T9 - Deployment

This tutorial provides several useful recipes for deploying Covasim.

Click here to open an interactive version of this notebook.

Dask

Dask is a powerful library for multiprocessing and “scalable” analytics. Using Dask (rather than the built-in multiprocess) for parallelization is relatively straightforward:

import dask
from dask.distributed import Client
import numpy as np
import covasim as cv


def run_sim(index, beta):
    ''' Run a standard simulation '''
    sim = cv.Sim(beta=beta, label=f'Sim {index}, beta={beta}')
    sim.run()
    return sim


if __name__ == '__main__':

    # Run settings
    n = 8
    n_workers = 4
    betas = np.sort(np.random.random(n))

    # Create and queue the Dask jobs
    client = Client(n_workers=n_workers)
    queued = []
    for i,beta in enumerate(betas):
        run = dask.delayed(run_sim)(i, beta)
        queued.append(run)

    # Run and process the simulations
    sims = list(dask.compute(*queued))
    msim = cv.MultiSim(sims)
    msim.plot(color_by_sim=True)

Jupyter/IPython

Using Jupyter and Voilà, you can build a Covasim-based webapp in minutes. First, install the required dependencies:

pip install jupyter jupyterlab jupyterhub ipympl voila

Here is a very simple interactive webapp that runs a multisim (in parallel!) when the button is pressed, and displays the results:

import numpy as np
import covasim as cv
import ipywidgets as widgets

# Create the button and output area
button = widgets.Button(description='Run')
output = widgets.Output()

@output.capture()
def run():
    ''' Stochastically run a parallelized multisim '''
    sim = cv.Sim(verbose=0, pop_size=20e3, n_days=100, rand_seed=np.random.randint(99))
    msim = cv.MultiSim(sim)
    msim.run(n_runs=4)
    return msim.plot()

def click(b):
    ''' Rerun on click '''
    output.clear_output(wait=True)
    run()

# Create and show the app
button.on_click(click)
app = widgets.VBox([button, output])
display(app)

If you save this as e.g. msim.ipynb, then you can turn it into a web server simply by typing voila msim.ipynb.