Building with the MOOSE Conda Environment

1. Installing the MOOSE Environment

Gnat is a MOOSE-based application, and therefore requires an appropriate MOOSE environment. More detailed instructions for installing Mambaforge3 (a dependency manager) can be found on the MOOSE installation page. You can install Mambaforge3 with the following shell commands:

Linux:

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
bash Mambaforge-Linux-x86_64.sh -b -p ~/mambaforge3

Macintosh without Apple Silicon:

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-MacOSX-x86_64.sh
bash Mambaforge-MacOSX-x86_64.sh -b -p ~/mambaforge3

Macintosh with Apple Silicon:

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-MacOSX-arm64.sh
bash Mambaforge-MacOSX-arm64.sh -b -p ~/mambaforge3

Once Mambaforge3 has been installed for your platform of choice, you need to configure it to add the MOOSE environment. To do so, add Mambaforge3 to your system PATH:

export PATH=$HOME/mambaforge3/bin:$PATH

Then, add the INL public channel:

conda config --add channels https://conda.software.inl.gov/public

Finally, initialize the Mambaforge3 shell:

mamba init

and create+install the MOOSE environment:

conda create -n moose moose-dev=2025.05.13=mpich
conda activate moose

This will take some time, so feel free to walk away and get yourself a coffee (or other beverage of your choice). Once it's complete deactivate your MOOSE environment to ensure the installation is applied.

mamba deactivate

After the installation is finished you can move on to cloning Gnat and MOOSE.

2. Cloning Gnat and MOOSE

Gnat comes with the MOOSE framework included as a Git submodule. For users who wish to develop applications alongside Gnat, use other sub-applications of Caribou, or use other MOOSE applications: it's advised that you install MOOSE separately. This can be done by following all of the detailed instructions on the MOOSE installation page.

For users who only wish to use Gnat:

git clone https://github.com/OTU-Center-for-SMRs/gnat.git
cd gnat
git submodule update --init moose

For users who want to develop/use other MOOSE applications:

git clone https://github.com/OTU-Center-for-SMRs/gnat.git

Before continuing with the compilation process, ensure that the MOOSE environment has been activated:

mamba activate moose

Once you're in the Gnat directory and have activated your MOOSE environment, proceed to the next step.

3. Getting Cardinal

Gnat allows for neutronics coupling with the continuous-energy Monte Carlo code OpenMC through Cardinal. If you don't want to build with Cardinal, you can skip this step. If you want to build Gnat with Cardinal, you need to update the Cardinal submodule and fetch it's dependencies:

git submodule update --init cardinal
./cardinal/scripts/get-dependencies.sh

In addition to fetching Cardinal's dependencies, you'll need to export the following environment variables:

# [REQUIRED] for builds with Cardinal
export ENABLE_CARDINAL=yes

# [REQUIRED WHEN USING THE MOOSE CONDA ENVIRONMENT] you must set the location of the
# root HDF5 directory provided by MOOSE for OpenMC to find
export HDF5_ROOT=$CONDA_PREFIX

# [REQUIRED ON SOME SYSTEMS] for some systems, libraries won't be linked properly unless
# you explicitly point this variable. We're working on a more elegant fix.
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH

# [OPTIONAL] it's a good idea to explicitly note that you are using MPI compiler wrappers
export CC=mpicc
export CXX=mpicxx
export FC=mpif90

# [REQUIRED WHEN RUNNING OPENMC] you will need cross section data at runtime;
# ythis variable must be set to point to a 'cross_sections.xml' file.
export OPENMC_CROSS_SECTIONS=${HOME}/cross_sections/endfb-vii.1-hdf5/cross_sections.xml

4. Building and Testing Gnat

To build Gnat, you can use the make buildsystem:

make -j{NUM_PROCESSES}

Where {NUM_PROCESSES} is the number of concurrent processes you want building both Gnat and the MOOSE framework. You may also compile a debug version of Gnat by running METHOD=dbg make -j{NUM_PROCESSES}.

Finally, run all tests to ensure that Gnat has been built successfully:

./run_tests -j{NUM_THREADS}

Where {NUM_THREADS} is the number of threads you want running tests.

5. Run Simulations

Gnat simulations use the hierarchical input text (HIT) input deck specification designed by INL for MOOSE-based applications. More information about HIT syntax can be found in the MOOSE tutorials. Gnat input decks can be executed with the following shell command:

./gnat-opt -i input-file.i

Replace input-file.i with the name of your input file. Gnat can be executed in parallel using MPI and the following shell command:

mpirun -n{NUM_THREADS} ./gnat-opt -i input-file.i

Where {NUM_THREADS} is the number of threads you want executing the input deck.

Now that Gnat has been successfully installed and tested, feel free to check out the tutorials to learn how to write a Gnat input deck.