Moved DuMuX-specific rules into a dedicated Snakefile and use environment_benchmarks in the DuMuX workflow file.

Author: Sarbani-Roy

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

@@ -27,7 +27,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
             miniforge-version: latest
-            activate-environment: rc-dumux
+            activate-environment: model-validation
             use-mamba: true
 
       - name: Set strict channel priority
@@ -39,7 +39,7 @@ jobs:
           apptainer-version: 1.4.5
 
       - name: Update environment
-        run: mamba env update -n rc-dumux -f $GITHUB_WORKSPACE/benchmarks/rotating-cylinders/environment_dumux.yaml
+        run: mamba env update -n model-validation -f environment_benchmarks.yml
 
       - name: generate-rc-config
         shell: bash -l {0}

benchmarks/rotating-cylinders/Snakefile

@@ -11,44 +11,44 @@ configfile: "rotating-cylinders_config.json"
 tools = config["tools"]
 configs = config["configurations"]
 benchmark = config["benchmark"]
-benchmark_uri = config.get("benchmark_uri", "https://nfdi-benchmark.org/rc") 
+benchmark_uri = config["benchmark_uri"]
 result_dir = f"snakemake_results/{benchmark}"
 shared_dir = os.getcwd()
-dumux_dir = f"{shared_dir}/dumux"
 
 rule all:
     input:
         expand(f"{result_dir}/{{tool}}/summary.json", tool=tools)
 
-rule generate_dumux_inputs:
-    input:
-        grid_t = f"{dumux_dir}/grid_files/grid_template.json",
-        dumux_t = f"{dumux_dir}/input_files/dumux_config.json"
-    output:
-        params = expand(f"{dumux_dir}/input_files/params_{{conf}}.input", conf=configs),
-        grids = expand(f"{dumux_dir}/grid_files/grid_{{conf}}.json", conf=configs)
-    shell:
-        "python3 dumux_input_gen.py --grid_template {input.grid_t} --dumux_template {input.dumux_t}"
-
 for tool in tools:
     include: f"{tool}/Snakefile"
 
 rule summary:
     input:
         script = "../common/summarize_results.py",
-        # We use the grids generated by the generator rule
-        parameters = expand(f"{dumux_dir}/grid_files/grid_{{conf}}.json", conf=configs),
-        mesh = expand(f"{dumux_dir}/grid_files/grid_{{conf}}.json", conf=configs), 
-        metrics = lambda wildcards: expand(
-            f"{result_dir}/{{tool}}/solution_metrics_{{conf}}.json",
-            tool=[wildcards.tool], conf=configs
+
+        parameters=lambda wc: expand(
+            f"{shared_dir}/{wc.tool}/grid_files/grid_{{conf}}.json",
+            conf=configs
+        ),
+
+        mesh=lambda wc: expand(
+            f"{shared_dir}/{wc.tool}/grid_files/grid_{{conf}}.json",
+            conf=configs
+        ),
+
+        metrics=lambda wc: expand(
+            f"{result_dir}/{wc.tool}/solution_metrics_{{conf}}.json",
+            conf=configs
         ),
-        solution_field_data = lambda wildcards: expand(
-            f"{result_dir}/{{tool}}/solution_field_data_{{conf}}.zip",
-            tool=[wildcards.tool], conf=configs
+
+        solution_field_data=lambda wc: expand(
+            f"{result_dir}/{wc.tool}/solution_field_data_{{conf}}.zip",
+            conf=configs
         )
+
     output:
-        summary_json = f"{result_dir}/{{tool}}/summary.json"
+        summary_json=f"{result_dir}/{{tool}}/summary.json"
+
     shell:
         """
         python3 {input.script} \

benchmarks/rotating-cylinders/dumux/Snakefile

@@ -1,13 +1,24 @@
+# benchmarks/rotating-cylinders/dumux/Snakefile
 import os
 
-# 1. Setup and Config
+# Setup and Config
 tool = "dumux"
+container_image = config["container_image"]
+dumux_dir = f"{shared_dir}/dumux"
 
-# Use .get() to prevent crashes if config isn't fully loaded yet
-benchmark_name = config.get("benchmark", "rotating-cylinders")
-container_image = config.get("container_image", "git.iws.uni-stuttgart.de:4567/benchmarks/rotating-cylinders:3.0")
+# Rule 1: Input generation
+rule generate_dumux_inputs:
+    input:
+        grid_t = f"{dumux_dir}/grid_files/grid_template.json",
+        dumux_t = f"{dumux_dir}/input_files/dumux_config.json",
+        input_gen_script = f"{dumux_dir}/dumux_input_gen.py"
+    output:
+        params = expand(f"{dumux_dir}/input_files/params_{{conf}}.input", conf=configs),
+        grids = expand(f"{dumux_dir}/grid_files/grid_{{conf}}.json", conf=configs)
+    shell:
+        "python3 {input.input_gen_script} --grid_template {input.grid_t} --dumux_template {input.dumux_t}"
 
-# Rule 1: Simulation
+# Rule 2: Simulation
 rule run_dumux_simulation:
     input:
         # Lambda prevents KeyError before the JSON is generated
@@ -28,7 +39,7 @@ rule run_dumux_simulation:
         ./test_ff_navierstokes_rotatingcylinders {input.params}
         """
 
-# Rule 2: Post-processing
+# Rule 3: Post-processing
 rule postprocess_dumux:
     input:
         sim_data = [

…ks/rotating-cylinders/dumux_input_gen.py …ating-cylinders/dumux/dumux_input_gen.pybenchmarks/rotating-cylinders/dumux_input_gen.py renamed to benchmarks/rotating-cylinders/dumux/dumux_input_gen.py benchmarks/rotating-cylinders/dumux_input_gen.py renamed to benchmarks/rotating-cylinders/dumux/dumux_input_gen.py

@@ -26,9 +26,8 @@ def write_benchmark_config():
         "benchmark": "rotating-cylinders",
         "benchmark_uri": "https://www.openfoam.com/documentation/guides/latest/doc/verification-validation-rotating-cylinders-2d.html",
         "tools": ["dumux"],
-        "configurations": configurations,
         "configuration_to_parameter_file": config_to_param,
-        "configuration_to_solution_vtu_files": config_to_vtu,
+        "configurations": configurations,
         "container_image": "git.iws.uni-stuttgart.de:4567/benchmarks/rotating-cylinders:3.0"
     }