signac
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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
Configuration
Overview
Project configuration
Advanced How-To
Migrating (changing) the project schema
Adding/renaming/deleting keys
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 using the command line
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
Glossary
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
|
J
|
M
|
N
|
O
|
P
|
R
|
S
|
W
B
body
E
executable
F
footer
fork
G
GPU:
H
header
J
job
job directory
job document
job id
M
memory
MPI parallelized:
MPI/OpenMP Hybrid:
N
ngpu
np
nranks
O
omp_num_threads
P
parallelized:
parameter
processor_fraction
project
project schema
project_header
R
resources
S
serial:
signac schema
state point
W
walltime
workspace
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