vivarium_nih_us_cvd

Cite as: Rajan Mudambi, Steve Bachmeier, Hussain Jafari, Kjell Swedin, Matthew Kappel, Sylvia Lutze, Alison Bowman, Caroline Kinuthia, & Abraham Flaxman. (2024). ihmeuw/vivarium_nih_us_cvd: Archival release (v1.0). Zenodo. https://zenodo.org/doi/10.5281/zenodo.10671674

Research repository for the vivarium_nih_us_cvd project.

Contents

• Installation
• Usage
• Running Simulations

Installation

You will need git, git-lfs and conda to get this repository and install all of its requirements. You should follow the instructions for your operating system at the following places:

• git
• git-lfs
• conda

Once you have all three installed, you should open up your normal shell (if you're on linux or OSX) or the git bash shell if you're on windows. You'll then make an environment, clone this repository, then install all necessary requirements as follows:

:~$ conda create --name=vivarium_nih_us_cvd python=3.11
...conda will download python and base dependencies...
:~$ conda activate vivarium_nih_us_cvd
(vivarium_nih_us_cvd) :~$ git clone https://github.com/ihmeuw/vivarium_nih_us_cvd.git
...git will copy the repository from github and place it in your current directory...
(vivarium_nih_us_cvd) :~$ cd vivarium_nih_us_cvd
(vivarium_nih_us_cvd) :~$ pip install -e .
...pip will install vivarium and other requirements...

Supported Python versions: 3.9, 3.10, 3.11

Note the -e flag that follows pip install. This will install the python package in-place, which is important for making the model specifications later.

Cloning the repository should take a fair bit of time as git must fetch the data artifact associated with the demo (several GB of data) from the large file system storage (git-lfs). If your clone works quickly, you are likely only retrieving the checksum file that github holds onto, and your simulations will fail. If you are only retrieving checksum files you can explicitly pull the data by executing git-lfs pull.

Vivarium uses the Hierarchical Data Format (HDF) as the backing storage for the data artifacts that supply data to the simulation. You may not have the needed libraries on your system to interact with these files, and this is not something that can be specified and installed with the rest of the package's dependencies via pip. If you encounter HDF5-related errors, you should install hdf tooling from within your environment like so:

(vivarium_nih_us_cvd) :~$ conda install hdf5

The (vivarium_nih_us_cvd) that precedes your shell prompt will probably show up by default, though it may not. It's just a visual reminder that you are installing and running things in an isolated programming environment so it doesn't conflict with other source code and libraries on your system.

Usage

You'll find six directories inside the main src/vivarium_nih_us_cvd package directory:

• artifacts

  This directory contains all input data used to run the simulations. You can open these files and examine the input data using the vivarium artifact tools. A tutorial can be found at https://vivarium.readthedocs.io/en/latest/tutorials/artifact.html#reading-data

• components

  This directory is for Python modules containing custom components for the vivarium_nih_us_cvd project. You should work with the engineering staff to help scope out what you need and get them built.

• data

  If you have small scale external data for use in your sim or in your results processing, it can live here. This is almost certainly not the right place for data, so make sure there's not a better place to put it first.

• model_specifications

  This directory should hold all model specifications and branch files associated with the project.

• results_processing

  Any post-processing and analysis code or notebooks you write should be stored in this directory.

• tools

  This directory hold Python files used to run scripts used to prepare input data or process outputs.

Running Simulations

You can run your simulation from the command line. With your conda environment active, you can run with, e.g.:

(vivarium_nih_us_cvd) :~$ simulate run -vvv /<REPO_INSTALLATION_DIRECTORY>/vivarium_nih_us_cvd/src/vivarium_nih_us_cvd/model_specifications/nih_us_cvd.yaml -o /FILE/PATH/TO/SAVE/RESULTS -i src/vivarium_nih_us_cvd/artifacts/<STATE_NAME>.hdf

The simulation will run in one location at a time, enter the state you wish to run the simulation for in your call. The state name should be in lower case with an underscore between words. For example 'alabama', 'new_jersey' and 'district_of_columbia'.

The -vvv flag will log verbosely, so you will get log messages every time step. For more ways to run simulations, see the tutorials at https://vivarium.readthedocs.io/en/latest/tutorials/running_a_simulation/index.html and https://vivarium.readthedocs.io/en/latest/tutorials/exploration.html