test_vivarium_research_template

Package to test vivarium research template updates.

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=test_vivarium_research_template python=3.8
...conda will download python and base dependencies...
:~$ conda activate test_vivarium_research_template
(test_vivarium_research_template) :~$ git clone https://github.com/ihmeuw/test_vivarium_research_template.git
...git will copy the repository from github and place it in your current directory...
(test_vivarium_research_template) :~$ cd test_vivarium_research_template
(test_vivarium_research_template) :~$ pip install -e .
...pip will install vivarium and other requirements...

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:

(test_vivarium_research_template) :~$ conda install hdf5

The (test_vivarium_research_template) 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/test_vivarium_research_template 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 test_vivarium_research_template 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

With your conda environment active, the first step to running simulations is making the model specification files. A model specification is a complete description of a vivarium model. The command to generate model specifications is installed with this repository and it can be run from any directory.:

(test_vivarium_research_template) :~$ make_specs -v
2020-06-18 18:18:28.311 | 0:00:00.679701 | build_model_specifications:48 - Writing model spec(s) to "/REPO_INSTALLATION_DIRECTORY/test_vivarium_research_template/src/test_vivarium_research_template/model_specifications"

As the log message indicates, the model specifications will be written to the model_specifications subdirectory in this repository. You can then run simulations by, e.g.:

(test_vivarium_research_template) :~$ simulate run -v /<REPO_INSTALLATION_DIRECTORY>/test_vivarium_research_template/src/test_vivarium_research_template/model_specifications/china.yaml

The -v 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