Quickstart Guide: Shardian Atmos
This guide describes how to configure and execute meteorological simulations in the WRF mesoscale model using the coupled boundary layer solver Shardian Atmos (shardian_atmos.sif).
1. Singularity/Apptainer Containerized Architecture
To eliminate dependency conflicts involving compilers, MPI versions, and NetCDF libraries, Shardian Atmos is distributed as a self-contained static Singularity image (shardian_atmos.sif).
The installer creates a global wrapper script on your system: shardian_atmos. This command dynamically forwards the execution call to the Singularity engine, mounting your current working directory and executing wrf.exe inside the container environment.
2. Running a Local Simulation (Single Core)
To run a basic WRF simulation on your local machine, navigate to your case directory (where your namelist.input, wrfinput_d01, and wrfbdy_d01 files are located) and run:
This is equivalent to calling Singularity directly from your terminal:
3. Distributed Parallel Execution (HPC / MPI)
In high-performance computing (HPC) environments or mesoscale clusters, Shardian Atmos interfaces with the parallel communication message-passing interface (MPI) installed on the host cluster.
You should wrap the Singularity call with mpirun or srun, specifying the path to the container and the target executable (wrf.exe):
Example SLURM Batch Script:
#!/bin/bash
#SBATCH --job-name=wrf_shardian
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=16
#SBATCH --time=12:00:00
#SBATCH --partition=compute
module load openmpi/4.1.2
# Execute WRF in parallel across 64 distributed cores
mpirun -np 64 singularity exec /usr/local/bin/shardian_atmos.sif wrf.exe
[!IMPORTANT] MPI Version Matching: The Shardian Atmos container is compiled against OpenMPI v4.1.2. For optimal parallel communication and to avoid interconnect messaging delays, the MPI library loaded in your HPC cluster environment should match this version.
4. Required Input Files
The solver expects to find the following files inside your current working directory when executed:
1. namelist.input (WRF physics, domain, and time control file).
2. wrfinput_d01 (Initial conditions field generated by real.exe).
3. wrfbdy_d01 (Lateral boundary conditions generated by real.exe).
4. Standard WRF physics and radiation tables (preconfigured and symbolic-linked inside /wrf/run/ inside the container, but overridable locally).