Running WRF-SFIRE with real data in the WRFx system

wrf-fire

Requirements and environment

Install requiered libraries

• General requirements:
  • C-shell
  • Traditional UNIX utilities: zip, tar, make, etc.
• WRF-SFIRE requirements:
  • Fortran and C compilers (Intel recomended)
  • MPI libraries (same compiler)
  • NetCDF libraries (same compiler)
• WPS requirements:
  • zlib compression library (zlib)
  • PNG reference library (libpng)
  • JasPer compression library
  • libtiff and geotiff libraries

See also https://www2.mmm.ucar.edu/wrf/users/prepare_for_compilation.html.

Set environtment

Set specific libraries installed

setenv NETCDF /path/to/netcdf
setenv JASPERLIB /path/to/jasper/lib
setenv JASPERINC /path/to/jasper/include
setenv LIBTIFF /path/to/libtiff
setenv GEOTIFF /path/to/libtiff
setenv WRFIO_NCD_LARGE_FILE_SUPPORT 1

And add all the library folders into your LD_LIBRARY_PATH

setenv LD_LIBRARY_PATH /path/to/netcdf/lib:/path/to/jasper/lib:/path/to/libtiff/lib:/path/to/libtiff/lib:$LD_LIBRARY_PATH

Installation

Clone github repositories

git clone https://github.com/openwfm/wrf-fire
git clone https://github.com/openwfm/wrf-fire wrf-fire-serial

Configure WRF-SFIRE

cd wrf-fire/wrfv2_fire
./configure

Options 7 (intel dmpar) and 1 (simple nesting) if available

Compile WRF-SFIRE

Compile em_real

./compile em_real >& compile_em_real.log & 
grep Error compile_em_real.log

If any compilation error, compile em_fire

./compile em_fire >& compile_em_fire.log & 
grep Error compile_em_fire.log

If any of the previous step fails:

./clean -a
./configure

Add -nostdinc in CPP flag, and repeat compilation. If this does not solve compilation, look for issues in your environment.

Configure WPS

cd ../WPS
./configure

Option 2 (serial) if available

Compile WPS

./compile >& compile_wps.log &
ls -l *.exe

It should contain geogrid.exe, metgrid.exe, and ungrib.exe. If not

./clean -a
./configure

Add -nostdinc in CPP flag, and repeat compilation. If this does not solve compilation, look for issues in your environment.

Configure and compile serial version of WRF-SFIRE

Sometimes, one needs to provide an installation of WRF-SFIRE in serial mode in order to run real.exe in serial. So, it is better to repeat the same steps but in serial mode.

cd wrf-fire-serial/wrfv2_fire
./configure

Options 5 (intel serial) and 0 (no nesting)

./compile em_real >& compile_em_real.log & 
grep Error compile_em_real.log

Again, if any of the previous step fails:

./clean -a
./configure

Add -nostdinc in CPP flag, and repeat compilation. If this does not solve compilation, look for issues in your environment.

Note: This time, we only need to compile em_real because we only need real.exe. However, if you want to test serial vs parallel for any reason, you can proceed to compile em_fire the same way.

Get static data

 cd ../..
 wget http://math.ucdenver.edu/~jmandel/tmp/WPS-GEOG.tbz
 tar xvfj WPS-GEOG.tbz

wrfxpy

Requirements and environment

Install Anaconda distribution

Download and install the Python 3 Anaconda Python distribution for your platform. We recommend an installation into the users' home directory.

wget https://repo.continuum.io/archive/Anaconda3-2019.10-Linux-x86_64.sh
chmod +x Anaconda3-2019.10-Linux-x86_64.sh
./Anaconda3-2019.10-Linux-x86_64.sh

Install necessary packages

We recommend the creation of an environment. Install pre-requisites:

conda update -n base -c defaults conda
conda create -n wrfxpy python=3 netcdf4 pyproj paramiko dill scikit-learn scikit-image h5py psutil proj4 pytz
conda activate wrfxpy
conda install -c conda-forge simplekml pygrib f90nml pyhdf xmltodict basemap
pip install MesoPy python-cmr

Note that conda and pip are package managers available in the Anaconda Python distribution.

Set environment

If you created the wrfxpy environment as shown above

setenv PROJ_LIB "$HOME/anaconda3/envs/wrfxpy/share/proj"

If not

setenv PROJ_LIB "$HOME/anaconda3/share/proj"

Installation

Clone github repository

git clone https://github.com/openwfm/wrfxpy

General configuration

An etc/conf.json file must be created with the keys discussed below. A template file etc/conf.json.initial is provided as a starting point.

cd wrfxpy
cp etc/conf.json.initial etc/conf.json

Configure the system directories, WPS/WRF-SFIRE locations, and workspace locations by editing the following keys in etc/conf.json:

"wps_install_path": "/path/to/WPS"
"wrf_install_path": "/path/to/WRF"
"sys_install_path": "/path/to/wrfxpy"
"wps_geog_path" : "/path/to/WPS-GEOG"
"wget" : /path/to/wget"

Note that all these paths are created from previous steps of this wiki unless wget path which needs to be specified. If not version of wget is prefered

which wget

Cluster configuration

Next, wrfxpy needs to know how jobs are submitted on your cluster. Create an entry for your cluster in etc/clusters.json, here we use speedy as an example:

{
  "speedy" : {
    "qsub_cmd" : "qsub",
    "qdel_cmd" : "qdel",
    "qstat_cmd" : "qstat",
    "qstat_arg" : "",
    "qsub_delimiter" : ".",
    "qsub_job_num_index" : 0,
    "qsub_script" : "etc/qsub/speedy.sub"
  }
}

And then the file etc/qsub/speedy.sub should contain a submission script template, that makes use of the following variables supplied by wrfxpy based on job configuration:

%(nodes)d the number of nodes requested
%(ppn)d the number of processors per node requested
%(wall_time_hrs)d the number of hours requested
%(exec_path)d the path to the wrf.exe that should be executed
%(cwd)d the job working directory
%(task_id)d a task id that can be used to identify the job
%(np)d the total number of processes requested, equals nodes x ppn

Note that not all keys need to be used, as shown in the speedy example:

#$ -S /bin/bash
#$ -N %(task_id)s
#$ -wd %(cwd)s
#$ -l h_rt=%(wall_time_hrs)d:00:00
#$ -pe mpich %(np)d
mpirun_rsh -np %(np)d -hostfile $TMPDIR/machines %(exec_path)s

The script template should be derived from a working submission script.

Note: wrfxpy has already configuration for colibri, gross, kingspeak, and cheyenne.

Tokens configuration

When running wrfxpy, sometimes the data needs to be accessed and downloaded using a specific token created for the user. For instance, in the case of running the Fuel Moisture Model, one needs a token from a valid MesoWest user to download data automatically. Also, when downloading satellite data, one needs a token from an Earthdata user. All of these can be specified with the creation of the file etc/tokens.json from the template etc/tokens.json.initial containing:

{
  "mesowest" : "token-from-mesowest",
  "appkey" : "token-from-earthdata"
}

So, if any of the previous capabilities are required, create a token from the specific page, do

cp etc/tokens.json.initial etc/tokens.json

and include your previously created token.

wrfxweb

Account creation

Create ~/.ssh directory (if you have not one)

mkdir ~/.ssh
cd ~/.ssh

Create an id_rsa key (if you have not one) doing

ssh-keygen

and following all the steps (you can select defaults, so always press enter).

Send an email to Jan Mandel (jan.mandel@gmail.com) asking for the creation of an account in demo server providing:

• Purpose of your request (including information about you)
• User id you would like (user_id)
• Short user id you would like (short_user_id)
• Public key (~/.ssh/id_rsa.pub file previously created)

After that, you will receive an answer from Jan and you will be able to ssh the demo server without any password (only the passcode from the id_rsa key if you set one).

Installation

Clone github repository

Clone wrfxweb in the demo server

ssh user_id@demo.openwfm.org
git clone https://github.com/openwfm/wrfxweb.git

Configuration

Change directory and copy template to create new etc/conf.json

cd wrfxweb
cp etc/conf.json.template etc/conf.json

Configure the following key in etc/conf.json:

"url_root": "http://demo.openwfm.org/short_user_id"

The next steps are going to be set in a desired installation of wrfxpy (generated in the previous section).

Configure the following keys in etc/conf.json in any wrfxpy installation

"shuttle_ssh_key": "/path/to/id_rsa"
"shuttle_remote_user": "user_id"
"shuttle_remote_host": "demo.openwfm.org"
"shuttle_remote_root": "/path/to/remote/storage/directory"
"shuttle_lock_path": "/tmp/short_user_id"

The "shuttle_remote_root" key is usually defined as "/home/user_id/wrfxweb/fdds/simulations". So, everything should be ready to send post-processing simulations into the visualization server.