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WRF case study

This case study uses the Weather Research and Forecasting (WRF) Model to demonstrate the usage of HDF5 log-layout based VOL. WRF can choose to use NetCDF4 I/O option which can perform underlying I/O using parallel HDF5. Enabling log-layout based VOL for this case is easy since all we need to do is to set up several environment variables.

Build Instructions

  • Prerequisite

    • HDF5 1.13.0 or higher, required by any HDF5 VOL
    • HDF5 log-layout based VOL version 1.3.0
    • netcdf 4.1.3 or higher
    • Jasper-1.900.1 or higher
    • libpng-1.2.50 or higher
    • zlib-1.2.7 or higher

  • Clone WRF from its github repository:

      git clone https://github.com/wrf-model/WRF/releases/download/v4.4.1/v4.4.1.tar.gz

  • Setup environment variables for configuring WRF

      export DIR=${HOME}
  export JASPERLIB=${HOME}/grib2/lib
  export JASPERINC=${HOME}/grib2/include
  export CC=mpicc
  export CXX=mpicxx
  export FC=mpif90
  export FCFLAGS=-m64
  export F77=mpif77
  export F90=mpif90
  export FFLAGS=-m64

  export NETCDF=${HOME}/NetCDF/4.9.0
  export HDF5=${HOME}/HDF5/1.13.2
  export ZLIB=${HOME}/zlib/1.2.7
  export WRF_DIR=${HOME}/WRF

  export NETCDFPAR=$NETCDF_DIR
  export PHDF5=$HDF5

  export CPPFLAGS="$CPPFLAGS -I${JASPERINC} -I$HDF5/include -I$NETCDF/include"
  export LDFLAGS="$LDFLAGS -L${JASPERLIB} -L$HDF5/lib -L$NETCDF/lib"
  export LD_LIBRARY_PATH="$HDF5/lib:$NETCDF/lib:$LD_LIBRARY_PATH"
  export PATH="$HDF5_DIR/bin:$NETCDF_DIR/bin:$PATH"

  • Configure WRF with NetCDF4 features enabled.

      cd WRF
  ./clean -a
  ./configure
    • The WRF configuration is interactive.
      • Select the distributed memory only (dmpar) option that corresponds to the target system.
      • Other options can be left default.

  • Compile one of WRF applications

    • An example compiling the em_les test case 
          ./compile em_les

    Two executables (ideal.exe, and wrf.exe) will be built under main forlder. The two executables should also exist in test/em_les, which are linked to those under main folder.

  • For more details, please refer to WRF's official compilation tutorial.

Run Instructions

  • Prepare the input data for WRF simulation 
      cd test/em_les
  ./ideal.exe
  • Enable log-layout based VOL by setting environment variables 
      source ${HOME}/logvol/1.3.0/bin/h5lenv.bash
  • Run em_les application with log-layout based VOL 
      mpiexec -np 4 ./wrf.exe

Example Results

We provide some example results running WRF with NetCDF4 via HDF5, with the log-layout based VOL enabled

WRF write two kinds of outputs: restart files and history files. An history file contains the simulatioin results for the user selected simulation timesteps. And a restart file serves as a check point and contains all the necessary information to restart the WRF simulation from a certain timestep. Each history file or restart file may contain multiple time steps.

In our experiments, we use the COUNS2.5 run case and produce one history file and one restart file.

The following table summarizes the information for the history and restart file in our experiment.

file type grid size (e_we x e_sn) num time steps num variables file size (GB)
history 1900 x 1300 13 202 103
restart 1900 x 1300 1 565 34

Example Results on Cori at NERSC

Performance chart below shows the execution time, collected in Oct/2022, on Cori at NERSC. All runs were on the KNL nodes, with 64 MPI processes allocated per node.

The Lustre file system is configured to use striping count of 8 OSTs and striping size of 1 MiB.

num nodes num MPI processes timing history (sec) timing restart (sec)
4 256 9.25 4.05
8 512 7.94 3.78
16 1024 7.83 3.75
32 2048 8.28 3.83