Welcome to AP-Nimbus’s documentation

Project Home:https://github.com/CardiacModelling/ap-nimbus Documentation:https://ap-nimbus.readthedocs.io/ Created:Aug 07, 2023 Version:1.0.1

IMPORTANT

This activity represents the next step in the development of the original AP-Portal work – towards a container-based / cloud solution.

AP-Nimbus is available at https://github.com/CardiacModelling/ap-nimbus and is being developed by the University of Nottingham’s School of Mathematical Sciences .

Preamble

• Unlike AP-Portal, this work includes the installation of ApPredict, the cardiac simulation software.
• Also unlike AP-Portal, this work, by nature of containerisation, means that AP-Nimbus work does not embody a single application, it is instead a collection of containers where each can operate in isolation, e.g. as a standalone Docker or Singularity container, or alternatively, orchestrated in a microservice architecture (e.g. Kubernetes or Docker Compose).

Singularity

This documentation predominantly covers Docker container environments, however it has been relatively straightforward to create Singularity containers (e.g. singularity build app-manager.img docker://cardiacmodelling/ap-nimbus-app-manager:0.0.10) and use those [1].

Sample invocation scripts can be found at ap-predict-online’s app-manager –> tools section.

Diagrammatic Representation

For the role each of the containers has in the overall AP-Nimbus activity please see Activity Overview.

ApPredict containers

ApPredict is the underlying cardiac simulation engine.

Building or installing ApPredict is a complex and time-consuming process and by distributing in container form it’s possible to have it installed in a fraction of the time [2].

AP-Nimbus containers

The following illustrates a Docker container setup.

It is equally feasible to run as .. :

• Containerised
  • docker run .. a single cardiacmodelling/ap-nimbus-app-manager container and call it with HTTP POST and GET requests, or;
  • docker run .. either of the cardiacmodelling/appredict-with-emulators or cardiacmodelling/appredict-no-emulators containers directly from a CLI to run their internal ApPredicts, or;
• Non-containerised
  • Running the various components without using containers is technically possible, but not reccomended or supported. See Developer Section for suggestions on how to develop the components using containers.

See also

For instructions on how to run containers, see the more detailed section on Running.

Activity Overview

• Activity Overview
  • Current work
  • Discontinued work

Installation

• Installation
  • Deployment Options

Security

• Security
  • Shared Computers / Browser Memory

Running

• Running
  • Running cardiacmodelling/ap-nimbus-app-manager
  • Running cardiacmodelling/appredict-no-emulators or cardiacmodelling/appredict-with-emulators
  • Running cardiacmodelling/ap-nimbus-client-direct

Troubleshooting

• Troubleshooting
  • Illegal Instruction
  • client-direct

Developer Section

• Developer Section
  • Building Options
  • Developing with Containers
  • Container Operations
  • Further Information
  • Networking and persistence
  • Backup
  • Starting simulations via command line
  • Updating ApPredict

Footnotes

[1]	Singularity containers (or rather, a Singularity version of just cardiacmodelling/ap-nimbus-app-manager so far) have been trialled operating in isolation, not in an orchestrated environment.

[2]	So long as there’s a container runtime, e.g. Docker, running somewhere!