Add a class to parse FMS profiling data.

om3utils/fms_profiling.py

@@ -0,0 +1,70 @@
+"""FMS profiling data parser."""
+
+from pathlib import Path
+import re
+
+from om3utils.utils import convert_from_string
+from om3utils.profiling import ProfilingParser
+
+
+class FMSProfilingParser(ProfilingParser):
+    """Defines a ProfilingParser for FMS profiling data, such as output by MOM6.
+
+    The data to be parsed is written in the following form:
+
+                                       hits          tmin          tmax          tavg          tstd  tfrac grain pemin pemax
+    Total runtime                         1    138.600364    138.600366    138.600365      0.000001  1.000     0     0    11
+    Ocean Initialization                  2      2.344926      2.345701      2.345388      0.000198  0.017    11     0    11
+    Ocean                                23     86.869466     86.871652     86.870450      0.000744  0.627     1     0    11
+    Ocean dynamics                       96     43.721019     44.391032     43.957944      0.244785  0.317    11     0    11
+    Ocean thermodynamics and tracers     72     27.377185     33.281659     29.950144      1.792324  0.216    11     0    11
+     MPP_STACK high water mark=           0
+    """
+
+    def __init__(self, filename: str):
+        super().__init__()
+
+        # FMS provides the following metrics:
+        self._metrics = ["hits", "tmin", "tmax", "tavg", "tstd", "tfrac", "grain", "pemin", "pemax"]
+        self._filename = filename
+
+    @property
+    def metrics(self) -> list:
+        return self._metrics
+
+    def read(self, path: Path) -> dict:
+        """Given a file path, returns a dictionary holding the parsed data.
+
+        Args:
+            path (Path): File to parse.
+
+        Returns:
+            dict: Profiling data.
+        """
+        profiling_file = path / self._filename
+        if not profiling_file.is_file():
+            raise FileNotFoundError(f"File not found: {profiling_file.as_posix()}")
+
+        # Regular expression to extract the profiling section from the file
+        header = r"\s*hits\s*tmin\s*tmax\s*tavg\s*tstd\s*tfrac\s*grain\s*pemin\s*pemax\s*"
+        footer = r" MPP_STACK high water mark=\s*\d*"
+        profiling_section_p = re.compile(header + r"(.*)" + footer, re.DOTALL)
+
+        # Regular expression to parse the data for each region
+        profile_line = r"^\s*(?P<region>[a-zA-Z:()_/\-*&\s]+(?<!\s))"
+        for metric in self.metrics:
+            profile_line += r"\s+(?P<" + metric + r">[0-9.]+)"
+        profile_line += r"$"
+        profiling_region_p = re.compile(profile_line, re.MULTILINE)
+
+        # Parse data
+        stats = {"region": []}
+        stats.update(dict(zip(self.metrics, [[] for _ in self.metrics])))
+        with open(profiling_file, "r") as f:
+            profiling_section = profiling_section_p.search(f.read()).group(1)
+            for line in profiling_region_p.finditer(profiling_section):
+                stats["region"].append(line.group("region"))
+                for metric in self.metrics:
+                    stats[str(metric)].append(convert_from_string(line.group(metric)))
+
+        return stats

tests/test_fms_profiling.py

@@ -0,0 +1,59 @@
+import pytest
+from pathlib import Path
+
+from test_utils import MockFile
+from om3utils.fms_profiling import FMSProfilingParser
+
+
+@pytest.fixture()
+def simple_fms_stats():
+    return {
+        "region": [
+            "Total runtime",
+            "Ocean Initialization",
+            "Ocean",
+            "Ocean dynamics",
+            "Ocean thermodynamics and tracers",
+        ],
+        "hits": [1.0, 2.0, 23.0, 96.0, 72.0],
+        "tmin": [138.600364, 2.344926, 86.869466, 43.721019, 27.377185],
+        "tmax": [138.600366, 2.345701, 86.871652, 44.391032, 33.281659],
+        "tavg": [138.600365, 2.345388, 86.87045, 43.957944, 29.950144],
+        "tstd": [1e-06, 0.000198, 0.000744, 0.244785, 1.792324],
+        "tfrac": [1.0, 0.017, 0.627, 0.317, 0.216],
+        "grain": [0.0, 11.0, 1.0, 11.0, 11.0],
+        "pemin": [0.0, 0.0, 0.0, 0.0, 0.0],
+        "pemax": [11.0, 11.0, 11.0, 11.0, 11.0],
+    }
+
+
+@pytest.fixture()
+def simple_fms_output_file(tmp_path):
+    file = tmp_path / "simple_output_file "
+    output_str = """Some random stuff
+over a few lines
+with some number: 1, 2, 3
+and special symbols: | /* #
+then the actual profiling output:
+                                   hits          tmin          tmax          tavg          tstd  tfrac grain pemin pemax
+Total runtime                         1    138.600364    138.600366    138.600365      0.000001  1.000     0     0    11
+Ocean Initialization                  2      2.344926      2.345701      2.345388      0.000198  0.017    11     0    11
+Ocean                                23     86.869466     86.871652     86.870450      0.000744  0.627     1     0    11
+Ocean dynamics                       96     43.721019     44.391032     43.957944      0.244785  0.317    11     0    11
+Ocean thermodynamics and tracers     72     27.377185     33.281659     29.950144      1.792324  0.216    11     0    11
+ MPP_STACK high water mark=           0
+"""
+    return MockFile(file, output_str)
+
+
+def test_fms_profiling_read(tmp_path, simple_fms_output_file, simple_fms_stats):
+    parser = FMSProfilingParser(simple_fms_output_file.file.name)
+    stats = parser.read(tmp_path)
+
+    assert stats == simple_fms_stats
+
+
+def test_read_missing_fms_profiling_file():
+    with pytest.raises(FileNotFoundError):
+        parser = FMSProfilingParser("benchmark")
+        parser.read(Path("garbage"))