Running MicroHH

Running MicroHH

MicroHH is a computational fluid dynamics code made for Direct Numerical Simulation (DNS) and Large-Eddy Simulation of turbulent flows in the atmospheric boundary layer. The code is written in C++.

A tutorial and documentation is available at: https://microhh.readthedocs.io/en/latest/.

MicroHH is described in detail in Van Heerwaarden et al. (2017).

Downloading the code

General information to download the code from GitHub can be found here: https://github.com/microhh/microhh/blob/main/README.md

For this tutorial, we will use Thijs’ fork, and in particular the lagtraj branch: git clone –recurse-submodules https://github.com/thijsheus/microhh.git

More details on how to compile and setup the code on your own can be found in the main README

Logging in to OSC

To run this tutorial, we first log in on the Ohio Super Computer through: ondemand.osc.edu and log in with the username that you got before the workshop.

From the side bar, select the Ascend Desktop to get in-browser access to the supercomputer.

Give the app a moment to start up, open it, and open a VNC window.

Quick Start to Running MicroHH

At the desktop, open a terminal and navigate to the summerschool folder:

cd /fs/project/PFS0220/summerschool

make your own folder, and copy all relevant data to your own folder:

cp template/* <yourname>/

and move to your own folder.

To submit a quick simulation to the supercomputer, you can submit a job to the queue: sbatch SGP.slurm

Changing the input parameters

The input parameters are in SGP.ini. Feel free to browse through and look at what can be easily changed. More info on individual options is available on https://microhh.readthedocs.io/en/latest/

After the simulation is done, you can evaluate the results, for instance with the analyze_microhh.ipynb script.

Selecting particular ERA5 use cases (Advanced and Experimental):

The eulerian_lagtraj.py code is based on the lagtraj Python package and pulls ERA5 data to drive the LES model. This is a bit too time consuming for the current tutorial, but the gist is as follows:

  1. Open config.yaml to set the location, time, name, etc. Note that you can elect to use a Eulerian (fixed in space) setup, or a Lagrangian (moving along with the atmospheric flow) setup. A Lagrangian setup over land is not recommended.

  2. Open SGP.ini.base to setup the case properties, such as domain size, grid points, etc. You can fill out None for anything that you want the system to decide

  3. Run the python script: python eulerian_lagtraj.py

  4. Initialize MicroHH following the instructions above.