Short Installation instructions¶
Starting BEAT v2.0.0 can be installed on any Unix based system with python>=3.9 that supports its prerequisites. Earlier versions must be installed on python3.8!
Please consider to use virtual environments to lower the risk of package conflicts.
Install and create a virtual environment¶
Install the virtual environment package:
sudo apt install python-venv
Create a directory virtualenvs where you want to keep your virtual environments, e.g. in user home:
cd ~
mkdir virtualenvs
cd virtualenvs
Create new environment e.g. beat_env using python3.11 (for other version just change the number e.g.: python3.9) and activate it:
python3.11 -m venv beat_env
source ~/virtualenvs/beat_env/bin/activate
The environment can be (later) deactivated NOT NOW!, with:
deactivate
Now we have created the beat_env environment into which we will install all the needed packages. Thus, we can avoid potential versioning conflicts with other packages.
Install beat, latest release¶
In the activated environment we install the latest release of beat through the package manager pip:
pip3 install beat
Install beat from source (github)¶
Please make sure to activate your virtual environment! e.g.:
source ~/virtualenvs/beat_env/bin/activate
Get the development version through the github repository:
cd ~/src # or wherever you keep the packages
git clone https://github.com/hvasbath/beat
cd beat
# get feature branch from online repository and create local branch
git fetch origin feature_branch_name:feature_branch_name
# switch to branch "feature_branch_name" locally
git checkout feature_branch_name
git pull origin feature_branch_name
pip3 install -e .
Once the development headers are installed. Only switching between gitbranches- is enough.:
git checkout $branch_name
Optional Dependencies¶
For using the BEM module¶
The new Boundary Element Modeling (BEM) module requires extra dependencies (and dependencies within):
pygmsh
cutde
To install pygmsh:
[sudo] apt install python3-gmsh # this will be a system wide installation of gmsh
pip install pygmsh # this will install the python abstraction library around gmsh
To install cutde:
pip install cutde
This will be sufficient to run cutde on the CPU using its C++ backend. However, that will render sampling slow to the point that it is not useful. In order to use the BEM module of BEAT for sampling a GPU is required. Install instructions for installing the GPU depending on your system architecture for cutde are here.
For using the PT sampler¶
For the Parallel Tempering (PT) algorithm OpenMPI and the python bindings are required. If you do not have any MPI library installed, this needs to be installed first.:
[sudo] apt install openmpi-bin libopenmpi-dev
Finally, the python wrapper:
pip3 install mpi4py
If a particular mpi version is required, they can be listed with the command:
apt-cache madison libopenmpi-dev
To install openmpi for a specific version for example version 2.1.1-8:
[sudo] apt install openmpi-bin=2.1.1-8 libopenmpi-dev=2.1.1-8 -V
Greens Function calculations¶
To calculate the Greens Functions we rely on modeling codes written by Rongjiang Wang. If you plan to use the GreensFunction calculation framework, these codes are required and need to be compiled manually. The original codes are packaged for windows and can be found here.
For Unix systems the codes had to be repackaged.
The packages below are also github repositories and you may want to use “git clone” to download:
git clone <url>
This also enables easy updating for potential future changes.
For configuration and compilation please follow the descriptions provided in each repository respectively.