WRF

How to compile WRF-SFIRE-Chem in Vega and Poznan // Meteogrid Project

Description

This repository contains the tests, configurations and scripts developed to run WRF model at Poznan HPC. It contains a directory with the collection of tests that have been carried out to ensure that the installation of the model at the HPC is correct and has all the modules needed and also some tests to study configuration and paralelization options and parameters.

A script to set up the environment and also create separate folders for each test is available. In this version, it is needed to configure this script to the folders and namelists in use but it is planned to improve this version when a stable configuration for both the HPC and the WRF model has been reached.

Installation

WRF Requirements

Libraries

WRF-SFIRE version 4.4

git clone https://github.com/openwfm/WRF-SFIRE
WPS version 4.3 git clone https://github.com/openwfm/WPS or version 4.4 https://github.com/wrf-model/WPS/releases

Note that WRF-SFIRE is only needed if the module SFIRE is going to be used, if not just install WRF:

https://github.com/wrf-model/WRF/releases

WRF-SFIRE INSTALLATION INSTRUCTION @Altair

Versions of the software used

openmpi 4.1.0 (available as a module)
zlib-1.2.7 (already installed in the system)
libpng-3.50.0 (already installed in the system)
jasper-1.900.1
hdf5-1.14.0
netcdf-c-4.9.2
netcdf-fortran-4.6.0
WRF-SFIRE 4.4
WPS 4.4

Installation

These steps will cover the installation of WRF with SFIRE and CHEM.

Allocate a lot of memory for your interactive task:
```
srun -n 1 -p altair --mem=30G --pty /bin/bash
```
Load a module with openmpi
```
module load openmpi/4.1.0_gcc620
```

Create a general software directory

export SOFTWARE_DIR=/mnt/storage_2/project_data/grant_627/Software

Download WRF and WPS

cd ${SOFTWARE_DIR}
git clone https://github.com/openwfm/WRF-SFIRE
wget https://github.com/wrf-model/WPS/archive/refs/tags/v4.4.tar.gz
tar -zxvf v4.4.tar.gz

Create a temporary directory for dependencies sources:

export DEP_SOURCES_DIR=${SOFTWARE}/build
mkdir -p ${DEP_SOURCES_DIR}

Download all the necessary sources

cd ${DEP_SOURCES_DIR}
wget https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz
wget https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.0/netcdf-fortran-4.6.0.tar.gz
wget https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.0/src/hdf5-1.14.0.tar.gz

Create a directory for all the dependencies installation

export DEP_DIR=${SOFTWARE_DIR}/dependencies
mkdir -p ${DEP_DIR}

Install library dependencies (jasper, HDF5, NETCDF-C, NETCDF-FORTRAN):

# Install Jasper
cd ${DEP_SOURCES_DIR}
unzip jasper-1.900.1.zip
cd ${DEP_SOURCES_DIR}/jasper-1.900.1
./configure --prefix=${DEP_DIR}
make
make install

# Install HDF5:
cd ${DEP_SOURCES_DIR}
tar -zxvf hdf5-1.14.0.tar.gz
cd ${DEP_SOURCES_DIR}/hdf5-1.14.0
CC=mpicc ./configure --with-zlib=/usr/ --prefix=${DEP_DIR} --enable-parallel --enable-fortran --enable-hl
make
make install

# Set PATH and LD_LIBRARY_PATH for further steps
export PATH=${DEP_DIR}/bin:${PATH}
export LD_LIBRARY_PATH=${DEP_DIR}/lib:${LD_LIBRARY_PATH}

# Install NETCDF-C:
cd ${DEP_SOURCES_DIR}
tar -zxvf netcdf-c-4.9.2.tar.gz
cd ${DEP_SOURCES_DIR}/netcdf-c-4.9.2
CC=mpicc CFLAGS=-fPIC CPPFLAGS=-I${DEP_DIR}/include LDFLAGS="-L${DEP_DIR}/lib -L/usr/lib64/" ./configure --enable-shared --disable-dap --enable-parallel-tests --enable-netcdf4 --enable-netcdf-4 --prefix=${DEP_DIR}
make
make install

# Install NETCDF-FORTRAN:
cd ${DEP_SOURCES_DIR}
tar -zxvf netcdf-fortran-4.6.0.tar.gz
cd ${DEP_SOURCES_DIR}/netcdf-fortran-4.6.0
CC=mpicc CPPFLAGS=-I${DEP_DIR}/include CFLAGS=$(nc-config --cflags) LDFLAGS=$(nc-config --libs --static) ./configure --prefix=${DEP_DIR} --enable-shared
make
make install

Install WRF-SFIRE:

cd ${SOFTWARE_DIR}/WRF-SFIRE
# in arch/Config.pl file set $I_really_want_to_output_grib2_from_WRF = "TRUE"
export NETCDF=${DEP_DIR}
export HDF5=${DEP_DIR}
export PHDF5=${DEP_DIR}
export JASPERLIB=${DEP_DIR}/lib
export JASPERINC=${DEP_DIR}/include
ulimit -s unlimited
export WRF_CHEM=1
./clean -a
./configure chem
# Choose option 34
# Choose option 1
./compile -j 1 em_real >& compile.log

Note that in order for CHEM to work properly it might be needed to make this change:

in chem/depend.chem change line number 232 from:

module_mosaic_addemiss.o: module_data_mosaic_asect.o module_data_sorgam.o

to:

module_mosaic_addemiss.o: module_data_mosaic_asect.o module_data_sorgam.o module_gocart_dust.o

continue with the compilation

./compile -j 1 em_real >& compile.log2

Create link for WRF-SFIRE
```
cd ${SOFTWARE_DIR}
ln -s WRF-SFIRE WRF
```

Install WPS

cd ${SOFTWARE_DIR}
tar -zxvf v4.4.tar.gz
cd ${SOFTWARE_DIR}/WPS-4.4
./clean
./configure
# Choose option 3
./compile >& log.compile

Once the installation is finished each time the user will run the model, it is needed to set up this environment parameters. This can be done using the script that will be used to submit the jobs or using a dedicated set up script created for this purpose.

module load openmpi/4.1.0_gcc620
export DEP_DIR=/path/to/userhome/grant_XXX/project_data/grant_627/Software/dependencies/
export PATH=${DEP_DIR}/bin:${PATH}
export LD_LIBRARY_PATH=${DEP_DIR}/lib:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH=${DEP_DIR}/lib64:${LD_LIBRARY_PATH}
ulimit -s unlimited

WRF-SFIRE INSTALLATION INSTRUCTION @Vega

Versions of the software used

openmpi 4.1.4 (available as a module)
zlib-1.2.12 (available as a module)
jasper-2.0.33
libpng-1.6.37
hdf5-1.14.0
netcdf-c-4.9.2
WRF-SFIRE 4.4
WPS 4.4

Set environment variables and modules

export SOFTWARE_DIR=/ceph/hpc/data/d2023d08-038-users/Software
export DEP_SOURCES_DIR=${SOFTWARE_DIR}/build
mkdir -p ${DEP_SOURCES_DIR}
export DEP_DIR=${SOFTWARE_DIR}/dependencies
export PATH=${DEP_DIR}/bin:${PATH}
export LD_LIBRARY_PATH=${DEP_DIR}/lib:${LD_LIBRARY_PATH}

module load OpenMPI/4.1.4-GCC-12.2.0
module load zlib/1.2.12-GCCcore-12.2.0

Download software

Libraries

cd ${DEP_SOURCES_DIR}
wget https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz
wget https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.0/netcdf-fortran-4.6.0.tar.gz
wget https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.0/src/hdf5-1.14.0.tar.gz

WRF & WPS

cd ${SOFTWARE_DIR}
git clone https://github.com/openwfm/WRF-SFIRE
wget https://github.com/wrf-model/WPS/archive/refs/tags/v4.4.tar.gz
tar -zxvf v4.4.tar.gz

Install library dependencies (jasper, HDF5, NETCDF-C, NETCDF-FORTRAN):

Install Jasper

cd ${DEP_SOURCES_DIR}
unzip jasper-1.900.1.zip
cd ${DEP_SOURCES_DIR}/jasper-1.900.1
./configure --prefix=${DEP_DIR}
make
make install

Install libpng

cd ${DEP_SOURCES_DIR}
tar xvzf libpng-1.6.37.tar.gz
cd ${DEP_SOURCES_DIR}/libpng-1.6.37
./configure --prefix=${DEP_DIR}
make
make install

* Install HDF5
```bash
cd ${DEP_SOURCES_DIR}
tar -zxvf hdf5-1.14.0.tar.gz
cd ${DEP_SOURCES_DIR}/hdf5-1.14.0
CC=mpicc ./configure --with-zlib=/usr/ --prefix=${DEP_DIR} --enable-parallel --enable-fortran --enable-hl
make
make install

Install NETCDF-C

module load cURL
cd ${DEP_SOURCES_DIR}
tar -zxvf netcdf-c-4.9.2.tar.gz
cd ${DEP_SOURCES_DIR}/netcdf-c-4.9.2
CC=mpicc CFLAGS=-fPIC CPPFLAGS=-I${DEP_DIR}/include LDFLAGS="-L${DEP_DIR}/lib -L/usr/lib64/" ./configure --enable-shared --disable-dap --enable-parallel-tests --enable-netcdf4 --enable-netcdf-4 --prefix=${DEP_DIR}
make
make install

Install NETCDF-FORTRAN

cd ${DEP_SOURCES_DIR}
tar -zxvf netcdf-fortran-4.6.0.tar.gz
cd ${DEP_SOURCES_DIR}/netcdf-fortran-4.6.0
CC=mpicc CPPFLAGS=-I${DEP_DIR}/include CFLAGS=$(nc-config --cflags) LDFLAGS=$(nc-config --libs --static) ./configure --prefix=${DEP_DIR} --enable-shared
make
make install

Install WRF-SFIRE

cd ${SOFTWARE_DIR}/WRF-SFIRE
# in arch/Config.pl file set $I_really_want_to_output_grib2_from_WRF = "TRUE"
export NETCDF=${DEP_DIR}
export HDF5=${DEP_DIR}
export PHDF5=${DEP_DIR}
export JASPERLIB=${DEP_DIR}/lib
export JASPERINC=${DEP_DIR}/include
ulimit -s unlimited
export WRF_CHEM=1
./clean -a
./configure chem
# Choose option 34
# Choose option 1

Note that in order for CHEM to work properly it might be needed to make this change:

in chem/depend.chem change line number 232 from:

module_mosaic_addemiss.o: module_data_mosaic_asect.o module_data_sorgam.o

to:

module_mosaic_addemiss.o: module_data_mosaic_asect.o module_data_sorgam.o module_gocart_dust.o

continue with the compilation

Failed compilation:

Tried:

switching to bash
adding flag -DLANDREAD_STUB CFLAGS in configure.wrf
compiling with 4 & 1 core

What worked:

Before compiling wrf edit the compile.wrf file and at line 139 change (https://forum.mmm.ucar.edu/threads/compiling-wrf-4-0-2-test-em_b_wave-failed.8991/):

FC = time $(DM_FC)

to

FC = $(DM_FC)

./compile -j 1 em_real | tee compile.log

Note: it might be interesting to test with "-j 4 "

Create link for WRF-SFIRE:

WRF Requirements

Install WPS

cd ${SOFTWARE_DIR}
tar -zxvf v4.4.tar.gz
cd ${SOFTWARE_DIR}/WPS-4.4
./clean
./configure
# Choose option 3
./compile >& log.compile

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WRF

Description

Installation

WRF Requirements

Libraries

WRF-SFIRE version 4.4

WRF-SFIRE INSTALLATION INSTRUCTION @Altair

Versions of the software used

Installation

WRF-SFIRE INSTALLATION INSTRUCTION @Vega

Versions of the software used

WRF Requirements

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WRF

Description

Installation

WRF Requirements

Libraries

WRF-SFIRE version 4.4

WRF-SFIRE INSTALLATION INSTRUCTION @Altair

Versions of the software used

Installation

WRF-SFIRE INSTALLATION INSTRUCTION @Vega

Versions of the software used

WRF Requirements

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