Welcome to idmtools

idmtools is a collection of Python scripts and utilities created to streamline user interactions with disease models. This framework provides the user with tools necessary to complete projects, starting from the creation of input files (if required), to calibration of the model to data, to commissioning and running simulations, through the analysis of results. Modelers can use idmtools to run models locally or send suites of simulations to an HPC or other computing source. This framework is free, open-source, and model agnostic: it can be used to interact with a variety of models, such as custom models written in R or Python, or IDM’s own EMOD. Additional functionality for interacting with EMOD is provided in the emod_api package and emodpy package.

idmtools workflow

idmtools includes a variety of options for each step of the modeling process. Because of this, the tool suite was developed in a modular fashion, so that users can select the utilities they wish to use. In order to simplify the desired workflow, facilitate the modeling process, and make the model (and its results) reusable and sharable, idmtools allows the user to create assets. Assets can be added at any level of the process, from running a specific task, through creating a simulation, to creating a experiment. This allows the user to create inputs based on their specific needs: they can be transient, or sharable across multiple simulations.

The diagram below shows how idmtools and each of the related packages are used in an end-to-end workflow using EMOD as the disease transmission model.

Exact workflows for using idmtools is user-dependent, and can include any of the tasks listed below.

• Install
  • Basic installation
  • Developer installation
• Configure
  • Global parameters
  • Logging overview
  • idmtools.ini wizard
• Platforms
  • COMPS Platform
    • Configuration and options
    • Add to asset collection
    • Assetize outputs workitem
    • DownloadWorkItem
    • COMPS errors
    • COMPS scheduling
    • Singularity build
  • Slurm Platform
    • Configuration and options
    • Cancel jobs
    • Run script as Slurm job
  • Container Platform
    • ContainerPlatform Docker utilities
    • Container CLI commands
    • Examples for ContainerPlatform attributes
    • ContainerPlatform Docker image
  • Create platform plugin
• Simulations
  • Create simulation tags
  • Create EMOD simulations
• CLI
  • CLI COMPS Platform
    • Templates
    • CLI examples
    • Troubleshooting
  • CLI Slurm Platform
    • CLI Slurm examples
  • CLI Container Platform
    • Container CLI commands
• Singularity
  • Services on COMPS with containers
  • Container builder service
  • Using Singularity in COMPS
• Parameter sweeps and model iteration
  • Running parameter sweeps with Python models
  • Running parameter sweeps with EMOD
• Output data
• Introduction to analyzers
  • Example analyzers
    • Force working directory
    • Partial analysis
  • Create an analyzer
  • Using analyzers with SSMT
  • Convert analyzers from DTK-Tools
    • DTK-Tools example analyzer
    • DTK-Tools converted to idmtools
• Plot data
• Architecture and packages reference
  • idmtools
    • idmtools package
  • idmtools_models
    • idmtools_models package
  • idmtools_platform_comps
    • idmtools_platform_comps package
  • idmtools_platform_slurm
    • idmtools_platform_slurm package
  • idmtools_slurm_utils
    • idmtools_slurm_utils package
  • idmtools_platform_container
    • idmtools_platform_container package
• Plugin documentation
  • ID generation plugins
• User recipes
  • Asset collections
  • Builders
  • COMPS recipes
    • Assetize outputs
    • SSMT recipes
  • Environment
  • Experiments
  • Logging
  • Python
• Convert scripts from DTK-Tools
• FAQ
• Glossary
• Changelog
  • 2.0.1
  • 2.0.0
  • 1.7.11
  • 1.7.10
  • 1.7.9
  • 1.7.8
  • 1.7.7
  • 1.7.6
  • 1.7.5
  • 1.7.4
  • 1.7.3
  • 1.7.1
  • 1.7.0
  • 1.6.7
  • 1.6.6
  • 1.6.5
  • 1.6.4
  • 1.6.3
  • 1.6.2
  • 1.6.1
  • 1.6.0
  • 1.5.2
  • 1.5.1
  • 1.5.0
  • 1.4.0
  • 1.3.0
  • 1.2.2
  • 1.2.0
  • 1.1.0
  • 1.0.1
  • 1.0.0
  • 0.1.0