Set up Docker-based workflow for macOS

Author: Sarbani-Roy

.gitignore

@@ -1,2 +1,31 @@
 .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/
+
+# (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

@@ -21,9 +21,11 @@ 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}
         """
 
@@ -54,9 +56,11 @@ 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

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

dockerfiles/Dockerfile

@@ -0,0 +1,46 @@
+# -----------------------------
+# Dockerfile for NFDI_Benchmark
+# -----------------------------
+
+# Base image similar to GitHub Actions ubuntu-latest
+FROM --platform=linux/amd64 ubuntu:22.04
+
+# Avoid interactive prompts during apt installs
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install basic dependencies
+RUN apt-get update && apt-get install -y \
+    wget curl git unzip zip bzip2 libbz2-dev python3 python3-pip \
+    build-essential && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Miniforge3 for amd64 architecture
+RUN wget https://github.com/conda-forge/miniforge/releases/download/24.11.0-0/Miniforge3-24.11.0-0-Linux-x86_64.sh && \
+    bash Miniforge3-24.11.0-0-Linux-x86_64.sh -b -p /opt/miniforge && \
+    rm Miniforge3-24.11.0-0-Linux-x86_64.sh
+
+# Add conda/mamba to PATH
+ENV PATH="/opt/miniforge/bin:$PATH"
+
+ENV OMP_NUM_THREADS=1
+ENV KMP_AFFINITY=disabled
+ENV OMP_PROC_BIND=FALSE
+
+# Set working directory inside container
+WORKDIR /NFDI_Benchmark
+
+# Copy only environment yaml first to leverage Docker caching
+COPY environment_benchmarks.yml /NFDI_Benchmark/
+
+# Create model-validation environment
+RUN mamba env create -n model-validation -f environment_benchmarks.yml && \
+    echo "conda activate model-validation" >> ~/.bashrc
+
+# Copy the rest of the repo into container
+COPY . /NFDI_Benchmark
+
+# Use bash login shell by default
+SHELL ["bash", "-l", "-c"]
+
+# Drop into interactive bash shell when container starts
+CMD ["/bin/bash"]

dockerfiles/Dockerfile_base_env_ready

@@ -0,0 +1,40 @@
+# Use Ubuntu base image under x86_64 emulation for Apple Silicon Macs
+FROM --platform=linux/amd64 ubuntu:22.04
+
+# Prevent interactive prompts during package installs
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Update system and install required packages
+RUN apt-get update && apt-get install -y \
+    wget git build-essential curl unzip \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Miniforge (Conda for ARM/x86 compatible builds)
+ENV CONDA_DIR=/opt/miniforge
+RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O /tmp/miniforge.sh && \
+    bash /tmp/miniforge.sh -b -p $CONDA_DIR && \
+    rm /tmp/miniforge.sh
+ENV PATH=$CONDA_DIR/bin:$PATH
+
+# Initialize Conda shell integration
+RUN conda init bash
+
+# Create default working directory
+WORKDIR /NFDI_Benchmark
+
+# Copy your repository into the image (optional; or mount it later)
+# COPY . /NFDI_Benchmark
+
+# Pre-install mamba (faster environment management)
+RUN conda install -y mamba -n base -c conda-forge
+
+# Create and activate a base environment for model validation
+RUN mamba create -n model-validation python=3.10 -y && \
+    echo "source $CONDA_DIR/etc/profile.d/conda.sh && conda activate model-validation" >> ~/.bashrc
+
+# Set environment variables for stability under emulation
+ENV OMP_NUM_THREADS=1
+ENV KMP_AFFINITY=disabled
+
+# Default command starts bash with Conda activated
+ENTRYPOINT ["/bin/bash", "-l"]