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WRF-Chem
Overview
WRF-Chem is the Weather Research and Forecasting (WRF) model coupled with Chemistry. The model simulates the emission, transport, mixing, and chemical transformation of trace gases and aerosols simultaneously with the meteorology. The model is used for investigation of regional-scale air quality, field program analysis, and cloud-scale interactions between clouds and chemistry.
Versions 3.8 and 3.4.1 are installed on the CSF.
Compilation information
3.8
WPS + WRF-Chem and their dependency libraries were compiled using Intel 15.0, using the following compiler flags:
-w -O3 -ip -msse2 -axSSE4.2,AVX,CORE-AVX2
See here for further detail about how this version was compiled.
3.4.1/water_n2o5het_bburn
WPS + WRF-Chem and their dependency libraries were compiled using Intel 15.0, using the following compiler flags:
-w -O3 -ip -xCORE-AVX2
See here for further detail about how this version was compiled
Restrictions on use
None – Public domain software.
Set up procedure
To access the software you must first load the appropriate modulefile (if you’re unsure, you probably want the first one):
module load apps/intel-15.0/WRF-Chem/3.8 module load apps/intel-15.0/WRF-Chem/3.4.1/water_n2o5het_bburn
Settings applied by the WRF-Chem modulefile
The WRF-Chem modulefiles will automatically load the following modulefiles, which indicate the dependencies used when compiling WRF-Chem:
compilers/intel/c/15.0.3 compilers/intel/fortran/15.0.3 mpi/intel-15.0/openmpi/1.8.3-ib libs/intel-15.0/hdf/5/1.8.16 libs/intel-15.0/zlib/1.2.8 libs/intel-15.0/netcdf/4.4.0
Running the application
Please do not run WRF-Chem on the login node. Jobs should be submitted to the compute nodes via batch.
Important: you must run WRF-Chem in your scratch directory, not your home directory. WRF-Chem input and output files can be large and you can generate lots of them. You will very likely fill up the home filesystem which is shared with other members of your group. This will cause your jobs and other users’ jobs to fail – resulting in very unhappy colleagues! Please run in scratch. Any important results (and small input/config files such as namelist files and batch jobscripts) can be copied back to home for safe-keeping (home is backed up, scratch is not).
Loading the modulefile gives you an environment variable WRF_CHEM_RUN_DIR, which points to the run directory in the WRF-Chem installation. You should copy the files in this directory into your run directory e.g.
cp $WRF_CHEM_RUN_DIR your_scratch/run_dir
Your run directory should also contain your case-specific input files.
The WRF-Chem and WPS executables were built as dmpar executables during WRF config (i.e. they use MPI). The following are available:
- In
$WRF_DIR/run/: ndown.exe, nup.exe, real.exe tc.exe wrf.exe - In
$WPS_DIR/: geogrid.exe, metgrid.exe, ungrib.exe(this one is not an MPI executable)
3.8
This version of WRF-Chem has been compiled to run on any of the Intel nodes. WRF-Chem has been compiled for Real cases (dmpar – Distributed Memory PARallelism), with basic nesting and the Kinetic Pre-Processor (KPP). As such all “out of the box” chemistry schemes are included.
3.4.1/water_n2o5het_bburn
This version of WRF-Chem has been compiled to run on haswell nodes only. WRF-Chem has been compiled for Real cases (dmpar – Distributed Memory PARallelism), with basic nesting and the Kinetic Pre-Processor (KPP). It includes chemistry schemes written by members of the Gordon McFiggans’ research group in the Centre For Atmospheric Science.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script. An example job submission script is already in the $WRF_CHEM_RUN_DIR directory. You should modify this script for your own use. The contents of the job script are similar to the example below:
#!/bin/bash #$ -S bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -N wrfchem_job # Give the job a name of your choosing ##### Multi-node MPI ##### #$ -pe orte-24-ib.pe 48 -l haswell mpirun -n $NSLOTS ./wrf.exe # $NSLOTS is automatically set to number of cores
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
- WRF-Chem website
- How to modify chemistry schemes (This will require you to recompile WRF-Chem)
Updates
None.