Getting Started
Initialising and Startup
1. Install OpenCOR
Download and install OpenCOR version 0.8.1 from this link. I recommend installing with zip/tarball in a directory where you have access and edit rights, such as ~/Desktop.
Note
If you are not familiar with OpenCOR, you should go through the OpenCOR Tutorial before starting this
Download the OpenCOR tutorial, which is a comprehensive tutorial including many examples: OpenCOR Tutorial.
2. Clone the project
Clone the Circulatory Autogen project from the GitHub repository.
Note
If you have not worked with git and GitHub, firstly download and install git, and then open the terminal and navigate (with terminal in Linux/Mac or gitbash in Windows) to a directory where you want the repository to be. Then write these commands to clone the project on your pc:
git clone https://github.com/FinbarArgus/circulatory_autogen
If you want to develop the code, then create a fork of the above repo in GitHub, then do the following lines instead of the above:
-
git clone https://github.com/<YourUsername>/circulatory_autogen -
git remote add upstream https://github.com/FinbarArgus/circulatory_autogen
Directory Definition
In this tutorial, we define the project_dir as the directory where the Github Circulatory Autogen project has been cloned. For example, on our computer, this directory is as below:
[project_dir]: ~/Documents/git_projects/Circulatory_autogen
Also, the OpenCOR directory is needed for installing the necessary python libraries, which we defined as the OpenCOR_dir, e.g.:
[OpenCOR_dir]: ~/Desktop/OpenCOR-0-8-1-Linux/
Info
If running on the ABI HPC, you can use the installed OpenCOR version at the path: /hpc/farg967/OpenCOR-0-8-1-Linux/ and Ignore the below installation steps, as the libraries are already installed. See running on hpc
Python and Libraries Installation
To run openCOR, you need to use the Python version that is shipped with openCOR.
To install required python packages, navigate to [OpenCOR_dir] directory and run the below command.
Note
./pip install <packagename>
./pythonshell -m pip install <packagename>
./pythonshell.bat -m pip install <packagename>
Note
Required packages for autogeneration: pandas pyyaml rdflib
Recommended (but not required) packages for autogeneration (allows for better error checking): libcellml
Required packages for parameter identification: mpi4py sympy
Required packages for mcmc bayesian identification: emcee corner schwimmbad tqdm statsmodels
Required for some utilities: ruamel.yaml
Setting up your python path
Open [project_dir]/user_run_files/opencor_pythonshell_path.sh file and change the opencor_pythonshell_path to the directory of pythonshell in the OpenCOR_dir:
Note
opencor_pythonshell_path=`<OpenCOR_dir>/pythonshell`.
opencor_pythonshell_path=`C:\<OpenCOR_dir>\pythonshell.bat`.
Note that the windows path conventions need to be used with C: and "\ rather than "/".
Note
This tutorial assumes you will be running .sh commands (if you're on Windows, you should download gitbash from here so that you can run the bash scripts).
However, alternatively (especially if you want to debug), you can use an IDE of your choice, set the python path equal to the opencor_pythonshell_path and run the python scripts that are called to within the bash scripts (open the relevent .sh file to find the corresponding python script name). The scripts are located at project_dir]/src/scripts/
Warning
Installing mpi4py requires mpi to be available. Therefore, the following lines may be required to install the mpi software on your computer.
sudo apt install libopenmpi-dev
sudo apt install libffi7
brew install openmpi
''' To be able to import mpi4py, you may have to do the following:
Download MS MPI, install both .mis and SDK.
Set up environmental variables. Open Control Panel and select Advanced System Settings. Then select Environmental Variables and add the following.
C:\Program Files\Microsoft MPI\
C:\Program Files (x86)\Microsoft SDKs\MPI\
'''
Warning
In versions of OpenCOR < 0.8 you needed to nagivate to the [OpenCOR_dir]/python/bin directory and run the below command instead.
./python -m pip install <packagename>
Warning
For OpenCOR < 0.8 if you get an SSL error you must do the following before the pip install:
cd [OpenCOR_dir]/python/bin
export LD_LIBRARY_PATH=[OpenCOR_dir]/lib
This would let the system know where to look for libcrypto.so.3 when loading the ssl module.
Changes to be made
Currently vessels is used interchangeabley with modules. This will be changed to use modules in all instances, as the project now allows all types of modules, not just vessels.
The connections between terminals and the venous system is hardcoded, as a terminal_venous_connection has to be made to sum up the flows and get an avergae concentration. This is being improved in development.