Merge pull request #61 from converged-computing/cleanup-osu-parsing

add support for more specific osu parsing

Author: vsoch

examples/python/network-osu-benchmark/README.md

@@ -40,3 +40,5 @@ $ python run-metric-multiple.py --iter 5
 ![img/multiple/OSU-MPI_Put-Latency-Test-v5.8.png](img/multiple/OSU-MPI_Put-Latency-Test-v5.8.png)
 
 
+Note that if you add the option `timed: true` this will add extra 'wrapper' times around the above,
+and an extra data output for it in your results.

sdk/python/v1alpha1/CHANGELOG.md

@@ -14,6 +14,8 @@ and **Merged pull requests**. Critical items to know are:
 The versions coincide with releases on pip. Only major versions will be released as tags on Github.
 
 ## [0.0.x](https://github.com/converged-computing/metrics-operator/tree/main) (0.0.x)
+ - More specific parsing / control for OSU benchmarks (0.0.21)
+ - Support for OSU benchmark parsing with timed wrappers (0.0.2)
  - Allow getting raw logs for any metric (without parser) (0.0.19)
  - Refactor of structure of Operator and addition of metrics (0.0.18)
  - Add wait for delete function to python parser (0.0.17)

sdk/python/v1alpha1/metricsoperator/metrics/network/__init__.py

@@ -0,0 +1,2 @@
+from .netmark import network_netmark
+from .osu_benchmark import network_osu_benchmark

sdk/python/v1alpha1/metricsoperator/metrics/network.py renamed to sdk/python/v1alpha1/metricsoperator/metrics/network/netmark.py

@@ -1,85 +1,7 @@
 # Copyright 2023 Lawrence Livermore National Security, LLC
 # (c.f. AUTHORS, NOTICE.LLNS, COPYING)
 
-
-from .base import MetricBase
-
-
-class network_osu_benchmark(MetricBase):
-    """
-    Parse the OSU benchmarks output into data!
-    """
-
-    container_name = "launcher"
-
-    @property
-    def pod_prefix(self):
-        return f"{self.name}-l-0"
-
-    def parse_row(self, row):
-        """
-        Given a row of two values with spaces, parse.
-        """
-        row = row.split(" ", 1)
-        return [x.strip() for x in row]
-
-    def parse_log(self, lines):
-        """
-        Given lines of output, parse and return json
-        """
-        # Get the log metadata
-        metadata = self.get_log_metadata(lines)
-
-        # Split lines by separator
-        results = []
-        sections = self.get_log_sections(lines)
-        for section in sections:
-            if not section.strip():
-                continue
-            section = section.split("\n")
-            section = [x.strip() for x in section if x.strip()]
-
-            try:
-                datum = self.parse_benchmark_section(section)
-            except Exception:
-                print(f"Issue parsing section {section}")
-                continue
-            results.append(datum)
-
-        return {"data": results, "metadata": metadata, "spec": self.spec}
-
-    def parse_benchmark_section(self, section):
-        """
-        A wrapper for parsing in case there is an error we can catch!
-        """
-        # Command is the first entry
-        command = section.pop(0)
-
-        # Each section has some number of header lines (with #)
-        header = []
-        while section and section[0].startswith("#"):
-            header.append(section.pop(0))
-
-        # Last row of the header are the column names
-        columns = header.pop()
-        columns = columns.replace("# ", "").strip()
-        columns = self.parse_row(columns)
-
-        # The remainder is data, again always two points
-        data = []
-        for line in section:
-            if not line:
-                continue
-            row = self.parse_row(line)
-            row = [float(x) for x in row]
-            data.append(row)
-
-        return {
-            "matrix": data,
-            "columns": columns,
-            "header": header,
-            "command": command,
-        }
+from metricsoperator.metrics.base import MetricBase
 
 
 class network_netmark(MetricBase):

sdk/python/v1alpha1/metricsoperator/metrics/network/osu_benchmark.py

@@ -0,0 +1,286 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC
+# (c.f. AUTHORS, NOTICE.LLNS, COPYING)
+
+import os
+import re
+
+from metricsoperator.metrics.base import MetricBase
+
+# prepare more consistent / formatted columns
+latency_size_header = ["Size", "Latency(us)"]
+average_latency_header = ["Size", "Avg Latency(us)"]
+bandwidth_size_header = ["Size", "Bandwidth (MB/s)"]
+column_lookup = {
+    "osu_ibarrier": ["Overall(us)", "Compute(us)", "Pure Comm.(us)", "Overlap(%)"],
+    "osu_barrier": ["Avg Latency(us)"],
+    "osu_mbw_mr": ["Size", "MB/s", "Messages/s"],
+    "osu_init": ["nprocs", "min", "max", "avg"],
+    "osu_multi_lat": latency_size_header,
+    "osu_get_acc_latency": latency_size_header,
+    "osu_latency": latency_size_header,
+    "osu_fop_latency": latency_size_header,
+    "osu_put_latency": latency_size_header,
+    "osu_get_latency": latency_size_header,
+    "osu_acc_latency": latency_size_header,
+    "osu_mt_latency": latency_size_header,
+    "osu_get_latency": latency_size_header,
+    "osu_cas_latency": latency_size_header,
+    "osu_latency_mp": latency_size_header,
+    "osu_latency_mt": latency_size_header,
+    "osu_bibw": bandwidth_size_header,
+    "osu_get_bw": bandwidth_size_header,
+    "osu_put_bw": bandwidth_size_header,
+    "osu_put_bibw": bandwidth_size_header,
+    "osu_bw": bandwidth_size_header,
+    "osu_allgather": average_latency_header,
+    "osu_allreduce": average_latency_header,
+}
+
+
+def parse_commented_header(section):
+    """
+    Parse a commented (#) header
+    """
+    # Each section has some number of header lines (with #)
+    header = []
+    while section and section[0].startswith("#"):
+        header.append(section.pop(0))
+    return header
+
+
+def parse_row(row):
+    """
+    Given a row of two values with spaces, parse.
+    """
+    row = row.split(" ", 2)
+    return [x.strip() for x in row if x]
+
+
+def parse_multi_value_row(row):
+    """
+    Parse a row with multiple values.
+    """
+    row = row.split(" ")
+    return [x.strip() for x in row if x]
+
+
+def parse_hello_section(section):
+    """
+    Parse the osu hello section
+
+    This only has a print line for output
+    """
+    # Command is the first entry
+    command = section.pop(0)
+    header = parse_commented_header(section)
+
+    # The next row is just a print line
+    message = section.pop(0)
+    timed = parse_timed_section(section)
+    result = {
+        "matrix": [[message]],
+        "columns": ["message"],
+        "header": header,
+        "command": command,
+    }
+    if timed:
+        result["timed"] = timed
+    return result
+
+
+def parse_init_section(section):
+    """
+    Parse the osu init section
+
+    This section has one column, and all the values there!
+    """
+    # Command is the first entry
+    command = section.pop(0)
+    header = parse_commented_header(section)
+
+    # The next row has all the data!
+    row = section.pop(0)
+    values = [x.strip() for x in row.split(",")]
+    data = {}
+    for entry in values:
+        field, value = [x.strip() for x in entry.split(":")]
+        # Do we have a unit?
+        unit = ""
+        if " " in value:
+            value, unit = [x.strip() for x in value.split(" ")]
+        if unit:
+            field = f"{field}-{unit}"
+        data[field] = float(value)
+
+    # If we have additional sections (possibly with times)
+    timed = parse_timed_section(section)
+    result = {
+        "matrix": [list(data.values())],
+        "columns": list(data.keys()),
+        "header": header,
+        "command": command,
+    }
+    if timed:
+        result["timed"] = timed
+    return result
+
+
+def parse_timed_section(section):
+    """
+    If the remainder is wrapped in time, parse it.
+    """
+    timed = {}
+    for line in section:
+        if line and re.search("^(real|user|sys\t)", line):
+            time_type, ts = line.strip().split("\t")
+            timed[time_type] = ts
+    return timed
+
+
+def parse_barrier_section(section):
+    """
+    Parse a barrier section.
+
+    This section is unique in that it has two columns
+    but the header is not preceded with a #
+    """
+    # Command is the first entry
+    command = section.pop(0)
+    header = parse_commented_header(section)
+
+    # The columns are the last row of the header
+    section.pop(0)
+    result = parse_value_matrix(section)
+    result.update({"header": header, "command": command})
+    return result
+
+
+def parse_multi_section(section):
+    """
+    Parse a multi-value section.
+
+    This section has standard format, but >2 values in the matrix
+    """
+    # Command is the first entry
+    command = section.pop(0)
+    header = parse_commented_header(section)
+
+    # The columns are the last row of the header
+    header.pop()
+    result = parse_value_matrix(section)
+    result.update({"header": header, "command": command})
+    return result
+
+
+def parse_value_matrix(section):
+    """
+    Parse a matrix of times
+    """
+    # The remainder is data, again always two points
+    # If there are real / user / sys at the end, we ran with timed:true
+    data = []
+    timed = {}
+    for line in section:
+        if not line:
+            continue
+
+        # We found a time
+        if re.search("^(real|user|sys\t)", line):
+            time_type, ts = line.strip().split("\t")
+            timed[time_type] = ts
+            continue
+
+        row = parse_multi_value_row(line)
+        row = [float(x) for x in row]
+        data.append(row)
+
+    result = {"matrix": data}
+    if timed:
+        result["timed"] = timed
+    return result
+
+
+def run_parsing_function(section):
+    """
+    Parsing functions for different sections
+    """
+    # The command is the first line
+    command = os.path.basename(section[0])
+    result = None
+    if command in ["osu_ibarrier"]:
+        result = parse_barrier_section(section)
+    elif command in [
+        "osu_bw",
+        "osu_bibw",
+        "osu_barrier",
+        "osu_get_bw",
+        "osu_put_bw",
+        "osu_put_bibw",
+        "osu_mbw_mr",
+        "osu_multi_lat",
+        "osu_allgather",
+        "osu_latency",
+        "osu_cas_latency",
+        "osu_put_latency",
+        "osu_get_latency",
+        "osu_latency_mp",
+        "osu_latency_mt",
+        "osu_fop_latency",
+        "osu_acc_latency",
+        "osu_get_acc_latency",
+        "osu_allreduce",
+    ]:
+        result = parse_multi_section(section)
+
+    # Special snowflakes
+    elif command == "osu_init":
+        result = parse_init_section(section)
+
+    # This only potentially has a time :)
+    elif command == "osu_hello":
+        result = parse_hello_section(section)
+
+    # Columns aren't predictible, so we ensure they are more consistent this way
+    # Some parsers do their own columns
+    if "columns" not in result:
+        result["columns"] = column_lookup[command]
+
+    return result
+
+
+class network_osu_benchmark(MetricBase):
+    """
+    Parse the OSU benchmarks output into data!
+
+    For pair to pair we had a common format (two values with size and another field)
+    but adding on the multi- benchmarks, we have a new challenge that there is slight
+    variance in format, so I needed to extend the class to be more specific to parsing.
+    """
+
+    container_name = "launcher"
+
+    @property
+    def pod_prefix(self):
+        return f"{self.name}-l-0"
+
+    def parse_log(self, lines):
+        """
+        Given lines of output, parse and return json
+        """
+        # Get the log metadata
+        metadata = self.get_log_metadata(lines)
+
+        # Split lines by separator
+        results = []
+        sections = self.get_log_sections(lines)
+        for section in sections:
+            if not section.strip():
+                continue
+            section = section.split("\n")
+            section = [x.strip() for x in section if x.strip()]
+
+            # Parse the section. If this fails, we want to know
+            datum = run_parsing_function(section)
+            results.append(datum)
+
+        return {"data": results, "metadata": metadata, "spec": self.spec}