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To use and/or contribute to PyBaMM, you must have Python 3.6 or 3.7 installed (note that 3.8 is not yet supported).
To install Python 3 on Debian-based distribution (Debian, Ubuntu, Linux mint), open a terminal and run
sudo apt update
sudo apt install python3
On Fedora or CentOS, you can use DNF or Yum. For example
sudo dnf install python3
On Mac OS distributions, you can use homebrew. First install
``brew` <https://docs.python-guide.org/starting/install3/osx/>`__:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
then follow instructions in link on adding brew to path, and run
brew install python3
We recommend to install PyBaMM within a virtual environment, in order
not to alter any distribution python files. To create a virtual
environment env within your current directory type:
python3 -m venv env
You can then “activate” the environment using:
source env/bin/activate
Now all the calls to pip described below will install PyBaMM and its
dependencies into the environment env. When you are ready to exit
the environment and go back to your original system, just type:
deactivate
PyBaMM can be installed via pip:
pip install pybamm
PyBaMM’s dependencies (such as numpy, scipy, etc) will be
installed automatically when you install PyBaMM using pip.
For an introduction to virtual environments, see (https://realpython.com/python-virtual-environments-a-primer/).
Users can install scikits.odes in order to use the wrapped SUNDIALS ODE and DAE solvers.
A pre-requisite is the installation of a BLAS library (such as openblas). On Ubuntu/debian
sudo apt install libopenblas-dev
and on Mac OS
brew install openblas
After installing PyBaMM, the following command can be used to
automatically install scikits.odes and its dependencies
$ pybamm_install_odes --install-sundials
The --install-sundials option is used to activate automatic
downloads and installation of the sundials library, which is required by
scikits.odes.
If you wish to contribute to PyBaMM, you should get the latest version from the GitHub repository. To do so, you must have Git and graphviz installed. For instance run
sudo apt install git graphviz
on Debian-based distributions, or
brew install git graphviz
on Mac OS.
To install PyBaMM, the first step is to get the code by cloning this repository
git clone https://github.com/pybamm-team/PyBaMM.git
cd PyBaMM
Then, to install PyBaMM as a developer, type
pip install -e .[dev,docs]
KLU sparse solver If you wish so simulate large systems such as the 2+1D models, we recommend employing a sparse solver. PyBaMM currently offers a direct interface to the sparse KLU solver within Sundials, but it is unlikely to be installed as you may not have all the dependencies available. If you wish to install the KLU from the PyBaMM sources, see the instructions for compiling the KLU sparse solver.
To check whether PyBaMM has installed properly, you can run the tests:
python3 run-tests.py --unit
Before you start contributing to PyBaMM, please read the contributing guidelines.
PyBaMM can be uninstalled by running
pip uninstall pybamm
in your virtual environment.
Problem: I’ve made edits to source files in PyBaMM, but these are not being used when I run my Python script.
Solution: Make sure you have installed PyBaMM using the -e flag,
i.e. pip install -e .. This sets the installed location of the
source files to your current directory.
Problem: When running python run-tests.py --quick, gives error
FileNotFoundError: [Errno 2] No such file or directory: 'flake8': 'flake8.
Solution: make sure you have included the [dev,docs] flags when
you pip installed PyBaMM, i.e. pip install -e .[dev,docs]
Problem: Errors when solving model
ValueError: Integrator name ida does not exsist, or
ValueError: Integrator name cvode does not exsist.
Solution: This could mean that you have not installed
scikits.odes correctly, check the instructions given above and make
sure each command was successful.
One possibility is that you have not set your LD_LIBRARY_PATH to
point to the sundials library, type echo $LD_LIBRARY_PATH and make
sure one of the directories printed out corresponds to where the
sundials libraries are located.
Another common reason is that you forget to install a BLAS library such as OpenBLAS before installing sundials. Check the cmake output when you configured Sundials, it might say:
-- A library with BLAS API not found. Please specify library location.
-- LAPACK requires BLAS
If this is the case, on a Debian or Ubuntu system you can install
OpenBLAS using sudo apt-get install libopenblas-dev (or
brew install openblas for Mac OS) and then re-install sundials using
the instructions above.