Updating Malaria Models in MultiMalModPy

This guide describes how to update EMOD, malariasimulation, and OpenMalaria versions in MultiMalModPy, including dependency handling, configuration updates, and validation steps.

⚠️ If you’re updating any model version, you must also review the changes in manifest.py, containers (Docker/Singularity), and the documentation.

General Update Workflow

  1. Update or install the new version of the model or its dependencies.
  2. Adjust manifest.py to reflect new supported version ranges or paths.
  3. Rebuild containers if used (Docker/Singularity).
  4. Validate backward compatibility with existing configurations.
  5. Update the Simulation Guide and Changelog.

EMOD

EMOD is installed via pip from IDM’s private PyPI, and optionally uses a pre-built .sif image for HPC execution.

Follow the Installation Guide and run:

pip install emodpy-malaria==<new_version> --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple pip install idmtools[slurm] --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple

Test using: 

python launch_sim.py --models EMOD --test

Document Changes Update Simulation Guide sections related to EMOD behavior, parameter sets, or performance changes.

malariasimulation

  • Update R version if required
  • Update versions in dependencies/install_packages.R
  • Update R package: via
  • source("dependencies/install_packages.R")
  • remotes::install_github(“mrc-ide/malariasimulation”)
  • Update manifest.py with supported versions and R_PATH

Test using: 

python launch_sim.py --models malariasimulation --test

OpenMalaria

  • Follow the installation instructions , and place files under: dependencies/OpenMalaria/om_v<NEW_VERSION>
  • If on HPC (NUCLUSTER), edit modules/openmalaria/<version>.lua.
  • Update manifest.py
  • OPENMALARIA_PATH = “/gpfs/projects/…/om_v46”
  • OPENMALARIA_SUPPORTED_VERSIONS = [“v43”, “v46”] # Add latest version

Test using: 

python launch_sim.py --models OpenMalaria --test