FabSim3 Plugins¶

Installing plugins¶

By default, FabSim3 comes with the FabDummy plugin, which is available in ~/FabSim3/plugins.

Other plugins can be installed in FabSim3, and are listed in fabsim/deploy/plugins.yml file.

To install a specific plugin, simply type:

fabsim localhost install_plugin:<plug_name>

To install plugin from a specific github branch, you can use branch keyword
```
fabsim localhost install_plugin:<plug_name>,branch=<branch_name>
```

List of available FabSim3 plugins¶

FabChemShell¶

FabChemShell is a ChemShell plugin for FabSim3.

FabChemShell github repository :
FabChemShell documentation :

FabCovid19¶

FabCovid19 is a FabSim3 plugin for Flu And Coronavirus Simulator (FACS).

FabCovid19 github repository :
FabCovid19 documentation :

FabCovidsim¶

FabCovidsim is a FabSim3/EasyVVUQ plugin for COVID-19 CovidSim microsimulation model developed Imperial College, London.

FabCovidsim github repository :
FabCovidsim documentation :

FabDummy¶

FabDummy is a dummy example plugin for FabSim3. It is meant to showcase a minimal implementation for a FabSim3 plugin.

FabDummy github repository :
FabDummy documentation :

FabDynamics¶

FabDynamics is a plugin for Dynamics which is used for analysis of ODE systems.

FabDynamics github repository :
FabDynamics documentation :

FabFlee¶

FabFlee is a plugin for automated Flee agent-based simulations. It provides an environment to construct, modify and execute simulations as a single run or ensemble runs. FabFlee aims to predict the distribution of incoming refugees across destination camps under a range of different policy situations.

FabFlee github repository :
FabFlee documentation :

FabMD¶

FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.

This plugin provides functionality to extend FabSim3's workflow and remote submission capabilities to LAMMPS specific tasks.

FabMD github repository :
FabMD documentation :

FabMUSCLE¶

FabMUSCLE is a preliminary launcher for the MUSCLE3 toolkit. It serves to automatically set up MUSCLE3 simulations, launch the manager and its submodels, and keep all the associated data organized.

FabMUSCLE github repository :
FabMUSCLE documentation :

FabParticleDA¶

FabParticleDA is a FabSim3 plugin for ParticleDA.jl).

FabParticleDA github repository :
FabParticleDA documentation :

FabSMD¶

FabSMD is a Steered Molecular Dynamics (SMD) plugin for FabSim3.

FabSMD github repository :
FabSMD documentation :

FabUQCampaign¶

FabUQCampaign is a FabSim3 plugin for a climate modelling. It used to run an ensemble of EasyVVUQ samples on HPC resources.

FabUQCampaign github repository :
FabUQCampaign documentation :
- FabUQCampaign 2D ocean model documentation :

FabDummy testing on localhost¶

FabDummy Plugin Installation¶

Open a terminal, and simply type:

fabsim localhost install_plugin:FabDummy

Info

FabDummy plugin will be downloaded under FabSim3/plugins/FabDummy.

Testing¶

To run a dummy job, type:
```
fabsim localhost dummy:dummy_test
```

To run an ensemble of dummy jobs, type:

fabsim localhost dummy_ensemble:dummy_test

For both cases, i.e. a single dummy job or an ensemble of dummy jobs, you can fetch the results by using:
```
fabsim localhost fetch_results
```

For more advanced testing features, please refer to the FabDummy tutorial at https://github.com/djgroen/FabDummy/blob/master/README.md.