/dtk-tools

Facilitating DTK disease model configuration, submission, and analysis

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Documentation is currently being updated.

Older developer-written docs are available at: http://institutefordiseasemodeling.github.io/dtk-tools Docs currently under construction are available at: https://institutefordiseasemodeling.github.io/Documentation/dtk-tools/index.html

The dtk package is intended to strengthen and simplify the interaction between researchers and the EMOD model.

Modules contained in this package are intended to:

  • Empower the user to configure diverse simulations and arbitrarily complex campaigns built up from a standardized library of configuration fragments and utility functions;
  • Facilitate transparent switching between local and remote HPC commissioning, job-status queries, and output analysis;
  • Enable the configuration of arbitrary collections of simulations (e.g. parameteric sweeps) through an extensible library of builder classes;
  • Collect a library of post-processing analysis functionality, e.g. filtering, mapping, averaging, plotting.

Recommended Installation steps

Make sure you have Python 3.6 x64 installed (available here).

Install python virtualenv:

> pip install virtualenv

Create a python virtual environment:

> virtualenv idmtools

Activate the virtual environment, on Windows:

> cd idmtools\Scripts
> activate

On unix platform:

> cd idmtools/bin
> ./activate

Create a pip.ini file (pip.conf if on Unix) in your virtual environment folder (here idmtools) with the following content:

[global]
index-url = https://packages.idmod.org/api/pypi/pypi-production/simple

Install dtk-tools:

> pip install dtk-tools

Run the initialization:

> dtksetup init

If you want to access the examples, navigate to the desired folder and run:

> dtkseup examples

It will create an examples directory containing all the built-in dtk-tools examples.

Installation for development

To install the dtk-tools, first clone the repository:

> git clone https://github.com/InstituteforDiseaseModeling/dtk-tools.git

Create a pip.ini file (pip.conf if on Unix) in your virtual environment folder (here idmtools) with the following content:

[global]
index-url = https://packages.idmod.org/api/pypi/pypi-production/simple

From a command-prompt, run the following from the dtk-tools directory:

> pip install -e .

Run the initialization:

> dtksetup init

Setup

To configure your user-specific paths and settings for local and HPC job submission, please create a simtools.ini file in the same folder that contains your scripts.

Simulation job management is handled through the various dtk command-line options, e.g. dtk run example_sweep or dtk analyze example_plots. For a full list of options, execute dtk --help.