This project presents a general transmission model implemented in ixa, the Center for Forecasting and Outbreak Analytics' agent-based modeling framework. Our goal is to develop a model that can appropriately represent all stages of a respiratory disease outbreak, including case importation, a detailed transmission model accounting for time-varying infectiousness and immunity, and the assessment of non-pharmaceutical interventions. This model is a next generation update of ixa-epi-isolation.
Community Mitigation and Economic Impacts team of the CDC Center for Forecasting and Outbreak Analytics. Team lead: Guido Camargo España (CDC/IOD/ORR/CFA)
This repo uses uv for dependency management, be sure that uv is installed on your machine. To run any python script, you will need to initialize the uv environment first:
make uv-syncTo use this model, you need to have Rust and Cargo installed. You can find instructions for installing Rust here. To run the main example, use the following command:
cargo run -- -c input/input.json -o outputThe model requires a compatible synthetic population CSV in the person-record format supported by pop_reader. A small test file is included at input/people_test.csv. To generate larger populations, first install R dependencies and set up a Census Bureau API key in .env as CENSUS_API_KEY:
make setup-r
make synthetic-population # default: WY, 1000 people
make synthetic-population STATE=NY N=50000 # custom state and size| Target | Description |
|---|---|
make run |
Run the model with default config |
make run-1m |
Generate a 1M WY population and run the model with it |
make run-10m |
Generate a 10M WY population and run the model with it |
make synthetic-population |
Generate a synthetic population (configurable via STATE and N) |
make profile |
Profile the model with samply (configurable, see below) |
make setup-r |
Install required R packages |
You can also override the population file directly via CLI with --synth-population:
cargo run --release -- -c input/input.json -o output --synth-population path/to/population.csvmake profile runs the model under samply, which opens the Firefox Profiler with a call tree and flame graph. Press Ctrl+C to stop early — samply will still capture the profile. You can also Ctrl+C any make run-* target to kill the simulation early.
make profile # 1M population, no ixa spans
make profile PROFILE_SIZE=10m # 10M population
make profile PROFILE_FEATURES=profiling # with ixa span instrumentation
make profile PROFILE_SIZE=10m PROFILE_FEATURES=profiling # bothThe profiling Cargo feature enables ixa's built-in span timing (open_span/Span::drop). This adds ~25% overhead, so it's off by default for samply runs. The run, run-1m, and run-10m targets enable it for ixa's own profiling output.
make calibrate-phase-1-dev is the easiest way to run the calibration routine of Phase 1, in which we compare the first observed deaths in the model to the first observed death in the State of Indiana. Running this command with setting SIZE will generate a toy synthetic population of that size based on Indiana PUMs census data and then run the Phase 1 calibration script. For example, to run routines in popualtions 50K, 100K, and 1 million:
make calibrate-phase-1-dev SIZE=50_000
make calibrate-phase-1-dev SIZE=100_000
make calibrate-phase-1-dev SIZE=1_000_000By default, the calibration routine uses four parallel worker threads to run simulations. Depending on your computer specs, this can be altered by setting the MAX_WORKERS parameter
make calibrate-phase-1-dev SIZE=50_000 MAX_WORKERS=10In general, for local parallelized computing, you should select a maximum number of workers that will not exhaust your memory. Check the amount of memory that a single simulation of the model requires and divide your working memory by that number. Flooring that value should arrive at a reasonable estimate of the number of workers that can run concurrently for a particular model calibration run. For example, if each simulation takes 2.3 GB of memory to run and your machine has 16 GB of RAM, then 16 / 2.3 = 6.9 -> 6 workers should be allowed for the parallel execution. Allowing for a higher number of workers runs the risk of fatal memory overflow errors.
To run the post-calibration projection of the accepted particles on a longer time horizon, use the command make projections-phase-1-dev, which also accepts the SIZE and MAX_WORKERS command and will generate the calibration if it deos not exist.
To run the whole routine through generating figures, use
make plot-phase-1-projection-dev SIZE={n} MAX_WORKERS={m}This command can be called without calling the others explicitly.
Production code follows the same format, but drops the dev suffix (for example the calibration command is make calibrate-phase-1). To run this, please ensure that you have specified a path to a valid synthetic population in the .env file under SYNTH_POP_FILE.
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