Add Docker-based workflow setup, environment fixes, and improved .gitignore

.github/workflows/docker_ci.yml

@@ -0,0 +1,107 @@
+name: Docker-based CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+  # schedule:
+  #   - cron: '3 16 * * *'
+
+permissions:
+  contents: write
+
+jobs:
+  build-docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+            persist-credentials: false
+
+      # -----------------------------
+      # Build Docker images
+      # -----------------------------
+      - name: Build base image (mesh generation included)
+        run: docker build -t ci-base -f dockerfiles/Dockerfile.base .
+
+      - name: Build Fenics image (simulations included)
+        run: docker build -t ci-fenics -f dockerfiles/Dockerfile.fenics .
+
+      - name: Build Kratos image (simulations included)
+        run: docker build -t ci-kratos -f dockerfiles/Dockerfile.kratos .
+
+      # -----------------------------
+      # Extract Fenics results
+      # -----------------------------
+      - name: Extract Results from Fenics container
+        run: |
+          docker create --name fenics_temp ci-fenics
+          # Copy the results folder as-is from container to host
+          docker cp fenics_temp:/sim/benchmarks/linear-elastic-plate-with-hole/results ./benchmarks/linear-elastic-plate-with-hole/
+          docker rm fenics_temp
+
+      # -----------------------------
+      # Extract Kratos results
+      # -----------------------------
+      - name: Extract Kratos results
+        run: |
+          docker create --name kratos_temp ci-kratos
+          # Copy the results folder as-is from container to host
+          docker cp kratos_temp:/sim/benchmarks/linear-elastic-plate-with-hole/results ./benchmarks/linear-elastic-plate-with-hole/
+          docker rm kratos_temp
+
+      # -----------------------------
+      # Upload Artifacts
+      # -----------------------------
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: workflow-results
+          path: |
+            benchmarks/linear-elastic-plate-with-hole/results/fenics
+            benchmarks/linear-elastic-plate-with-hole/results/kratos
+
+      # # -----------------------------
+      # # Optional: commit generated results to GitHub
+      # # -----------------------------
+      # - name: Commit generated results
+      #   env:
+      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      #   run: |
+      #     git config --global user.name "github-actions[bot]"
+      #     git config --global user.email "github-actions[bot]@users.noreply.github.com"
+
+      #     # Create a flat zip of the simulation results
+      #     cd benchmarks/linear-elastic-plate-with-hole
+      #     tar -cJf simulation_results.tar.xz results
+      #     cd ../..
+
+      #     # Add only the zip
+      #     git add -f benchmarks/linear-elastic-plate-with-hole/simulation_results.tar.xz
+
+      #     git commit -m "Add generated simulation results" || echo "No changes to commit"
+      #     git push https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git HEAD:main
+
+      # - name: Build Postprocessing image
+      #   run: |
+      #     docker build -t ci-postprocessing -f dockerfiles/Dockerfile.postprocessing .
+
+      # - name: Postprocessing (metadata + extraction + plot)
+      #   run: |
+      #     docker run --rm \
+      #       -v ${{ github.workspace }}:/workspace \
+      #       -w /workspace/benchmarks/linear-elastic-plate-with-hole \
+      #       ci-postprocessing \
+      #       bash -c '
+      #         echo "Generating metadata...";
+      #         python parameter_extractor.py ./results metadata4ing_provenance.zip;
+      #
+      #         echo "Extracting ZIP...";
+      #         mkdir -p ./metadata4ing_provenance;
+      #         unzip -o metadata4ing_provenance.zip -d ./metadata4ing_provenance;
+      #
+      #         echo "Plotting provenance...";
+      #         python plot_provenance.py ./metadata4ing_provenance
+      #       '

.gitignore

@@ -1,2 +1,32 @@
 .snakemake
-site
+site
+
+# macOS system files
+.DS_Store
+
+# Python cache files
+__pycache__/
+*.py[cod]
+
+# Benchmark and workflow output files
+benchmarks/linear-elastic-plate-with-hole/element_size_vs_stress.pdf
+benchmarks/linear-elastic-plate-with-hole/metadata4ing_provenance.zip
+benchmarks/linear-elastic-plate-with-hole/workflow_config.json
+
+# Generated folders and outputs
+benchmarks/linear-elastic-plate-with-hole/metadata4ing_provenance/
+benchmarks/linear-elastic-plate-with-hole/snakemake_results/
+benchmarks/linear-elastic-plate-with-hole/results/
+
+# (Optional) ignore all ZIP and PDF files in benchmarks if they are always generated
+# benchmarks/**/*.zip
+# benchmarks/**/*.pdf
+
+# VS Code / IDE settings (optional, if you use editors)
+.vscode/
+.idea/
+
+# Conda and environment files (optional safety)
+*.lock
+*.log
+.env

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

@@ -22,9 +22,11 @@ rule create_mesh:
         parameters = lambda wildcards: configuration_to_parameter_file[wildcards.configuration],
     output:
         mesh = f"{result_dir}/mesh/mesh_{{configuration}}.msh",
-    conda: "environment_mesh.yml"
+    # conda: "environment_mesh.yml"
     shell:
         """
+        source /opt/miniforge/etc/profile.d/conda.sh
+        conda activate mesh
         python3 {input.script} --input_parameter_file {input.parameters} --output_mesh_file {output.mesh}
         """
 
@@ -55,9 +57,11 @@ rule summary:
         ),
     output:
         summary_json = f"{result_dir}/{{tool}}/summary.json",
-    conda: "environment_postprocessing.yml",
+    # conda: "environment_postprocessing.yml",
     shell:
         """
+        source /opt/miniforge/etc/profile.d/conda.sh
+        conda activate postprocessing
         python3 {input.script} \
             --input_configuration {configurations} \
             --input_parameter_file {input.parameters} \

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

@@ -15,9 +15,23 @@ rule run_fenics_simulation:
     output:
         zip = f"{result_dir}/{{tool}}/solution_field_data_{{configuration}}.zip",
         metrics = f"{result_dir}/{{tool}}/solution_metrics_{{configuration}}.json",
-    conda:
-        "environment_simulation.yml",
+    # conda:
+    #     "environment_simulation.yml",
     shell:
         """
-        python3 {input.script} --input_parameter_file {input.parameters} --input_mesh_file {input.mesh} --output_solution_file_zip {output.zip} --output_metrics_file {output.metrics}
+        # Disable 'unbound variable' errors to avoid ADDR2LINE issues
+        set +u
+        # Load conda
+        source /opt/miniforge/etc/profile.d/conda.sh
+        # Activate the FEniCS environment
+        conda activate fenics-sim
+        # Prevent OpenMP crash under qemu (macOS/arm64 emulation)
+        export OMP_NUM_THREADS=1
+
+        # Run the actual simulation
+        python3 {input.script} \
+            --input_parameter_file {input.parameters} \
+            --input_mesh_file {input.mesh} \
+            --output_solution_file_zip {output.zip} \
+            --output_metrics_file {output.metrics}
         """

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

@@ -16,10 +16,12 @@ rule mesh_to_mdpa:
         script = f"{tool}/msh_to_mdpa.py",
     output:
         mdpa = f"{result_dir}/{tool}/mesh_{{configuration}}.mdpa",
-    conda:
-        "environment_simulation.yml",
+    # conda:
+    #     "environment_simulation.yml",
     shell:
         """
+        source /opt/miniforge/etc/profile.d/conda.sh
+        conda activate kratos-sim
         python3 {input.script} \
             --input_parameter_file {input.parameters} \
             --input_mesh_file {input.mesh} \
@@ -44,10 +46,12 @@ rule create_kratos_input_and_run_simulation:
         kratos_inputfile = f"{result_dir}/{tool}/ProjectParameters_{{configuration}}.json",
         kratos_materialfile = f"{result_dir}/{tool}/MaterialParameters_{{configuration}}.json",
         result_vtk = f"{result_dir}/{tool}/{{configuration}}/Structure_0_1.vtk",
-    conda:
-        "environment_simulation.yml",
+    # conda:
+    #     "environment_simulation.yml",
     shell:
         """
+        source /opt/miniforge/etc/profile.d/conda.sh
+        conda activate kratos-sim
         python3 {input.script_create_kratos_input} \
             --input_parameter_file {input.parameters} \
             --input_mdpa_file {input.mdpa} \
@@ -70,10 +74,12 @@ rule postprocess_kratos_results:
     output:
         zip = f"{result_dir}/{tool}/solution_field_data_{{configuration}}.zip",
         metrics = f"{result_dir}/{tool}/solution_metrics_{{configuration}}.json",
-    conda:
-        "environment_simulation.yml",
+    # conda:
+    #     "environment_simulation.yml",
     shell:
         """
+        source /opt/miniforge/etc/profile.d/conda.sh
+        conda activate kratos-sim
         python3 {input.script} \
             --input_parameter_file {input.parameters} \
             --input_result_vtk {input.result_vtk} \

benchmarks/linear-elastic-plate-with-hole/kratos/environment_simulation.yml

@@ -9,7 +9,7 @@ dependencies:
   - python-gmsh
   - pint
   - pyvista
+  - sympy
   - pip
   - pip:
-    - KratosMultiphysics-all
-  - sympy
+    - KratosMultiphysics-all==9.0.2