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dtyagi
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Add FEniCS Nextflow benchmark and update environment configurations
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‎.github/workflows/run-benchmark.yml

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run: |
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cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/FEniCS/
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snakemake --use-conda --force --cores 'all'
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- name: run-fenics-nextflow-benchmark
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shell: bash -l {0}
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run: |
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cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/
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nextflow run main.nf
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- name: run-Kratos-benchmarks
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shell: bash -l {0}

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/create_input_files.py

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import json
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import sys
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import gmsh
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from pint import UnitRegistry
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ureg = UnitRegistry()
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# Parameters
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name = sys.argv[1]
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#experiment_file = sys.argv[2]
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parameter_file = sys.argv[2]
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# Load parameters
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with open(parameter_file) as f:
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parameters = json.load(f)
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print(parameters)
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length = (
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ureg.Quantity(parameters["length"]["value"], parameters["length"]["unit"])
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.to_base_units()
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.magnitude
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)
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radius = (
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ureg.Quantity(parameters["radius"]["value"], parameters["radius"]["unit"])
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.to_base_units()
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.magnitude
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)
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# create mesh
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"""
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4---------3
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| |
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5_ |
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\ |
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1______2
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"""
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gmsh.initialize()
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gmsh.model.add(name)
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element_size = (
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ureg.Quantity(
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parameters["element-size"]["value"], parameters["element-size"]["unit"]
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)
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.to_base_units()
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.magnitude
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)
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gmsh.option.setNumber("Mesh.CharacteristicLengthMin", element_size)
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gmsh.option.setNumber("Mesh.CharacteristicLengthMax", element_size)
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gmsh.option.setNumber("Mesh.CharacteristicLengthFactor", 1.0)
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gmsh.option.setNumber("Mesh.ElementOrder", parameters["element-order"])
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z = 0.0
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lc = 1.0
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x0 = 0.0
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x1 = x0 + radius
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x2 = x0 + length
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y0 = 0.0
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y1 = y0 + radius
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y2 = y0 + length
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center = gmsh.model.geo.addPoint(x0, y0, z, lc)
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p1 = gmsh.model.geo.addPoint(x1, y0, z, lc)
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p2 = gmsh.model.geo.addPoint(x2, y0, z, lc)
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p3 = gmsh.model.geo.addPoint(x2, y2, z, lc)
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p4 = gmsh.model.geo.addPoint(x0, y2, z, lc)
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p5 = gmsh.model.geo.addPoint(x0, y1, z, lc)
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l1 = gmsh.model.geo.addLine(p1, p2)
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l2 = gmsh.model.geo.addLine(p2, p3)
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l3 = gmsh.model.geo.addLine(p3, p4)
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l4 = gmsh.model.geo.addLine(p4, p5)
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l5 = gmsh.model.geo.addCircleArc(p5, center, p1)
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curve = gmsh.model.geo.addCurveLoop([l1, l2, l3, l4, l5])
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plane = gmsh.model.geo.addPlaneSurface([curve])
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gmsh.model.geo.synchronize()
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gmsh.model.geo.removeAllDuplicates()
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gmsh.model.addPhysicalGroup(2, [plane], 1, name="surface")
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gmsh.model.addPhysicalGroup(1, [l4], 1, name="boundary_left")
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gmsh.model.addPhysicalGroup(1, [l1], 2, name="boundary_bottom")
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gmsh.model.addPhysicalGroup(1, [l2], 3, name="boundary_right")
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gmsh.model.addPhysicalGroup(1, [l3], 4, name="boundary_top")
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gmsh.model.mesh.generate(2)
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#gmsh.write("data/mesh_" + name + ".msh")
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gmsh.write("mesh_" + name + ".msh")
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gmsh.finalize()
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#parameters["mesh-file"] = "data/mesh_" + name + ".msh"
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parameters["mesh-file"] = "mesh_" + name + ".msh"
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#with open("data/input_" + name + ".json", "w") as f:
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with open("input_" + name + ".json", "w") as f:
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json.dump(parameters, f, indent=4)

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/environment.yml

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name: plate-with-hole
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channels:
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- conda-forge
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- defaults
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dependencies:
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- python>=3.10
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- fenics-dolfinx
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- libadios2=2.10.1
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- petsc4py
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- python-gmsh
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- pint

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/experiment.json

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{
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"name": "linear elastic plate with hole",
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"description": "Benchmark for linear elasticity with a plate with a hole"
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}

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/main.nf

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// Default parameter input
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params.ip_files_script = Channel.value(file('create_input_files.py'))
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params.run_sim_script = Channel.value(file('run_simulation.py'))
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//params.summary_script = Channel.value(file('summary.py'))
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// split process
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process generate_input_files {
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publishDir "data/"
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conda 'environment.yml'
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input:
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path python_script
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val name
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path parameters_json
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output:
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tuple val(name), path("input_${name}.json"), path("mesh_${name}.msh"), path(parameters_json)
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script:
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"""
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python3 $python_script $name $parameters_json
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"""
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}
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process run_simulation {
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publishDir "data/"
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conda 'environment.yml'
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input:
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path python_script
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tuple val(name), path(input_json), path(mesh_msh), path(parameters_json)
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output:
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tuple val(name), path("output_${name}.vtk"), path(input_json), path(mesh_msh), path(parameters_json)
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script:
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"""
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python3 $python_script $name $input_json
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"""
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}
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process summary {
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publishDir "data/"
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//conda 'environment.yml'
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input:
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//path python_script
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tuple val(name), path(output_vtk), path(input_json), path(mesh_msh), path(parameters_json)
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output:
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path("summary_${name}.json")
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script:
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"""
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#!/usr/bin/env python
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import json
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import pyvista
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from xml.etree import ElementTree as ET
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from pathlib import Path
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import sys
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import os
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summary = {}
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summary["name"] = "$name"
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summary["parameters"] = "$parameters_json"
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summary["input"] = "$input_json"
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summary["mesh"] = "$mesh_msh"
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summary["output"] = "$output_vtk"
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# Load the mesh and output data
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max_mises_stress = 42.0
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tree = ET.parse(summary["output"])
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root = tree.getroot()
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pvtu_filenames = []
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path = Path(os.path.realpath(summary["output"])).parent
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for dataset in root.findall(".//DataSet"):
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pvtu_filenames.append(path / dataset.get("file"))
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meshes = [pyvista.read(pvtu_filename) for pvtu_filename in pvtu_filenames]
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for mesh in meshes:
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print("Mesh:", mesh)
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# Assuming the mesh has a 'von_mises_stress' array
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try:
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max_mises_stress = float(mesh["von_mises_stress"].max())
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except KeyError:
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print("von_mises_stress not found in mesh.")
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summary["max_mises_stress"] = max_mises_stress # Replace with actual computation
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with open(f"summary_{summary["name"]}.json", "w") as f:
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json.dump(summary, f, indent=4)
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"""
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}
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// Workflow block
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workflow {
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def ch_parameter_files = Channel.fromPath('parameters_*.json', checkIfExists: true)
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//ch_parameter_files.view()
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def parameters_files = files('parameters_*.json')
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def names = parameters_files.baseName.collect{it.split('_')[1]}
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//println names
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def ch_file_names = Channel.fromList(names)
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output_gen_input_files = generate_input_files(params.ip_files_script, ch_file_names, ch_parameter_files)
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//output_gen_input_files.view()
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output_run_sim = run_simulation(params.run_sim_script, output_gen_input_files)
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//output_run_sim.view()
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summary(output_run_sim)
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}

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/nextflow.config

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profiles {
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conda {
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process.conda = 'environment.yml'
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}
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}
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//No need to specify profile each time
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conda.enabled = true // this or use -with-conda in command line
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//plugins {
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// id 'nf-prov'
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//}
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//
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//prov {
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// enabled = true
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// formats {
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// legacy {
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// file = 'provenance.json'
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// overwrite = true
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// }
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// }
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//}

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/parameters_003125.json

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{
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"radius": {
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"value": 0.33,
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"unit": "m"
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},
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"length": {
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"value": 1.0,
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"unit": "m"
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},
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"load": {
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"value": 100.0,
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"unit": "MPa"
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},
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"element-size": {
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"value": 0.003125,
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"unit": "m"
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},
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"element-order": 1,
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"element-degree": 1,
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"quadrature-rule": "gauss",
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"quadrature-degree": 1,
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"young-modulus": {
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"value": 210e9,
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"unit": "Pa"
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},
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"poisson-ratio": {
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"value": 0.3,
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"unit": ""
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}
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}

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/parameters_00625.json

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{
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"radius": {
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"value": 0.33,
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"unit": "m"
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},
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"length": {
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"value": 1.0,
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"unit": "m"
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},
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"load": {
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"value": 100.0,
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"unit": "MPa"
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},
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"element-size": {
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"value": 0.00625,
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"unit": "m"
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},
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"element-order": 1,
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"element-degree": 1,
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"quadrature-rule": "gauss",
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"quadrature-degree": 1,
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"young-modulus": {
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"value": 210e9,
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"unit": "Pa"
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},
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"poisson-ratio": {
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"value": 0.3,
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"unit": ""
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}
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}

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/parameters_0125.json

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{
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"radius": {
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"value": 0.33,
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"unit": "m"
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},
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"length": {
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"value": 1.0,
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"unit": "m"
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},
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"load": {
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"value": 100.0,
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"unit": "MPa"
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},
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"element-size": {
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"value": 0.0125,
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"unit": "m"
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},
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"element-order": 1,
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"element-degree": 1,
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"quadrature-rule": "gauss",
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"quadrature-degree": 1,
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"young-modulus": {
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"value": 210e9,
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"unit": "Pa"
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},
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"poisson-ratio": {
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"value": 0.3,
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"unit": ""
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}
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}

‎benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/parameters_025.json

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{
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"radius": {
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"value": 0.33,
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"unit": "m"
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},
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"length": {
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"value": 1.0,
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"unit": "m"
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},
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"load": {
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"value": 100.0,
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"unit": "MPa"
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},
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"element-size": {
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"value": 0.025,
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"unit": "m"
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},
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"element-order": 1,
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"element-degree": 1,
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"quadrature-rule": "gauss",
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"quadrature-degree": 1,
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"young-modulus": {
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"value": 210e9,
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"unit": "Pa"
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},
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"poisson-ratio": {
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"value": 0.3,
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"unit": ""
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}
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}

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