config-generator: non-interactive mode

examples/config-generator/README.md

@@ -42,6 +42,8 @@ This file has the following structure:
 
 ### Usage
 1. Navigate to the target directory for the `couette.xml` file (most likely the MaMiCo build folder)
-2. Execute `$MAMICO_DIR/examples/config-generator/run`
+2. Execute `$MAMICO_DIR/examples/config-generator/run`  
+Specific values can be fixed by providing them as a command line argument, e.g. `--override=domain_size=large,use_checkpoint=False,multi_md=2`.  
+The corresponding entries will be removed from the interactive menu. If all configurations are overwritten, the script will run non-interactively. (May be used for automated testing.)
 3. Customize the generator settings and generate the `couette.xml` file
-3. Customize the generated configuration even further according to the [documentation](https://github.com/HSU-HPC/MaMiCo/wiki/couette.xml) (optional)
+4. Customize the generated configuration even further according to the [documentation](https://github.com/HSU-HPC/MaMiCo/wiki/couette.xml) (optional)

examples/config-generator/assets/configuration_template.json

@@ -1,22 +1,19 @@
 [
   {
-    "key": "domain",
+    "key": "domain_size",
     "label": "domain size",
     "options": [
       {
         "selected": true,
-        "value": 1,
-        "label": "small",
+        "value": "small",
         "description": "MD/CFD domain size = 30\u00B3/50\u00B3"
       },
       {
-        "value": 2,
-        "label": "medium",
+        "value": "medium",
         "description": "MD/CFD domain size = 60\u00B3/100\u00B3"
       },
       {
-        "value": 3,
-        "label": "large",
+        "value": "large",
         "description": "MD/CFD domain size = 120\u00B3/200\u00B3"
       }
     ]
@@ -188,4 +185,4 @@
       }
     ]
   }
-]
+]

examples/config-generator/run

@@ -4,7 +4,7 @@
 # Any dependencies are automatically installed.
 # The output of the script is saved to the current working directory.
 
-OUTPUT="$(pwd)/couette.xml"
+OUTPUT="$(pwd)"
 
 cd "$(dirname "$0")" || exit
 
@@ -22,4 +22,4 @@ fi
 source .venv/bin/activate
 
 # Run the config builder
-python3 src/main.py "$OUTPUT"
+python3 src/main.py --output "$OUTPUT" "$@"

examples/config-generator/src/generators/domain.py → examples/config-generator/src/generators/domain_size.py

@@ -2,19 +2,22 @@
 from generators.mpi_ranks import get_ranks_xyz
 
 
-def _get_domain_size(get_config_value) -> int:
+def get_domain_size(get_config_value) -> int:
     key = __name__.split(".")[-1]
-    return get_config_value(key)
+    domain_size_name = get_config_value(key)
+    domain_size_names = ["small", "medium", "large"]
+    return domain_size_names.index(domain_size_name) + 1
 
 
 def get_domain_sizes(get_config_value) -> int:
-    size = _get_domain_size(get_config_value)
+    size = get_domain_size(get_config_value)
     md_base_size = 30
     cfd_base_size = 50
     md_domain_size = md_base_size * size
     cfd_domain_size = cfd_base_size * size
     if size == 3:
         md_domain_size = 120  # instead of 90
+        cfd_domain_size = 200  # instead of 150
     return md_domain_size, cfd_domain_size
 
 
@@ -35,7 +38,7 @@ def validate(get_config_value) -> str:
 def apply(partial_xml, get_config_value) -> None:
     equilibration_steps = 10000
     equilibration_steps_max = 20000
-    size = _get_domain_size(get_config_value)
+    size = get_domain_size(get_config_value)
     md_domain_size, cfd_domain_size = get_domain_sizes(get_config_value)
     domain_offset_xy = (cfd_domain_size - md_domain_size) / 2  # Centered
     partial_xml.substitute("md-size", md_domain_size)

examples/config-generator/src/generators/filtering.py

@@ -25,7 +25,7 @@ def apply(partial_xml, get_config_value) -> None:
 """.strip()
 
     if filtering == False:
-        per_instance_filtering_xml = "<per-instance output=\"md\"></per-instance>"
+        per_instance_filtering_xml = '<per-instance output="md"></per-instance>'
     elif filtering == "gauss":
         per_instance_filtering_xml = xml_2d_gaussian
     elif filtering == "nlm":

examples/config-generator/src/generators/simulation.py

@@ -1,7 +1,10 @@
+from generators.domain_size import get_domain_size
+
+
 def apply(partial_xml, get_config_value) -> None:
     key = __name__.split(".")[-1]
     simulation_type = get_config_value(key)
-    domain_size = get_config_value("domain")
+    domain_size = get_domain_size(get_config_value)
     match simulation_type:
         case "test":
             partial_xml.substitute("coupling-cycles", 50)

examples/config-generator/src/generators/solver_md.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from generators.cell_size import get_molecules_per_direction
-from generators.domain import get_domain_sizes
+from generators.domain_size import get_domain_sizes
 from utils import get_asset_text
 from xml_templating import PartialXml
 
@@ -15,7 +15,7 @@ def _create_ls1_config(get_config_value) -> None:
     xml.substitute("grid-filler-lattice", grid_filler_lattice)
     boundary_condition = get_config_value("boundary")
     xml.substitute("boundary-condition", boundary_condition)
-    filename = Path(get_config_value("output_filename")).parent / "ls1config.xml"
+    filename = Path(get_config_value("output_dir")) / "ls1config.xml"
     with open(filename, "w") as file:
         file.write(xml.get())
 

examples/config-generator/src/generators/use_checkpoint.py

@@ -1,14 +1,16 @@
 import shutil
 from pathlib import Path
 
+from generators.domain_size import get_domain_size
+
 
 def validate(get_config_value) -> str:
     """MaMiCo config validation:
     A pre-computed checkpoint is (currently) only available for Simple MD with a 30x30x30 domain.
     """
     key = __name__.split(".")[-1]
     use_checkpoint = get_config_value(key)
-    domain_size = get_config_value("domain")
+    domain_size = get_domain_size(get_config_value)
     solver_md = get_config_value("solver_md")
     if use_checkpoint and (domain_size > 1 or solver_md != "md"):
         return f"Example checkpoint file only provided for small Simple MD simulation."
@@ -29,8 +31,7 @@ def apply(partial_xml, get_config_value) -> None:
             / f"CheckpointSimpleMD_10000_{boundary_condition}_0.checkpoint"
         )
         checkpoint_dst_path = (
-            Path(get_config_value("output_filename")).parent
-            / "CheckpointSimpleMD.checkpoint"
+            Path(get_config_value("output_dir")) / "CheckpointSimpleMD.checkpoint"
         )
         # Avoid reading and writing the contents of the file, because it is rather large
         shutil.copyfile(checkpoint_src_path, checkpoint_dst_path)