WPS met_em files

ln -sf /scratch/<group>/<user>/WPS_RUN_<TAG>/met_em.d0*.nc .

# Confirm
ls -1 met_em.d01.*.nc | head
ls -1 met_em.d01.*.nc | tail

4.4 Link WRF executables

ln -sf $WRF_DIR/main/real.exe .
ln -sf $WRF_DIR/main/wrf.exe .

4.5 Copy namelist and create logs directory

cp -p <PATH_TO_YOUR_NAMELIST>/namelist.input .
mkdir -p logs

5. real.exe

What it does: Converts WPS forcing files (met_em*) into:

• wrfinput_d01 — initial conditions
• wrfbdy_d01 — boundary conditions

If real.exe fails, the answer is almost always in rsl.error.0000.

Clean old outputs:

rm -f wrfinput_d0* wrfbdy_d0* rsl.out.* rsl.error.*
rm -f logs/real.log

Run:

./real.exe |& tee logs/real.log

Validate:

ls -lh wrfinput_d01 wrfbdy_d01
tail -n 80 logs/real.log

If it fails:

ls -1 rsl.error.* | head
tail -n 120 rsl.error.0000

Confirm your run matches requirements:

grep -nE "run_(days|hours|minutes|seconds)|start_(year|month|day|hour)|end_(year|month|day|hour)|history_interval|frames_per_outfile|time_step" namelist.input

grep -nE "max_dom|e_we|e_sn|dx|dy|map_proj|ref_lat|ref_lon|truelat1|truelat2|stand_lon" namelist.input

6. wrf.exe (WRF-SFIRE simulation)

What it does: Runs the full atmospheric model with SFIRE enabled. Advances the fire-spread model alongside the atmospheric simulation.

Produces: wrfout_d01_YYYY-MM-DD_HH:MM:SS — one file per history_interval minutes. For history_interval = 30 over a 3-day run, expect 145 output files.

Clean old outputs:

rm -f rsl.out.* rsl.error.*
rm -f logs/wrf.log
rm -f wrfout_d0*   # only if OK with deleting prior outputs

Run:

./wrf.exe |& tee logs/wrf.log

Monitor progress while running:

tail -f logs/wrf.log
ls -lt wrfout_d01_* | head

# Check timestep progress without tailing full log
grep -n "Timing for main" logs/wrf.log | tail

Validate output after completion:

# Count output files
ls -1 wrfout_d01_* | wc -l

# Check first and last timestamps
ls -1 wrfout_d01_* | head -n 3
ls -1 wrfout_d01_* | tail -n 3

# Inspect times inside a file (NetCDF)
f=$(ls -1 wrfout_d01_* | head -n 1)
ncdump -v Times "$f" | sed -n '1,35p'

If wrf.exe fails:

1. Check the first error file:

tail -n 200 rsl.error.0000

2. Check for missing input/boundary:

   • wrfinput_d01 missing → real.exe did not complete
   • wrfbdy_d01 missing → real.exe did not complete

3. Check your forcing set:

ls -1 met_em.d01.*.nc | head

4. Confirm library paths:

ldd ./wrf.exe | head

7. Slurm Monitoring

Submit and capture job ID:

jid=$(sbatch --parsable <your_job>.slurm)
echo "JOBID=$jid"

Monitor:

squeue -j "$jid"
sacct -j "$jid" --format=JobID,JobName,State,ExitCode,Elapsed,Timelimit -n

Tail logs:

tail -F logs/wrf.log