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Parallel MODFLOW Course

WSL and Parallel MODFLOW

Instructions are provided here for setting up Ubuntu on the Windows Subsystem for Linux (WSL) to work with MODFLOW.

Installing WSL

On a Windows machine it is relatively easy to get parallel MODFLOW compiled and running in a WSL Ubuntu virtual machine.

Install a latest version of Ubuntu.

  wsl --install -d Ubuntu-22.04

You will be asked to provide a username and password. You'll need to remember this information for some future sudo operations.

Firewall Considerations

If you are on a networked computer behind a firewall, you may need to take additional steps at this point to configure WSL to handle SSL intercept requirements. If your computer is on the USGS internal network, or needs to be, then there are a specific set of instructions that must be run before continuing. These instructions are located in a file called usgs_wsl_security.txt.

Installing Miniconda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh -b
eval "$(/home/langevin/miniconda3/bin/conda shell.bash hook)"
conda init
exit

The exit command will close the Ubuntu shell. At this point, you will need to restart the shell, which you can typically find through the Windows Start button, to allow the miniconda installation to complete.

Cloning MODFLOW Resources from GitHub

The next step is to clone the GitHub repositories for MODFLOW 6 and the MODFLOW 6 parallel class.

git clone https://github.com/jdhughes-usgs/parallel-modflow6-class.git
git clone https://github.com/MODFLOW-USGS/modflow6.git

Installing the mf6pro Conda Environment

Next, you will create a conda environment, called mf6pro, that will be used for thie class. The mf6pro environment will have all of the software needed to compile serial and parallel versions of MODFLOW 6, and the Python packages needed to pre- and post-process MODFLOW models.

The steps for creating the mf6pro conda environment are as follows

conda env create -f ./parallel-modflow6-class/environment/flopy_environment.yml -f ./parallel-modflow6-class/environment/mf6_environment.yml

In order to run jupyter notebooks, it will also be necessary to install jupyter. Activate the mf6pro conda environment and then install jupyter from the conda-forge channel, as shown with the following commands.

conda activate mf6pro
conda install -c conda-forge jupyter jupyterlab

Note that you may have to type Y to continue the conda install of jupyter packages.

Building MODFLOW

cd modflow6
meson setup builddir -Ddebug=false -Dparallel=true --prefix=$(pwd) --libdir=bin
meson install -C builddir
meson test --verbose --no-rebuild -C builddir

If everything is working properly, then the last command should show that the tests completed ok and without errors.

To make this new MODFLOW 6 executable available for future simulations, add a symbolic link to the newly compiled version of mf6 (./bin/mf6) from the mf6pro bin folder (~/miniconda3/envs/mf6pro/bin).

ln ./bin/mf6 ~/miniconda3/envs/mf6pro/bin/mf6