WRF

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.

 

Download WRF:

cd /nesi/project/<your_project_code>
wget https://github.com/wrf-model/WRF/archive/v4.1.1.tar.gz
tar xf v4.1.1.tar.gz

This guide is based on WRF 4.1.1 and WPS 4.2 (it was also tested with Polar WRF 4.1.1 but for that, you would need to apply the Polar WRF and WPS patches before compiling).

WRF needs NetCDF, NetCDF-Fortran, PnetCDF and their dependencies to be installed. On Maui, these are available as modules. On Mahuika, we recommend to download these packages and build them by hand (instructions are provided below).

 

WRF on Mahuika

 

Environment on Mahuika

We'll use the Intel compiler and Intel MPI library. 

module purge
module load HDF5/1.12.2-iimpi-2022a

Although NeSI has NetCDF modules installed, WRF wants the C and Fortran NetCDF libraries, include files and modules all installed under the same root directory. Hence we build those by hand.

 

Building WRF dependencies on Mahuika

Copy-paste the commands below to build WRF on Mahuika:

# create build directory for WRF's dependencies
export WRF_DEPS_DIR=$PWD/wrf-deps
mkdir $WRF_DEPS_DIR
cd $WRF_DEPS_DIR

# required for building and running
export LD_LIBRARY_PATH=$WRF_DEPS_DIR/lib:$LD_LIBRARY_PATH

# to access the nc-config anf nf-config commands
export PATH=$WRF_DEPS_DIR/bin:$PATH

# set the compilers
export CC=icc
export CXX=icc
export FC=ifort
export F77=ifort
export MPICC=mpiicc
export MPICXX=mpiicc
export MPIF77=mpiifort
export MPIF90=mpiifort

# now install the dependencies

# netcdf-c
wget https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz
tar xf netcdf-c-4.9.2.tar.gz
cd netcdf-c-4.9.2/
./configure --prefix=$WRF_DEPS_DIR
make & make install
cd ..

# netcdf-fortran
wget https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.1/netcdf-fortran-4.6.1.tar.gz
tar xf netcdf-fortran-4.6.1.tar.gz
cd netcdf-fortran-4.6.1
CPPFLAGS="$(../bin/nc-config --cflags)" LDFLAGS="$(../bin/nc-config --libs)" \
./configure --prefix=$WRF_DEPS_DIR
make & make install
cd ..

# pnetcdf
wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz
tar xf pnetcdf-1.12.3.tar.gz
cd pnetcdf-1.12.3
./configure --prefix=$WRF_DEPS_DIR --with-netcdf4=$WRF_DEPS_DIR
make & make install
cd ..

# back to the top directory
cd ..

 

Then proceed to configure WRF by setting

export NETCDF=$WRF_DEPS_DIR
export HDF5=$WRF_DEPS_DIR
export PNETCDF=$WRF_DEPS_DIR

cd WRF-4.1.1
./configure
[select 15]

and build the code with

./compile em_real >& log.compile

This may take several hours to compile. Check the log file to ensure that the compilation was successful. 

 

Running WRF on Mahuika

 

An example Slurm script for running WRF on Mahuika extension, which can be submitted with sbatch name_of_script.sl:

#!/bin/bash -e
#SBATCH --job-name=wrf
#SBATCH --time=01:00:00
#SBATCH --ntasks=240
#SBATCH --hint=nomultithread
#SBATCH --partition=milan

module purge
module load HDF5/1.12.2-iimpi-2022a
module list
export LD_LIBRARY_PATH=$WRF_DEPS_DIR/lib:$LD_LIBRARY_PATH

# run real
srun --output=real.log ./real.exe

# run wrf
srun --output=wrf.log ./wrf.exe

 

 

WRF on Maui

Building WRF

Load environment modules and set up the build environment (here we will build with the Intel compiler):

# load PrgEnv-intel (this assumes you currently have PrgEnv-cray loaded)
module switch PrgEnv-cray PrgEnv-intel

# load dependencies
module load cray-netcdf cray-hdf5 cray-parallel-netcdf

# the following two lines are optional and may improve performance
module switch craype-x86-skylake craype-broadwell
module load craype-hugepages2M

export NETCDF=$NETCDF_DIR
export HDF5=$HDF5_DIR
export PNETCDF=$PNETCDF_DIR

Apply patches for Polar WRF if required and then configure WRF:

./configure
# choose option 50 - INTEL (ftn/icc) Cray XC (dmpar)
# choose an appropriate nesting option or leave it at the default

The configure script takes some options, for example, to configure for a debug build (no optimisations and debug symbols enabled) you could run ./configure -d instead.

The configure script writes out a configure.wrf file which can also be edited manually if desired. For example, if you want an optimised build with debug symbols included, you could add -g to the FCDEBUG variable.

Next compile WRF:

./compile em_real >& log.compile

It is important to check the output in log.compile as the command will not exit with an error if it fails. Check the end of the log file for a message saying compilation was successful. You could also check the timestamps of the executables in the main subdirectory (main/wrf.exe, main/real.exe, etc).

Running WRF

An example Slurm script for running WRF on Maui, which can be submitted with sbatch name_of_script.sl:

#!/bin/bash -e
#SBATCH --job-name=wrf
#SBATCH --time=01:00:00
#SBATCH --ntasks=240
#SBATCH --hint=nomultithread

# important, required on Maui
export HDF5_USE_FILE_LOCKING=FALSE

# optional, may improve performance
module load craype-hugepages2M

# run real
srun --output=real.log ./real.exe

# run wrf
srun --output=wrf.log ./wrf.exe

Parallel netCDF

For some model configurations enabling parallel IO can be beneficial. By default WRF uses serial netCDF IO, which can be verified by looking in the namelist.input file for the io_form_* variables (these will mostly be in the time_control section of the namelist). If these variables are set to "2" then they will use serial netCDF. Setting them to 11 will use parallel netCDF instead. It is also recommended (possibly required) to set nocolons = .true. in the time_control section of the namelist when using parallel IO.

Building WPS

Download WPS:

wget https://github.com/wrf-model/WPS/archive/v4.2.tar.gz
tar xf v4.2.tar.gz
cd WPS-4.2

Load environment modules and set up the build environment (here we will build with the Intel compiler). We will build WPS using dynamic linking so that we can link against the system JasPer shared library.

# load PrgEnv-intel (this assumes you currently have PrgEnv-cray loaded)
module switch PrgEnv-cray PrgEnv-intel

# load dependencies
module load cray-netcdf cray-hdf5 cray-parallel-netcdf

# the following two lines are optional and may improve performance
module switch craype-x86-skylake craype-broadwell
module load craype-hugepages2M

export NETCDF=$NETCDF_DIR
export HDF5=$HDF5_DIR
export PNETCDF=$PARALLEL_NETCDF_DIR
export JASPERLIB=/usr/lib/libjasper.so.1
export JASPERINC=/usr/include/jasper/jasper.h
export WRF_DIR=../WRF-4.1.1
export CRAYPE_LINK_TYPE=dynamic

Configure WPS:

./configure
# choose option 39 - Cray XC Intel parallel build

This creates the configure.wps file, which can be edited in a similar way to configure.wrf above, if desired.

Now compile WPS:

./compile >& log.compile

Check that the executables were successfully created: geogrid.exe, ungrib.exe and metgrid.exe.

Running WPS

Both geogrid and metgrid are parallel applications and can be run on Maui compute nodes. However, ungrib is serial and should not be run on a compute node unless it is very quick to finish. Alternatively you could run ungrib on an interactive/login node if it will not take up many resources, or you could compile WRF and WPS on a Maui Ancillary node and run it there. 

Note that WPS does a lot of file IO and therefore probably won't scale up to as many processes as WRF.

This example shows running geogrid in a Slurm job:

#!/bin/bash -e
#SBATCH --job-name=wps
#SBATCH --time=01:00:00
#SBATCH --ntasks=40
#SBATCH --hint=nomultithread

# need to specify modules as we linked dynamically
module unload PrgEnv-cray PrgEnv-intel PrgEnv-gnu
module load PrgEnv-intel cray-netcdf cray-hdf5 cray-parallel-netcdf

# the following two lines are optional and may improve performance
module switch craype-x86-skylake craype-broadwell
module load craype-hugepages2M

# important, required on Maui
export HDF5_USE_FILE_LOCKING=FALSE

# run geogrid
srun --output=geogrid.log ./geogrid.exe