Seismic wavefield simulation - CWL implementation

This repository contains a Common Workflow Language (CWL) implementation of a seismic wavefield simulation workflow based on the SPECFEM3D software package.

Description

The main SPECFEM3D workflow is described in the specfem3d.cwl file. It accepts four input parameters:

• The meshdir folder, which stores a pre-generated mesh for the region under consideration;
• The cmtsolution file, which is the earthquake source parameter file;
• The stations file, which contains the coordinates of the receivers;
• The parfile file, which is the configuration file for the simulation process.

The workflow comprises three sequential steps:

• Mesh decomposition: given an input mesh stored in the meshdir folder and a number of target processes configured in the parfile input, the xdecompose_mesh partitions the mesh to allow for parallel processing;
• Database generation: after the decomposition step, the xgenerate_databases command creates all the missing information needed by the SEM parallel solver;
• Wavefield simulation: finally, the xspecfem3D command executes the wavefield simulation.

The first step is always sequential, while the other two rely on MPI for parallel/distributed execution whenever the number of processes exceeds one.

This workflow can also run multiple simulations on the same mesh in parallel. The main.cwl file accepts an array of input simulation files (i.e., cmtsolutions, parfiles, and stations files) and runs an entire simulation process for each configuration. The config.yml file shows an example of input parameters for the workflow.

Usage

Running this workflow requires a CWL runner. For example, the CWL reference implementation, called cwltool, can be installed as follows:

python3 -m venv venv
source venv/bin/activate
pip install cwlref-runner

Note that this workflow does not build the SPECFEM3D suite from scratch. Instead, it expects that all SPECFEM3D-related commands are available in the user's $PATH. Please follow the official documentation to build and configure SPECFEM3D in your target execution environment.

Once all software and data dependencies are installed, the workflow can be launched using the following command:

cwl-runner main.cwl config.yml

Acknowledgment

This work has been partially supported by the EUPEX project, "European Pilot for Exascale," which has received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No. 101033975.

This work partially builds on a previous CWL implementation of SPECFEM3D workflow realised in the context of the DARE project, "Delivering Agile Research Excellence on European e-Infrastructures," which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 777413.