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Getting Started

  • Concept
  • Packages
  • Installation
    • Install with conda
    • Install with pip
    • Installation from Source
    • Build Status
      • signac
      • signac-flow
      • signac-dashboard
  • Quickstart
  • Tutorial
    • Basics
      • Initializing the data space
      • Exploring the data space
      • Interacting with the signac project
      • Operating on the data space
    • Workflows
      • Implementing a simple workflow
      • Extending the workflow
      • Grouping Operations
      • The job document
      • Job.data and Job.stores
    • Submit operations to a scheduling system
  • Examples
    • Workflow Examples
      • 1.1 Getting started
        • Prerequisites
        • A minimal example
        • The Basics
      • 1.2 Exploring Data
        • Finding jobs
        • Views
      • 1.3 A Basic Workflow
        • Operations
        • Execution
        • Data Space Initialization
        • Classification
        • Parallelization
      • 1.4 Modifying the Data Space
      • 1.5 signac-flow Ideal Gas Example
        • About
        • Author
        • Before you start
      • 1.6 signac-flow HOOMD-blue Example
        • About
        • Author
        • Before you start
      • 1.7 Integration with Sacred
    • Analysis Examples
      • 2.2 Integration with pandas DataFrames
    • Aggregation Examples
      • 3.1 Aggregation Tutorial
        • About
        • Author
        • Prerequisites
        • Definition
        • Objective
        • Project Setup
        • Initializing the data space
        • Creating a FlowProject with aggregate operations
        • Executing the workflow
        • Summary

Package API Reference

  • signac (core) API
  • signac-flow API
  • signac-dashboard API

Topic Guide

  • Projects
    • Introduction
    • Project Initialization
    • The Data Space
      • Jobs
      • Finding jobs
      • Grouping
        • Basic Grouping by Key
        • Grouping by Multiple Keys
        • Searching and Grouping
        • Custom Grouping Functions
      • Moving, Copying and Removal
    • Centralized Project Data
    • Schema Detection
    • Importing and Exporting Data
      • Exporting a Workspace
      • Importing a Data Space
    • Linked Views
    • Synchronization
  • Jobs
    • Overview
    • The Job State Point
      • Modifying the State Point
    • The Job Document
    • Job Data Storage
      • Reading and Writing data
      • Accessing arrays
      • Data organization
      • Accessing keys
      • File handling
      • Low-level API
    • Job Stores
  • Query API
    • Query Namespaces
    • Basic Expressions
      • Select All
      • Simple Selection
      • Nested Keys
    • Operator Expressions
      • Arithmetic Expressions
      • Near Operator
      • Logical Operators
      • Exists Operator
      • Array Operator
      • Regular Expression Operator
      • Type Operator
      • Where Operator
    • Simplified Syntax on the Command Line
  • The Dashboard
    • Quickstart
    • Included modules
    • Specifying a custom job title
    • Running dashboards on a remote host
    • Dissecting the dashboard structure
    • Searching jobs
  • The FlowProject
    • Setup and Interface
    • Operations
    • Conditions
    • The Project Status
  • Cluster Submission
    • The submit interface
    • Submitting specific Operations
    • Bundling
    • Submission Directives
      • Available directives
      • Execution Modes
  • Manage Environments
    • How to Use Environments
    • Packaged Environments
    • Defining New Environments
    • Contributing Environments to the Package
  • Templates
    • Replacing the default template
    • Customize provided templates
    • The base template
  • FlowGroups
    • Definition
    • Basic Usage
    • Group-Specific Directives
  • Aggregation
    • Definition
    • Types of Aggregation
      • Group By
      • Groups Of
      • Sorting jobs for aggregation
      • Selecting jobs for aggregation
    • Aggregate ID
    • Aggregation with FlowGroups
  • Hooks
    • Introduction
    • Triggers
    • Operation Hooks
    • Project-Level Hooks
  • Collections
    • Creating collections
    • Searching collections
    • Command Line Interface
  • Configuration
    • Overview
    • Project configuration
    • Host configuration
      • Configuring a new host
      • Changing the password
      • Copying a configuration
      • Manual host configuration
  • Advanced How-To
    • Migrating (changing) the data space schema
      • Adding/renaming/deleting keys
      • Initializing Jobs with Replica Indices
      • Applying document-wide changes
    • Initializing state points with replica indices
    • Defining a grid of state point values
    • Creating parameter-dependent operations
    • Using signac-flow with MATLAB or other software without Python interface
    • Running MPI-parallelized operations
      • MPI-operations with mpi4py or similar
      • MPI-operations with flow.cmd
      • MPI-operations with custom script templates
    • Forcing the execution of a specific operation for debugging
    • Running in containerized environments
    • Using multiple execution environments for operations
    • Passing command line options to operations run in a container or other environment
  • FAQ
    • How do I design a good schema?
    • What is the difference between the job state point and the job document?
    • How do I avoid replicating metadata in filenames?
    • How do I reference data/jobs in scripts?
    • How do I achieve optimal performance? What are the practical scaling limits for project sizes?

Reference

  • Community
    • NumFOCUS
    • Code of Conduct
    • Support
    • Contributions
  • Scientific Papers
  • GitHub
  • Twitter
  • License
  • How to cite signac
    • Preferred Citation
    • Badge
    • Logos
  • References
signac
  • Index
  • Edit on GitHub

Index

B | E | F | G | H | M | N | O | P | R | S | W

B

  • body

E

  • executable

F

  • footer
  • fork

G

  • GPU:

H

  • header

M

  • memory
  • MPI parallelized:
  • MPI/OpenMP Hybrid:

N

  • ngpu
  • np
  • nranks

O

  • omp_num_threads

P

  • parallelized:
  • processor_fraction
  • project_header

R

  • resources

S

  • serial:

W

  • walltime

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