SweepManager Workflow

Simplified parameter sweep using SweepManager

Introduction

Josh is an ecological simulation runtime for agent-based modeling developed by the Eric and Wendy Schmidt Center for Data Science and Environment. This demo assumes familiarity with Josh’s simulation language and runtime.

joshpy is a Python client that enables:

Orchestration: Define parameter sweeps, expand job configurations, and execute simulations programmatically
Tracking: Register runs in a DuckDB-backed registry with session and config tracking
Data Loading: Import cell-level CSV exports into queryable tables
Analysis: Query results across parameter values and replicates
Diagnostics: Quick matplotlib visualizations for simulation sanity checks
Visualization: Create publication-quality plots with R/ggplot2 integration

This demo walks through a complete parameter sweep workflow using SweepManager, which encapsulates the common workflow of expanding, running, and collecting sweep results. For a more detailed walkthrough using each component directly, see Manual Workflow.

We vary the maxGrowth parameter from 10 to 100 meters/step across 10 experiments, each with 3 replicates, then load, query, and visualize the results.

Prerequisites

Ensure the Josh JAR is available at jar/joshsim-fat.jar and joshpy is installed:

pip install -e '.[all]'

For visualization, ensure R is installed with the following packages:

install.packages(c("reticulate", "ggplot2", "dplyr"))

Step 1: Define Parameter Sweep

The first step is to define our experiment configuration. joshpy uses three key abstractions:

JobConfig: The top-level configuration specifying source files, templates, and sweep parameters
SweepConfig: Defines which parameters to sweep and their values
SweepParameter: A single parameter with a name and list of values

from pathlib import Path

from joshpy.jobs import JobConfig, SweepConfig, SweepParameter

# Paths to source files (optimized for fast tutorial builds)
SOURCE_PATH = Path("../../examples/tutorial_sweep.josh")
TEMPLATE_PATH = Path("../../examples/templates/sweep_config.jshc.j2")

# Parameter sweep: maxGrowth from 10 to 100 in steps of 10
MAX_GROWTH_VALUES = list(range(10, 101, 10))

config = JobConfig(
    template_path=TEMPLATE_PATH,
    source_path=SOURCE_PATH,
    simulation="Main",
    replicates=3,
    sweep=SweepConfig(
        parameters=[
            # maxGrowth is swept - creates one job per value
            SweepParameter(name="maxGrowth", values=MAX_GROWTH_VALUES),
            # Note: daysPerYear is a static value in the template (not swept)
        ]
    ),
)

The sweep creates one job per maxGrowth value (10, 20, …, 100). Static values like daysPerYear are defined directly in the template, not as sweep parameters.

Let’s examine the source files. The .josh file defines the simulation, and the .jshc.j2 template provides parameterized configuration:

Josh Source

print(SOURCE_PATH.read_text())

# Tutorial sweep simulation - optimized for fast documentation builds
# Uses larger grid cells (5000m) for faster execution with same extent

start simulation Main

  grid.size = 5000 m
  grid.low = 33.7 degrees latitude, -115.4 degrees longitude
  grid.high = 34.0 degrees latitude, -116.4 degrees longitude
  grid.patch = "Default"

  steps.low = 0 count
  steps.high = 10 count

  exportFiles.patch = "file:///tmp/tutorial_sweep_{maxGrowth}_{replicate}.csv"

end simulation

start patch Default

  ForeverTree.init = create 10 count of ForeverTree

  export.averageAge.step = mean(ForeverTree.age)
  export.averageHeight.step = mean(ForeverTree.height)

end patch

start organism ForeverTree

  # Static config value - same for all sweep runs (initial tree count)
  initialTreeCount.init = config sweep_config.initialTreeCount

  # Swept config value - varies across sweep runs
  maxGrowth.init = config sweep_config.maxGrowth

  age.init = 0 year
  age.step = prior.age + 1 year

  height.init = 0 meters
  # maxGrowth is swept via sweep_config.jshc
  height.step = prior.height + sample uniform from 0 meters to maxGrowth

end organism

start unit year

  alias years
  alias yr
  alias yrs

end unit

Template Configuration

print(TEMPLATE_PATH.read_text())

# Auto-generated configuration for tutorial_sweep.josh
# Parameter sweep: maxGrowth={{ maxGrowth }}

# =============================================================================
# STATIC CONFIG VALUES
# These values are the same for all runs in the sweep.
# Use static values for constants that don't need to vary across experiments.
# =============================================================================

# Initial tree count per organism (constant across all sweep runs)
initialTreeCount = 10 count

# =============================================================================
# SWEPT CONFIG VALUES
# These values vary across sweep runs. Each unique combination creates a job.
# Use swept values for parameters you want to explore or optimize.
# =============================================================================

# Maximum growth per timestep (meters) - SWEPT via Jinja template
maxGrowth = {{ maxGrowth }} meters

Notice how the configuration template has two types of values:

Static values (e.g., daysPerYear = 365 count): Fixed values that don’t use Jinja templating. These are the same for all runs in the sweep.
Swept values (e.g., maxGrowth = {{ maxGrowth }} meters): Values that use Jinja variables. These vary across sweep runs based on the SweepParameter definitions.

The .josh file references both via config sweep_config.variableName. At runtime, each config variable pulls its value from the generated .jshc file.

Step 2: Create SweepManager

The SweepManager encapsulates the entire sweep workflow. It uses a builder pattern for flexible configuration:

with_registry(): Configure DuckDB registry (path or existing instance)
with_cli(): Configure JoshCLI (JAR path or existing instance)
build(): Expand jobs, create session, and register configurations

from joshpy.sweep import SweepManager

# Registry path - saved to disk for use in analysis tutorial
REGISTRY_PATH = "demo_registry.duckdb"

# Create manager with builder pattern
manager = (
    SweepManager.builder(config)
    .with_registry(REGISTRY_PATH, experiment_name="growth_rate_sweep")
    .with_cli(jar_path=Path("../../jar/joshsim-fat.jar"))
    .build()
)

Step 3: Run Simulations

The run() method executes all jobs with automatic registry tracking:

# Run all jobs
results = manager.run()

Running 10 jobs (30 total replicates)
[1/10] Running (local): {'maxGrowth': 10}
  [OK] Completed successfully
[2/10] Running (local): {'maxGrowth': 20}
  [OK] Completed successfully
[3/10] Running (local): {'maxGrowth': 30}
  [OK] Completed successfully
[4/10] Running (local): {'maxGrowth': 40}
  [OK] Completed successfully
[5/10] Running (local): {'maxGrowth': 50}
  [OK] Completed successfully
[6/10] Running (local): {'maxGrowth': 60}
  [OK] Completed successfully
[7/10] Running (local): {'maxGrowth': 70}
  [OK] Completed successfully
[8/10] Running (local): {'maxGrowth': 80}
  [OK] Completed successfully
[9/10] Running (local): {'maxGrowth': 90}
  [OK] Completed successfully
[10/10] Running (local): {'maxGrowth': 100}
  [OK] Completed successfully
Completed: 10 succeeded, 0 failed

Step 4: Load Results

The load_results() method automatically discovers export paths from the Josh file, resolves template variables for each job, and loads CSV results:

manager.load_results()

Loading patch results from: /tmp/tutorial_sweep_{maxGrowth}_{replicate}.csv
  Loaded 1463 rows from tutorial_sweep_10_0.csv
  Loaded 1463 rows from tutorial_sweep_10_1.csv
  Loaded 1463 rows from tutorial_sweep_10_2.csv
  Loaded 1463 rows from tutorial_sweep_20_0.csv
  Loaded 1463 rows from tutorial_sweep_20_1.csv
  Loaded 1463 rows from tutorial_sweep_20_2.csv
  Loaded 1463 rows from tutorial_sweep_30_0.csv
  Loaded 1463 rows from tutorial_sweep_30_1.csv
  Loaded 1463 rows from tutorial_sweep_30_2.csv
  Loaded 1463 rows from tutorial_sweep_40_0.csv
  Loaded 1463 rows from tutorial_sweep_40_1.csv
  Loaded 1463 rows from tutorial_sweep_40_2.csv
  Loaded 1463 rows from tutorial_sweep_50_0.csv
  Loaded 1463 rows from tutorial_sweep_50_1.csv
  Loaded 1463 rows from tutorial_sweep_50_2.csv
  Loaded 1463 rows from tutorial_sweep_60_0.csv
  Loaded 1463 rows from tutorial_sweep_60_1.csv
  Loaded 1463 rows from tutorial_sweep_60_2.csv
  Loaded 1463 rows from tutorial_sweep_70_0.csv
  Loaded 1463 rows from tutorial_sweep_70_1.csv
  Loaded 1463 rows from tutorial_sweep_70_2.csv
  Loaded 1463 rows from tutorial_sweep_80_0.csv
  Loaded 1463 rows from tutorial_sweep_80_1.csv
  Loaded 1463 rows from tutorial_sweep_80_2.csv
  Loaded 1463 rows from tutorial_sweep_90_0.csv
  Loaded 1463 rows from tutorial_sweep_90_1.csv
  Loaded 1463 rows from tutorial_sweep_90_2.csv
  Loaded 1463 rows from tutorial_sweep_100_0.csv
  Loaded 1463 rows from tutorial_sweep_100_1.csv
  Loaded 1463 rows from tutorial_sweep_100_2.csv

Results:
  Jobs in sweep: 10
  Jobs with results loaded: 10
  Total rows loaded: 43890
43890

Step 5: Verify Data Loaded

Let’s verify the data is in the registry and ready for analysis:

# Get summary of loaded data
summary = manager.registry.get_data_summary()
print(summary)

Registry Data Summary
========================================
Sessions: 2
Configs:  10
Runs:     20
Rows:     87,780

Variables: averageAge, averageHeight
Entity types: patch
Parameters: maxGrowth
Steps: 0 - 10
Replicates: 0 - 2
Spatial extent: lon [-115.37, -114.40], lat [33.41, 33.68]

manager.registry.list_export_variables()

['averageAge', 'averageHeight']

manager.registry.list_config_parameters()

['maxGrowth']

Next Steps: Analysis

Now that data is loaded, see Analysis & Visualization Tutorial for comprehensive coverage of:

Diagnostic Plots (SimulationDiagnostics) - quick matplotlib visualizations
Custom Queries (DiagnosticQueries) - get pandas DataFrames
Direct SQL - full DuckDB access for advanced analysis
R/ggplot2 - publication-quality figures

Quick example using manager.query():

# Query with parameter grouping
df = manager.query("averageHeight", group_by="maxGrowth")
df.head(10)

	param_value	step	mean_value	std_value	n_cells
0	10.0	0	5.002052	0.949872	798
1	10.0	1	10.017796	1.316734	798
2	10.0	2	15.035342	1.586715	798
3	10.0	3	19.980981	1.825273	798
4	10.0	4	24.937082	2.022142	798
5	10.0	5	29.970522	2.196011	798
6	10.0	6	34.976634	2.380003	798
7	10.0	7	39.937856	2.495450	798
8	10.0	8	44.960226	2.691332	798
9	10.0	9	49.950621	2.836932	798

from joshpy.diagnostics import SimulationDiagnostics

diag = SimulationDiagnostics(manager.registry)
diag.plot_comparison(
    "averageHeight",
    group_by="maxGrowth",
    title="Tree Height by Growth Rate Parameter",
)

Figure 1: Tree height trajectories across maxGrowth values.

Summary

This demo illustrated the SweepManager workflow:

Define a parameter sweep using JobConfig and SweepConfig
Build a SweepManager with builder pattern (handles expansion and registration)
Execute with manager.run() - single method replaces manual loops
Load outputs with manager.load_results() - automatic path discovery
Analyze - see Analysis Tutorial for visualization and queries

SweepManager Benefits:

Encapsulation: One object manages registry, CLI, and job set
Context manager: Automatic cleanup with with statement
Builder pattern: Flexible configuration with sensible defaults
Convenience methods: run(), load_results(), query() for common operations

Alternative Creation Methods:

# From dictionary
manager = SweepManager.from_dict(config.to_dict(), registry=":memory:")

# From YAML file
manager = SweepManager.from_yaml(Path("experiment.yaml"))

# With existing components
manager = (
    SweepManager.builder(config)
    .with_registry(existing_registry, session_id="existing-session")
    .with_cli(existing_cli)
    .build()
)

Related Tutorials:

Manual Workflow - Step-by-step control using individual components
Analysis & Visualization - Analysis and visualization (decoupled from orchestration)

Cleanup

# SweepManager cleanup (also works as context manager)
manager.cleanup()  # Remove temporary config files
manager.close()    # Close registry connection

The registry has been saved to demo_registry.duckdb. Run the Analysis Tutorial to explore the results.

Alternative: Context Manager

# Automatic cleanup with context manager
with SweepManager.from_dict(config.to_dict()) as manager:
    manager.run()
    manager.load_results()
    df = manager.query("averageHeight", group_by="maxGrowth")
# Resources automatically cleaned up here