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

OpenMalaria on NUCLUSTER

These instructions were adapted from the original setup notes by Scott Coughlin, who provided the module file and Singularity definition file.

Download and extract OpenMalaria i.e. v48

cd /gpfs/projects/b1139/OpenMalaria/  
wget https://github.com/SwissTPH/openmalaria/releases/download/schema-48.0/openMalaria-ubuntu-24.04.tar.gz  
tar -xvzf openMalaria-ubuntu-24.04.tar.gz  
rm openMalaria-ubuntu-24.04.tar.gz  
mv openMalaria-ubuntu-24.04 om_v48

Copy modules and definition file from previous version 

cp -r /gpfs/projects/b1139/OpenMalaria/om_v46/modules/ /gpfs/projects/b1139/OpenMalaria/om_v48/  
cp /gpfs/projects/b1139/OpenMalaria/OpenMalaria.def /gpfs/projects/b1139/OpenMalaria/om_v48/

Build the container on Quest using the remote Sylabs build environment 

module load singularity  
singularity remote login  
# If prompted:  
# An access token is already set for this remote. Replace it? [N/y] y   
# Generate an access token at: https://cloud.sylabs.io/auth/tokens   
# Paste it when prompted   

singularity build --remote OpenMalaria.sif OpenMalaria.def

Update the module file

Example module file (openmalaria/48.0.lua): 

help([[  
This git-repository contains source-code for OpenMalaria, a simulator program for studying malaria epidemiology and the impacts of interventions against malaria.
]]) 

local pkgName = "openmalaria"  
local version = "48.0"  

whatis("Name: " .. pkgName)  
whatis("Version: " .. version)  

depends_on("singularity") 

local bashStr = 'singularity exec -B /gpfs/projects:/gpfs/projects /gpfs/projects/b1139/OpenMalaria/om_v48/OpenMalaria.sif /openmalaria/openMalaria-48.0/openMalaria "$@"' 

set_shell_function("openMalaria", bashStr)