HemeLB Setup Instructions

For the most comprehensive and updated information, refer to the full documentation.

2. Installation Steps

Step 1: Install Required Packages

sudo apt-get install cmake-curses-gui
sudo apt install cmake build-essential
sudo apt install libopenmpi-dev openmpi-bin
sudo apt-get install libtinyxml-dev
sudo apt install libboost-all-dev
sudo apt install libcgal-dev

Step 2: Clone and Configure HemeLB

git clone https://github.com/hemelb-codes/hemelb.git
cd hemelb
mkdir build && cd build
ccmake ..

During the CMake configuration, replace the broken Parmetis tarball URL with:

https://karypis.github.io/glaros/files/sw/parmetis/parmetis-4.0.2.tar.gz

Press c to configure, update any necessary values, then press c again and finally g to generate build files.

Step 3: Build the Project

make        # or use make -j4 for parallel build

Use sudo if you encounter permission errors.

3. Post-Installation Verification

Check if the binary is accessible via:

which hemelb

If not, you may need to add the binary directory to your system's PATH environment variable.

4. Geometry and Python Tool Setup

Step 1: Install Geometry Tool Dependencies

Download the required environment file hemelb-geometry-python-env.txt and create the environment:

conda create --name gmy-tool --file hemelb-geometry-python-env.txt --yes

Step 2: Install Python Tools

cd hemelb/python-tools
pip install .

Step 3: Install Geometry Tool (GUI)

cd ../geometry-tool
pip install '.[gui]'

Optional: Fix for VMTK Detection Error

If vmtk is installed but not detected, either:

Edit geometry-tool/setup.py and comment out the VMTK dependency line
Or follow Appendix 5.3 in the documentation.

Re-run the installation afterwards:

pip install '.[gui]'

Step 4: Validate Installation

pip install pytest
hemelb-tests

Ensure the tests complete successfully without errors. Look for output confirming that all tests passed.