run OpenFOAM with snakemake

Author: mschwarzmeier

.github/workflows/run-benchmark.yml

@@ -19,6 +19,8 @@ env:
 jobs:
   tests:
     runs-on: ubuntu-latest
+    container:
+      image: opencfd/openfoam-run:2412
 
     steps:
       - name: checkout repo content
@@ -35,11 +37,18 @@ jobs:
         run: mamba env update -n model-validation -f environment_benchmarks.yml
         if: steps.cache.outputs.cache-hit != 'true'
 
+      - name: Ensure log directory exists
+        run: mkdir -p benchmarks/rotating-cylinder-OpenFOAM/.snakemake/log
+
       - name: run-OpenFOAM-benchmarks
         shell: bash -l {0}
         run: |
           cd $GITHUB_WORKSPACE/benchmarks/rotating-cylinder-OpenFOAM/
-          snakemake --force --cores 'all'
+          mkdir -p ./.snakemake/log || true # bc. snakemake is not able to create this directory itself
+          chmod +x Allrun
+          echo "Starting snakemake"
+          snakemake --cores 1
+          echo "Finished job."
 
       - name: run-fenics-benchmarks
         shell: bash -l {0}
@@ -100,7 +109,7 @@ jobs:
         shell: bash -l {0}
         run: |
           cd $GITHUB_WORKSPACE/benchmarks/rotating-cylinder-OpenFOAM/
-          sudo apt-get update && sudo apt-get install -y gnuplot
+          # sudo apt-get update && sudo apt-get install -y gnuplot
           chmod +x ./plot
           bash ./Allrun
           echo "Finished job"

benchmarks/rotating-cylinder-OpenFOAM/Allrun

@@ -5,6 +5,8 @@ cd "${0%/*}" || exit                                # Run from this directory
 
 runApplication blockMesh
 runApplication $(getApplication)
-./plot
+
+echo "Simulation completed. You could now post-process (e.g. visualize) the results."
+# ./plot # disabled for benchmark/snakemake-setup
 
 #------------------------------------------------------------------------------

benchmarks/rotating-cylinder-OpenFOAM/Snakefile

@@ -1,8 +1,17 @@
 
 rule run_simulation_container:
     input:
-        ".",
-    output:
-        directory("."),
+        mesh="system/blockMeshDict",
+        config="system/controlDict",
+        initial_conditions="0/",
+        scripts="Allrun"
+    output: 
+        directory("1000"),
     container: "docker://opencfd/openfoam-run:2412"
-    shell: "./Allrun"
+    shell:
+        """
+        set -euo pipefail
+        echo "Starting simulation."
+        ./Allrun
+        ls -la
+        """