Tutorials

Application tutorials and documentations in M27 release

We have provided detailed documentations and tutorials in this M27 release and the previous M24 release. For each application tutorial, based on users feedback we obtained for this release and previous ones, we have made a huge improvement compared to the release on M21. We divided VECMAtk tutorials into two formats, namely static and interactive. The static tutorials are accompanied with the M24 VECMAtk release while the interactive tutorials are included in this release, both publicly available from the deliverable D3.5 published on 14 August 2020.

The links to the detailed tutorials for VECMAtk components and applications are provided below:

FabSim3 is an automation toolkit written in Python 3  featuring an integrated test infrastructure and a flexible plugin system. There are several plugins available from a diverse range of scientific domains, such as

  • FabUQCampaign for a climate modelling;
  • FabMD for a molecular dynamics modelling using Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS);
  • FabFlee for a migration modelling;
  • FabMogp for an earthquake modelling;
  • FabCovid19 for a Covid-19 modelling.

EasyVVUQ is a Python library designed to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations. It accounts for uncertainty quantification (UQ) and validation patterns in application to  earlier described domains.

 

UQ Sampling techniques and tutorials

  • Stochastic Collocation (SC) sampler examples:
  • Polynomial Chaos Expansion (PCE) sampler example:

 

Validation pattern tutorials:

 

QCG-Pilot Job is a Pilot Job system that allows to execute many subordinate jobs in a single scheduling system allocation.

EasyVVUQ-QCGPJ is a lightweight plugin for parallelization of EasyVVUQ with the QCG-PilotJob mechanism. To learn more, please see the tutorial example here.

QCG-Client is a command line client for execution of computing jobs on the clusters offered by QCG middleware.

QCG-Now is a desktop, GUI client for easy execution of computing jobs on the clusters offered by QCG middleware.

MUSCLE3 is the third incarnation of the Multiscale Coupling Library and Environment.

                                          

 

 

Application tutorials provided in M12 release 

We provide four application tutorials to show that VECMAtk can be applied to solve some real world problems. These are:

  • FabFlee (migration modelling)
  • FabUQCampaign (basic CFD models)
  • Fusion
  • FabMD (molecular dynamics)

Each tutorial highlights different components in VECMAtk, as indicated by the corresponding figures.

FabFlee

https://github.com/djgroen/FabFlee/blob/master/doc/Tutorial.md

In this tutorial we will explain how you can combine a simple stochastic conflict evolution model (Flare) with an agent-based migration model (Flee), perform a set of runs based on different conflict evolutions, and visualize the migrant arrivals with confidence intervals.

 

FabUQCampaign

https://github.com/wedeling/FabUQCampaign/blob/master/Tutorial_ADE.md

This tutorial describes how to create a Stochastic Collocation EasyVVUQ campaign.

Figure 2: Overview of VECMAtk components used in the FabUQCampaign tutorial.

HPC execution of EasyVVUQ with QCG
Pilot Job

 

This tutorial allows users to submit an entire integrated EasyVVUQ and QCG Pilot Job Manager workflow as a single job into the HPC cluster.

Figure 3: Overview of VECMAtk components used in the Fusion tutorial.

FabMD

https://github.com/UCL-CCS/FabMD/blob/master/doc/EasyVVUQ_FabMD_example.md

This example shows how to create an ensemble of LAMMPS simulations using EasyVVUQ, execute the jobs through FabMD, then analyse them within the EasyVVUQ architecture.

Figure 4: Overview of VECMAtk components used in the FabMD tutorial.