Cubie documentation

cubie provides GPU-accelerated tools for integrating large batches of initial value problems. The source code is available on Github. If you’re just getting started, check out “Getting Started” and the rest of the User Manual. If you need specific details about a function or class, the Reference Manual is the place to go.

Contents

• Getting Started with Cubie
  • Installation
  • Basic Usage
  • Features
  • Requirements
  • Optional Dependencies
• Tutorials
  • Tutorial 1: Your First Parameter Sweep
  • Tutorial 2: Summaries Instead of Trajectories
  • Tutorial 3: Stiff Systems, Implicit Methods, and Drivers
• User Manual
  • Creating a “System” of Differential Equations
  • Solving ODEs
  • Coming from SciPy
  • Coming from MATLAB
  • Configuration Reference
  • Batching and Parameter Sweeps
  • Working with Results
  • Drivers (Time-dependent functions)
  • Timing Parameters
  • Choosing an Algorithm
  • Solver Options Reference
  • User functions and derivatives
  • CellML Models
  • GPU Memory Management
  • Caching and Recompilation
  • Making it Faster (basic)
  • Troubleshooting
• Theory
  • Numerical Integration
  • Nonlinear Solvers
  • Jacobians and Symbolic Differentiation
  • CUDA and GPU Computing
• Developer Guide
  • Architecture Overview
  • Adding Algorithms
  • Code Generation Pipeline
  • Buffer Registry
  • Adding Summary Metrics
  • Testing Guide
• Reference Manual
  • Batch solving
  • ODE systems
  • Integrators
  • Output handling
  • Memory
  • GUI Editors

Indices and tables

• Index

• Module Index

• Search Page