The platform uses a hierarchical workflow system that incorporates:

  • Multiple simulation tools (e.g., FEniCS, Kratos) for solving a problem.
  • Standardized I/O streams to the simulation tools.
  • Multiple parameter configurations per benchmark.
  • Automated mesh generation.
  • Provenance reports generation.
  • Querying the research objects.

Workflow

The workflow has a hierarchical structure. The common tasks like mesh generation and results' summary creation are done by the top-level workflow. The top-level workflow interacts with the sub-workflows which are tool-specific. The sub-workflows are responsible for running the scripts containing simulation code and pre/post-processing scripts necessary for processing the mesh files or the simulation output.

The benchmark linear-elastic-plate-with-hole is implemented with nextflow and snakemake packages. For this benchmark, the structure of the snakemake workflow is exemplified below:

linear-elastic-plate-with-hole/Snakefile 
│                                  ├── executes ──> create_mesh.py
│                                  └── executes ──> summarize_results.py                       
│
├── calls ──> fenics/Snakefile 
│                       └── executes ──> run_fenics_simulation.py
│
└── calls ──> kratos/Snakefile 
                        ├── executes ──> msh_to_mdpa.py
                        ├── executes ──> create_kratos_input.py
                        ├── executes ──> run_kratos_simulation.py
                        └── executes ──> postprocess_results.py

Terminologies

Parameter JSON File

A parameter_*.json file defines all the user-adjustable parameters for mesh generation, material properties, boundary conditions, and solver settings for finite element simulations. Each parameter file represents a unique configuration of these parameters that will be processed by the workflow system, e.g. parameter_1.json.

{   
    "configuration": "1",    
}

The keyword "configuration" is a unique identifier for the provided parameter set. It is used in output file naming and workflow tracking and must be unique across all parameter files.

Configuration Generator

generate_config.py file writes a configuration file for the workflow managers (snakemake or nextflow) extracting the configuration information from parameter_*.json files. Further, it lists the simulation tools that are going to run the different parameter configurations, e.g. generate_config.py.

Mesh Generation

The create_mesh.py file contains the code for mesh generation. In case the mesh(es) are already available, the file is not needed. In the linear-elastic-plate-with-hole example the create_mesh.py file:

  1. receives inputs from \parameter_*.json and outputs .msh files.
  2. Uses gmsh library for mesh generation.
  3. Uses pint library for unit conversion to the SI units.

Summarize File

summarize_results.py creates a JSON file containing the solution metrics and their corresponding parameter configurations after simulation runs of a benchmark.

Environment Files

The environment files are YML files which configures the environment for running a script. They contain a list of software libraries that build up an environment. They are present inside the simulation tool's folder for the tool-specific scripts and inside the benchmark folder for common scripts. 

benchmarks/
    ├── linear-elastic-plate-with-hole/
        ├── environment_mesh.yml
        ├── environment_postprocessing.yml
        ├── fenics
            ├── environment_simulation.yml
        ├── kratos
            ├── environment_simulation.yml