vivarium-cluster-tools 1.0.6

A set of tools for running simulation using vivarium on cluster.

This package includes a tool that allows vivarium users to run simulations based on multiple scenarios conveniently. It requires an access to IHME cluster. To install this package, create or edit a file called ~/.pip/pip.conf which looks like this:

[global]

extra-index-url = http://dev-tomflem.ihme.washington.edu/simple

trusted-host = dev-tomflem.ihme.washington.edu

This file tells the pip package management system to check with IHME’s internal pypi server for packages.

You can then install this package with

> source activate <env-name>

> pip install vivarium-cluster-tools

In addition, this tool needs redis client and cython.

> conda install redis cython

How to use

The Vivarium ecosystem uses YAML configuration files throughout, including vivarium-cluster-tools. To run the multiple scenarios, you need to make a separate branch file (YAML) in addition to a usual vivarium model specification YAML file. You can specify how to vary a certain parameter in this branch file. For example,

input_draw_count: 25
random_seed_count: 10

branches:
  - intervention_name:
       intervention_coverage: [0, 1]
       efficacy: [0, .5, 1]

This branch shows that you want to have 25 different input draws, 10 different random seeds and 2 different intervention coverages and 3 different intervention efficacy. This implies 25*10*2*3=1500 different simulation scenarios. You can run all 1500 simulations by

psimulate run /path/to/your/model_configuration /path/to/your/branch_file

As an optional parameter, you can specify the name of project as well as result directory to save the outputs and logs. To specify those optional arguments,

psimulate run /path/to/your/model_configuration /path/to/your/branch_file -p project_name -o /path/to/output/

If your psimulate run has any failed jobs from the previous runs, you can restart failed jobs by specifying which output directory includes the partially completed jobs by,

psimulate restart /path/to/the/previous/results/