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). In case you decide to use MicroHH for your own research, the developers would appreciate to be notified and kindly request to cite their reference paper. The version described in the reference paper has been assigned a DOI via Zenodo.

Requirements

In order to compile MicroHH you need:

• C++ compiler
• FFTW3 libraries
• Boost libraries
• NetCDF4
• CMake
• MPI2/3 implementation (optional for MPI support)
• CUDA (optional for GPU support)
• Python + numpy + python-netcdf4 (optional for running example cases)
• Ipython + python-netcdf4 + matplotlib (optional for plotting results example cases)

Downloading the code

Check out the code from GitHub using

git clone --recurse-submodules https://github.com/microhh/microhh.git

In case you had already checked out the repository without checking out the submodules, use:

git submodule update --init --recursive

Compilation of the code

First, enter the config directory:

cd config

Here, you find a potential series of settings with the extension .cmake for different systems. Check whether your system is there. If not, you can try the generic configuration (generic.cmake), or create a file with the correct compiler settings and the proper location for all libraries on your system. Then, copy your system file to default.cmake, for example:

cp generic.cmake default.cmake

Then, go back to the main directory and create a subdirectory with an arbitrary name in which you will compile the code. Let us assume this directory is called "build":

cd ..  
mkdir build  
cd build   

From this directory, run cmake with the suffix .. to point to the parent directory where the CMakeLists.txt is found. This builds the model without Message Passing Interface (MPI) and CUDA support, using double precision floating point numbers.

cmake ..

In case you prefer to enable either MPI, CUDA, or single precision (4 byte) floating point numbers, run cmake with the following flags:

cmake .. -DUSEMPI=TRUE

or

cmake .. -DUSECUDA=TRUE

or

cmake .. -DUSESP=TRUE

Some combinations are possible, such as:

cmake .. -DUSEMPI=TRUE -DUSESP=TRUE

However, the combination of -DUSEMPI with -DUSECUDA is not (yet) supported.

NOTE: once the build has been configured and you wish to change the USECUDA, USEMPI, or USESP setting, you must delete the content of the build directory, or create an additional empty directory from which cmake is run.)

With the previous command you have triggered the build system and created the make files, if the default.cmake file contains the correct settings. Now, you can start the compilation of the code and create the microhh executable with:

make -j 2

Your directory should contain a file named microhh now. This is the main executable.

Running an example case

To start one of the included test cases, go back to the main directory and open the directory cases. Here, a collection of test cases has been included. In this example, we start the drycblles case, a simple large-eddy simulation of a dry convective boundary layer.

cd cases/drycblles

First, we have to create the vertical profiles for our prognostic variables:

python drycblles_input.py

Then, we have to copy or link the microhh executable to the current directory. Here we assume the executable is in the build directory that we have created before.

cp ../../build/microhh .

Now, we can start microhh in initialization mode to create the initial fields:

./microhh init drycblles

If everything works out properly, a series of files has been created. The model can be started now following:

./microhh run drycblles

This will take some time. Now, a statistics file called drycblles.default.0000000.nc has been created. You can open this file with your favorite plotting tool, or run some example plots using the provided plotting script that uses Python and matplotlib. This is most easily done in interactive python:

ipython  
run drycbllesstats

This should show you a set of basic plots. Congratulations, you have just completed your first run of MicroHH.

Happy MicroHHing!

Contributing

If you are planning to contribute code to MicroHH, first of all: thanks! But please consider a few things:

• For eventual merging of contributions into the main code, we use the pull request feature of Github. For this, you need to make of fork of the MicroHH repository in your own Github account, and commit the changes there, before creating a pull request.
• If you plan to make major changes to the code or code structure, it might be wise to discuss them with the main MicroHH devs, for example by opening an issue on Github.
• We like to keep our code structured and clean, so please stick to the MicroHH coding conventions.
• Be careful with what you add and commit to Git. Accidentally adding/committing some large binaries or MicroHH executables is an easy mistake, but even if you later remove the files in a new commit, the files will stay in the history of the repository, making the repository unnecessary bloaty.

Current and previous contributors to MicroHH can be found here