Basic Usage

Client

The core functionality of StochSS-Compute comes from GillesPy2. This documentation assumes basic familiarity with GillesPy2 and/or StochSS.

  1. To run a RemoteSimulation, you need a Model and optionally a Solver and Server. More information about models may be found here.

from gillespy2 import Model
from gillespy2 import TauHybridSolver, TauHybridCSolver, NumPySSASolver, SSACSolver, CLESolver, TauLeapingSolver, TauLeapingCSolver, ODESolver, ODECSolver
from stochss_compute import RemoteSimulation, ComputeServer

simulation = RemoteSimulation(model=model, host='localhost', solver=TauHybridSolver)

  1. That’s it.

results = simulation.run()
# returns right away

results.plot()
# polls the server, downloading results when complete

If a cached Results object has identical properties to the simulation you have requested, your results are processed instantly.

results2 = simulation.run()
# returns cached object

results2.plot()
# no need to fetch

Server

  1. Run the included command-line utility to launch a server and pre-configured Dask cluster.

stochss-compute-cluster

Connecting to a Dask Cluster

stochss-compute -H localhost -P 8786

Arguments

-p PORT --port PORT

The port to use for the server. Defaults to 29681.

-c CACHE, --cache CACHE

Path to use for the cache. Defaults to ./cache.

--rm

Whether to delete the cache upon exit. Default False.

-H DASK_HOST, --dask-host DASK_HOST

The host to use for the dask scheduler. Defaults to localhost.

-P DASK_SCHEDULER_PORT, --dask-scheduler-port DASK_SCHEDULER_PORT

The port to use for the dask scheduler. 0 for a random port. Defaults to a random port.

-W DASK_N_WORKERS, --dask-n-workers DASK_N_WORKERS

Configure the number of workers. Defaults to one per core.

-T DASK_THREADS_PER_WORKER, --dask-threads-per-worker DASK_THREADS_PER_WORKER

Configure the threads per worker. Default will let Dask decide based on your CPU.

--dask-processes DASK_PROCESSES

Whether to use processes (True) or threads (False). Defaults to True, unless worker_class=Worker, in which case it defaults to False.

-D DASK_DASHBOARD_ADDRESS, --dask-dashboard-address DASK_DASHBOARD_ADDRESS

Address on which to listen for the Bokeh diagnostics server like ‘localhost:8787’ or ‘0.0.0.0:8787’. Defaults to ‘:8787’. Set to None to disable the dashboard. Use ‘:0’ for a random port.

-N DASK_NAME, --dask-name DASK_NAME

A name to use when printing out the cluster, defaults to type name.