WRF

Owned by Chris Harris
Last updated: Sept 06, 2023 by Deva Kumar Deeptimahanti
4 min read

The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications. It features two dynamical cores, a data assimilation system, and a software architecture supporting parallel computation and system extensibility. The model serves a wide range of meteorological applications across scales from tens of meters to thousands of kilometres.

For more information, see:

Before you begin

Researchers using WRF on Pawsey supercomputing systems typically need to build their own custom version to support their simulations. For this reason, WRF is not provided as a module by Pawsey staff. However, the WRF dependencies are installed on the system.

Registration with WRF is also required to before downloading, which should be completed before following the instructions below.

See: WRF Registration (external site)

Installing WRF using an interactive session

The following instructions provide guidance to compile WRF on Setonix.

Step 1: Start an interactive session on the work partition

Terminal 1. Salloc command
$ salloc -p work --ntasks=1 --mem=25G --time=4:00:00
salloc: Granted job allocation 82652
salloc: Waiting for resource configuration
salloc: Nodes nid001007 are ready for job

Step 2: Change directory to the /software filesystem

We recommend building and compiling WRF on the /software filesystem, so it will not be purged by the 30 day purge policy on /scratch.

Move to your software directory using the $MYSOFTWARE environment variable shown below, and create and enter any additional directories if desired.

$ cd $MYSOFTWARE 

Step 3: Download WRF

Check the for the URL to the latest version on the releases page, this will likely be the file ending in tar.gz in the Assets box at the bottom of the latest release.

Use the wget utility to download the file on the debug node, as it is a relatively small file that should only takes a few seconds.

See: WRF Github Releases page (external site)

$ wget https://github.com/wrf-model/WRF/releases/download/v4.4/v4.4.tar.gz

Step 3: Extract WRF

Expand the WRF tarball using the tar utility.

$ tar zxvf v4.4.tar.gz

Step 4: Enter the WRF directory

Use the cd command to enter the WRFV4.4 directory:

$ cd WRFV4.4 

Step 5: Prepare the Environment

Swap to the PrgEnv-cray programming environment, load the modules containing dependencies needed by WRF, and set up the NETCDF environment variable.

Terminal 2. Module preparation
$ module swap PrgEnv-gnu/8.3.3 PrgEnv-cray/8.3.3 
$ module load cray-hdf5-parallel/1.12.2.3
$ module use /opt/cray/pe/modulefiles
$ module load cray-netcdf-hdf5parallel/4.9.0.3 
$ module load cray-parallel-netcdf/1.12.3.3
$ export NETCDF=$NETCDF_DIR

Step 6: Configure WRF

Run the WRF configuration script:

./configure 

Select the option that contains the Cray compiler and the corresponding type of parallelism desired.

For WRF 4.4 these options are:

  • 46. (dmpar) CRAY CCE (ftn $(NOOMP)/cc): Cray XE and XC for MPI support, or

  • 47. (smpar_dmpar) CRAY CCE (ftn $(NOOMP)/cc): Cray XE and XC for MPI and OpenMP support.

The dmpar configuration (option 46) is generally used over the hybrid approach (option 47).

Select the level of nesting as desired, which in most cases will the default option corresponding to basic nesting.

Step 7: Compile WRF

Run the relevant WRF compilation, which may take one to two hours:

./compile em_real 

Installing WRF using an Slurm batch script

WRF can also be installed using a Slurm batch script instead of an interactive session.

Note that the options to the interactive configure script must be provided.

The following is an example for Option 46 (described in the previous section) and the default nesting.

Listing 1. Installing WRF with batch script
#!/bin/bash --login

#SBATCH --account=project_id
#SBATCH --partition=work
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=25G
#SBATCH --time=4:00:00
#SBATCH --cpus-per-task=1

module swap PrgEnv-gnu/8.3.3 PrgEnv-cray/8.3.3 
module load cray-hdf5-parallel/1.12.2.3
module use /opt/cray/pe/modulefiles
module load cray-netcdf-hdf5parallel/4.9.0.3 
module load cray-parallel-netcdf/1.12.3.3
export NETCDF=$NETCDF_DIR

wget https://github.com/wrf-model/WRF/releases/download/v4.4/v4.4.tar.gz
tar zxfv v4.4.tar.gz
cd WRFV4.4

./configure <<< $'46'

./compile em_real

Using WRF on Setonix

To use the WRF installation on Setonix, we recommend:

  1. Copying your WRF installation to a directory for the simulation on /scratch
  2. Copy necessary input data files as needed to the directory
  3. Configure your simulation
  4. Prepare a Slurm batch script to launch the job, including the same environment commands used to compile WRF
  5. Submit your job to the scheduler

The following is an example jobscript for running an MPI-enabled (dmpar) version of WRF on 2 nodes, or 256 cores:

Listing 2. Using WRF
#!/bin/bash --login

#SBATCH --account=project_id
#SBATCH --partition=work
#SBATCH --ntasks=256
#SBATCH --ntasks-per-node=128
#SBATCH --time=24:00:00
#SBATCH --exclusive
#SBATCH --cpus-per-task=1
#SBATCH --nodes=2  

module swap PrgEnv-gnu/8.3.3 PrgEnv-cray/8.3.3 
module load cray-hdf5-parallel/1.12.2.3
module use /opt/cray/pe/modulefiles
module load cray-netcdf-hdf5parallel/4.9.0.3 
module load cray-parallel-netcdf/1.12.3.3
export NETCDF=$NETCDF_DIR

srun -N 2 -n 256 -c 1 ./wrf.exe

WRF Reference Data

The WPS Geog dataset has been placed in /scratch/references/wrf/wps_geog to avoid the need for repeated staging of data commonly used by WRF users.

For more information, see WPS Geographical Static Data webpage (external link).

Installing WPS

WPS can be compiled in a similar manner to WRF.

Solutions to Common Issues

WRF simulation crashes due to numerical accuracy in the noah_mp module.

WRF contains internal checks on the ongoing accuracy of the simulation, and will halt the simulation if accuracy conditions are not met.

In practice, this looks like the following in one of the many rsl.out.* files created when running a simulation:

Terminal 3. WRD simulation crash error
-------------- FATAL CALLED ---------------

FATAL CALLED FROM FILE:  <stdin>  LINE:    1650

Stop in Noah-MP

-------------------------------------------

In this example there is a known issue when using the noah_mp land surface model in WRF when compiled using the Cray Fortran compiler that causes numerical instabilities and model crash. This has been linked to compiler optimisation levels and a work-around is to compile the noah_mp module with -O1 optimisation, but the rest of WRF with -O3 optimisation. To do this, you first need to compile WRF as normal.

Then you need to manually delete the compiled noah_mp files, re-compile these with -O1, and then run ./compile em_real again. Note the compile example below may have different paths depending on the location of WRF.

Terminal 4. Fixing WRF error
$ cd phys
$ rm -f module_sf_noahmplsm.o
$ rm -f MODULE_SF_NOAHMPLSM.mod
$ ftn -hnoomp -o module_sf_noahmplsm.o -c -O1 -Ofp1 -N1023 -f free -h byteswapio -I../dyn_em -I/$MYSOFTWARE/setonix/WRF4.4/WRF/external/esmf_time_f90 -I/$MYSOFTWARE/setonix/WRF4.4/WRF/main -I/$MYSOFTWARE/setonix/WRF4.4/WRF/external/io_netcdf -I/$MYSOFTWARE/setonix/WRF4.4/WRF/external/io_int -I/$MYSOFTWARE/setonix/WRF4.4/WRF/frame -I/$MYSOFTWARE/setonix/WRF4.4/WRF/share -I/$MYSOFTWARE/setonix/WRF4.4/WRF/phys -I/$MYSOFTWARE/setonix/WRF4.4/WRF/wrftladj -I/$MYSOFTWARE/setonix/WRF4.4/WRF/chem -I/$MYSOFTWARE/setonix/WRF4.4/WRF/inc -I/opt/cray/pe/netcdf-hdf5parallel/4.8.1.1/crayclang/10.0/include -s integer32 -s real{{expr 8 * 4}} module_sf_noahmplsm.f90
$ cd ..
$ ./compile em_real

WRF 4.4 bug in phys/module_ra_clWRF_support.F

Be aware that the current 4.4 version of WRF contains a bug that will cause wrf.exe to crash:

This requires code changes in the phys/module_ra_clWRF_support.F file around line 171, specifically the lines:

Listing 3. WRF 4.4 code bug
IF (istatus /= -1) THEN
WRITE(message,*) " Not normal ending of CAMtr_volume_mixing_ratio file"
call wrf_error_fatal( message)
END IF

need to be changed to:

Listing 4. WRF 4.4 bode bugfix
IF (istatus == -1) THEN
WRITE(message,) "Normal ending of CAMtr_volume_mixing_ratio file"
CALL wrf_message( message)
ELSE IF (istatus == -4001) THEN ! Cray CCE compiler throws -4001 rather than -1
WRITE(message,) "Normal ending of CAMtr_volume_mixing_ratio file"
CALL wrf_message( message)
ELSE ! if not -1 or -4001, then abort
WRITE(message,*) " Not normal ending of CAMtr_volume_mixing_ratio file"
call wrf_error_fatal( message)
END IF

It is expected that versions newer than 4.4 will address this bug.