Merge remote-tracking branch 'origin/55-reporter-plugin-update-rohub-upload-issue' into 62-rocrate-merge

Author: M-Jafarkhani

.github/workflows/run-benchmark.yml

@@ -14,13 +14,12 @@ on:
 
 env:
   CACHE_NUMBER: 1  # increase to reset cache manually
+  SNAKEMAKE_RESULT_FILE: metadata4ing_provenance
+  PROVENANACE_FILE_NAME: element_size_vs_max_mises_stress.pdf
 
 jobs:
-  tests:
+  run-simulation:
     runs-on: ubuntu-latest
-
-
-
     steps:
       - name: checkout repo content
         uses: actions/checkout@v2
@@ -84,7 +83,7 @@ jobs:
 
   process-artifacts:
     runs-on: ubuntu-latest
-    needs: tests
+    needs: run-simulation
     steps:
       - name: Checkout repo content
         uses: actions/checkout@v2
@@ -108,14 +107,60 @@ jobs:
             activate-environment: postprocessing 
             use-mamba: true
             environment-file: benchmarks/linear-elastic-plate-with-hole/environment_postprocessing.yml
+      
+      - name: Validate Snakemake Result File
+        shell: bash -l {0}
+        run: |
+          python benchmarks/common/validate_provenance.py \
+            --provenance_folderpath "./$SNAKEMAKE_RESULT_FILE" 
 
       - name: Run plotting script
         shell: bash -l {0}
         run: |
           python benchmarks/linear-elastic-plate-with-hole/plot_metrics.py ./snakemake_fenics_provenance ./snakemake_kratos_provenance
 
-      - name: Upload PDF plot as artifact
+      - name: Upload snakemake results file as artifact
         uses: actions/upload-artifact@v4
         with:
           name: element-size-vs-stress-plot
-          path: element_size_vs_stress.pdf
+          path: ${{ env.PROVENANACE_FILE_NAME }}
+      
+      - name: Re-zip snakemake result folder
+        run: |
+          cd "./${SNAKEMAKE_RESULT_FILE}"
+          zip -r "../${SNAKEMAKE_RESULT_FILE}.zip" .
+
+      - name: Upload RoCrate Zip file onto RoHub
+        id: rohub_upload
+        shell: bash -l {0}
+        continue-on-error: true
+        run: |
+          LOG_FILE="${GITHUB_WORKSPACE}/rohub_upload_error.log"
+
+          # Run Python and capture stdout+stderr
+          OUTPUT="$(
+            python benchmarks/common/upload_provenance.py \
+              --provenance_folderpath "./${SNAKEMAKE_RESULT_FILE}.zip" \
+              --benchmark_name "linear-elastic-plate-with-hole" \
+              --username "${{ secrets.ROHUB_USERNAME }}" \
+              --password "${{ secrets.ROHUB_PASSWORD }}" \
+            2>&1
+          )"
+          PYTHON_EXIT_CODE=$?
+
+          # Standard convention: 0 = success, non-zero = failure
+          if [ "$PYTHON_EXIT_CODE" -eq 0 ]; then
+            echo "RoHub upload succeeded"
+            rm -f "$LOG_FILE" || true
+          else
+            echo "=== RoHub upload failed — writing log to $LOG_FILE ==="
+            printf '%s\n' "$OUTPUT" | tee "$LOG_FILE"
+          fi
+
+      - name: Upload RoHub error log
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: rohub-upload-error-log
+          path: ${{ github.workspace }}/rohub_upload_error.log
+          if-no-files-found: ignore

.github/workflows/run-julia-benchmark.yml

@@ -0,0 +1,54 @@
+name: Julia-CI
+on:
+  push:
+
+  pull_request:
+    branches: [ main ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+  # Runs the workflow once per day at 3:15am
+  schedule:
+    - cron: '3 16 * * *'
+
+env:
+  CACHE_NUMBER: 1  # increase to reset cache manually
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+
+
+
+    steps:
+      - name: checkout repo content
+        uses: actions/checkout@v2
+
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+            miniforge-version: latest
+            activate-environment: model-validation 
+            use-mamba: true
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.4.5
+      - name: Set strict channel priority
+        run: conda config --set channel_priority strict
+        
+      - name: Update environment
+        run: mamba env update -n model-validation -f environment_benchmarks.yml
+
+      - name: generate-config-files
+        shell: bash -l {0}
+        run: |
+          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
+          python generate_config.py
+
+      - name: run_linear-elastic-plate-with-hole-benchmarks_snakemake
+        shell: bash -l {0}
+        run: |
+          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
+          snakemake --use-conda --use-apptainer --cores=all --config tools=[extendablefem] configurations=["1","05","025","0125","00625","003125"]

benchmarks/linear-elastic-plate-with-hole/extendablefem/Project.toml

@@ -0,0 +1,14 @@
+[deps]
+ExtendableFEM = "a722555e-65e0-4074-a036-ca7ce79a4aed"
+ExtendableGrids = "cfc395e8-590f-11e8-1f13-43a2532b2fa8"
+Fire = "652a1917-b8e5-5d9b-be38-bbf27e56fe44"
+Gmsh = "705231aa-382f-11e9-3f0c-b7cb4346fdeb"
+GridVisualize = "5eed8a63-0fb0-45eb-886d-8d5a387d12b8"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+ZipArchives = "49080126-0e18-4c2a-b176-c102e4b3760c"
+
+[compat]
+LinearSolve = "~3.50.0"

benchmarks/linear-elastic-plate-with-hole/extendablefem/Snakefile

@@ -0,0 +1,32 @@
+
+import json
+import os
+
+tool = "extendablefem"
+result_dir = "snakemake_results/" + config["benchmark"] 
+configuration_to_parameter_file = config["configuration_to_parameter_file"]
+configurations = config["configurations"]
+
+rule setup_julia_environment:
+    input: f"{tool}/Project.toml"
+    output: manifest=f"{tool}/Manifest.toml"
+    singularity: "docker://julia:1.12.2-bookworm"
+    shell: 
+        """
+        julia --project={tool} -e 'using Pkg;Pkg.instantiate()'
+        """
+
+rule run_extendablefem_simulation:
+    input: 
+        parameters = lambda wildcards: configuration_to_parameter_file[wildcards.configuration],
+        mesh = f"{result_dir}/mesh/mesh_{{configuration}}.msh",
+        manifest = f"{tool}/Manifest.toml",
+    output:
+        zip = f"{result_dir}/{{tool}}/solution_field_data_{{configuration}}.zip",
+        metrics = f"{result_dir}/{{tool}}/solution_metrics_{{configuration}}.json",
+    singularity: "docker://julia:1.12.2-bookworm"
+    shell:
+        """
+        julia --project={tool} {tool}/run_extendablefem_simulation.jl --configfile {input.parameters} --meshfile {input.mesh} --outputzip {output.zip} --outputmetrics {output.metrics}
+        """
+

benchmarks/linear-elastic-plate-with-hole/extendablefem/run_extendablefem_simulation.jl

@@ -0,0 +1,173 @@
+using JSON
+using Fire
+using Gmsh
+using ExtendableGrids
+using ExtendableFEM
+using StaticArrays: @SArray
+using Unitful
+using LinearAlgebra
+using ZipArchives: ZipWriter, zip_newfile
+
+struct PlateConfig
+    id::String
+    F::Float64
+    E::Float64
+    ν::Float64
+    radius::Float64
+    length::Float64
+    element_order::Int64
+end
+
+struct Metrics
+    max_von_mises_stress_nodes::Float64
+end
+
+function value_with_unit(json::JSON.Object{String,Any})
+    res = uparse(string(json["value"])*json["unit"])
+    return res
+end
+
+
+function parse_config(configfile::String)
+    config = JSON.parsefile(configfile)
+    id =  config["configuration"]
+    F = ustrip(u"Pa",value_with_unit(config["load"]))
+    E = ustrip(u"Pa",value_with_unit(config["young-modulus"]))
+    ν = config["poisson-ratio"]["value"]
+    radius = ustrip(u"m",value_with_unit(config["radius"]))
+    length = ustrip(u"m",value_with_unit(config["length"]))
+    element_order = config["element-order"]
+    return PlateConfig(id,F,E,ν,radius,length,element_order)
+end
+
+
+function plane_stress_elasticity_tensor(E::Float64, ν::Float64)
+    G = (1 / (1 + ν)) * E * 0.5
+    λ = (ν / (1 - 2ν)) * 2 * G
+    return @SArray [
+        (λ + 2G) λ 0
+        λ (λ + 2G) 0
+        0 0 G
+    ]
+end
+
+
+function make_kernel(𝐂)
+    function LE_kernel_sym!(σ,εv,qpinfo)
+        mul!(σ,𝐂,εv)
+    end 
+    return LE_kernel_sym!
+end
+
+function u_ex_kernel!(result,qpinfo)
+    x = qpinfo.x[1]
+    y = qpinfo.x[2]
+    a = qpinfo.params[1]
+    T = qpinfo.params[2]
+    E = qpinfo.params[3]
+    ν = qpinfo.params[4]
+    r = sqrt(x^2+y^2)
+    θ = atan(y,x)
+    k = (3.0-ν)/(1.0+ν)
+    Ta_8mu = T*a*(1.0+ν)/(4.0*E)
+    ct = cos(θ)
+    c3t = cos(3.0*θ)
+    st = sin(θ)
+    s3t = sin(3.0*θ)
+    fac = 2.0 * (a/r)^3
+
+
+    result[1] = Ta_8mu * (
+          (r/a) * (k + 1.0) * ct
+        + 2.0*(a/r)*((1.0 + k) * ct + c3t)
+        - fac * c3t
+    )
+    result[2] = Ta_8mu * (
+          (r/a) * (k - 3.0) * st
+        + 2.0*(a/r)*((1.0 - k) * st + s3t)
+        - fac * s3t
+    )
+end
+
+function exact_error!(result,u, qpinfo)
+    u_ex_kernel!(result,qpinfo)
+    result .-= u 
+    result .= result .^2
+    return nothing
+end
+
+function solve_plate_with_hole(config::PlateConfig,grid::ExtendableGrid,outputzip::String,outputmetrics::String)
+
+    bfacemask!(grid,[0.,0.],[config.radius,config.radius],50)
+
+    PD = ProblemDescription("Linear elastic 2D Plate with hole, configuration "*config.id)
+    u = Unknown("u"; name= "displacement")
+    assign_unknown!(PD, u)
+    𝐂 = plane_stress_elasticity_tensor(config.E,config.ν)
+    LE_kernel_sym! = make_kernel(𝐂)
+    assign_operator!(PD, BilinearOperator(LE_kernel_sym!, [εV(u,1.0)]))
+    assign_operator!(PD, InterpolateBoundaryData(u, u_ex_kernel!; regions = [3,4], params = [config.radius,config.F,config.E,config.ν]))
+    assign_operator!(PD, HomogeneousBoundaryData(u; regions = [1], mask = [1,0]))
+    assign_operator!(PD, HomogeneousBoundaryData(u; regions = [2], mask = [0,1]))
+
+    FEType = H1Pk{2,2, config.element_order}
+    FES = FESpace{FEType}(grid)
+    sol = solve(PD,FES; timeroutputs = :hide)
+
+    u_ex = FEVector(FES; name="exact solution")
+    interpolate!(u_ex.FEVectorBlocks[1],ON_CELLS,u_ex_kernel!;params = [config.radius,config.F,config.E,config.ν])
+    u_exx = nodevalues(u_ex.FEVectorBlocks[1])[1,:]
+    u_exy = nodevalues(u_ex.FEVectorBlocks[1])[2,:]
+
+    u_x = nodevalues(sol[u])[1,:]
+    u_y = nodevalues(sol[u])[2,:]
+    u_mag = sqrt.(u_x.*u_x.+u_y.*u_y)
+    uex_mag = sqrt.(u_exx.*u_exx.+u_exy.*u_exy)
+
+    # TODO: Stress calculations
+
+    metrics = Metrics(0.)
+    # TODO: L2 error, see Example301
+    ErrorIntegrationExact = ItemIntegrator(exact_error!, [id(u)]; quadorder = 8,params = [config.radius,config.F,config.E,config.ν])
+
+    error = evaluate(ErrorIntegrationExact, sol)
+
+    L2error = sqrt(sum(error))
+
+    outputvtk = splitdir(outputzip)[1]*"/results_"*config.id*".vtu";
+    writeVTK(outputvtk,grid;compress=false, u_x=u_x,u_y=u_y,u_mag=u_mag,uexx=u_exx,uexy=u_exy,uex=uex_mag)
+    f = open(outputvtk,"r")
+    vtkcontent = read(f,String)
+    ZipWriter(outputzip) do w
+        zip_newfile(w, "result_"*config.id*".vtu";compress=true)
+        write(w,vtkcontent)
+    end
+    JSON.json(outputmetrics,metrics;pretty=true)
+
+end
+
+"run linear elastic plate with a hole using ExtendableFEM.jl"
+Fire.@main function run_simulation(;
+    configfile::String="", 
+    meshfile::String="",
+    outputzip::String="",
+    outputmetrics::String=""
+)
+    if(isempty(configfile))
+        @error "No configuration file given"
+    end
+    config = parse_config(configfile)
+    if(isempty(meshfile))
+        @error "No mesh file given"
+    end
+    if(isempty(outputzip))
+        @error "No output zip file given"
+    end
+    if(isempty(outputmetrics))
+        @error "No output metrics file given"
+    end
+    grid = simplexgrid_from_gmsh(meshfile)
+    solve_plate_with_hole(config,grid,outputzip,outputmetrics)
+
+    return
+end

benchmarks/linear-elastic-plate-with-hole/metadata4ing.config

@@ -0,0 +1,10 @@
+{
+    "researchProblem": {
+        "description": "This benchmark describes a linear-elastic plate with a hole test case used in the NFDI-4Ing Model Validation Platform for comparing and validating computational modelling methods."
+    },
+    "rocrate": {
+        "name": "NFDI4Ing Provenance",
+        "description": "Benchmark for linear-elastic plate with a hole",
+        "license": "https://opensource.org/licenses/MIT"
+    }
+}