Perf checker

.github/workflows/profiler.yml

@@ -0,0 +1,24 @@
+name: TileDB-SOMA Profiler run
+
+on:
+  pull_request:
+
+  push:
+    branches:
+      - main
+      - 'release-*'
+  workflow_dispatch:
+
+jobs:
+
+  check-links:
+
+  name: Setup profiler
+
+  run: |
+    python -m venv profiler_env
+    source profiler_env/bin/activate
+    pip install -e ./profiler
+
+  run: |
+    ./perf_checker.sh

profiler/ann_data.py

@@ -0,0 +1,22 @@
+from time import perf_counter
+
+import cellxgene_census
+
+import tiledbsoma as soma
+
+census_S3_latest = dict(census_version="2023-10-23")
+
+
+def main():
+    t1 = perf_counter()
+    with cellxgene_census.open_soma(**census_S3_latest) as census:
+        with census["census_data"]["homo_sapiens"].axis_query(
+            measurement_name="RNA",
+            obs_query=soma.AxisQuery(value_filter="""tissue_general == 'eye'"""),
+        ) as query:
+            query.to_anndata(X_name="raw")
+    t2 = perf_counter()
+    print(f"End to end time {t2 - t1}")
+
+
+main()

profiler/perf_checker.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+python -m venv perf
+source perf/bin/activate
+pip install gitpython
+pip install psutil
+pip install comacore
+pip install profiler
+pip install tiledbsoma
+pip install cellxgene_census
+python -m profiler "python ann_data.py" -t gtime
+
+python ./profile_report.py

profiler/profile_report.py

@@ -0,0 +1,28 @@
+import data
+
+# Processes the set of previously written logs
+
+threshold = 1.10  # Percent difference
+
+db = data.FileBasedProfileDB()
+actual_max_ts = 0
+dt = db.find("python ann_data.py")
+last_two = dt[-2:]
+c = 0
+
+for s in last_two:
+    new_db = sorted(dt, key=lambda ProfileData: ProfileData.timestamp)
+
+    L = []
+    L[0] = dt[0].user_time_sec + dt[0].elapsed_time
+    L[1] = dt[1].user_time_sec + dt[1].elapsed_time
+    for i in range(0, len(dt)):
+        print(f"{i} dt[{i}].user_time_sec = {dt[i].user_time_sec} ts {dt[i].timestamp}")
+    print(f"Prev = {L[0]} Curr = {L[1]}")
+
+    if threshold * float(L[1]) < float(L[0]) or float(L[1]) > threshold * float(L[0]):
+        raise SystemExit(f"Potential performance degradation detected {L[0]} va {L[1]}")
+    print("No recent performance degradation detected")
+    print(
+        f"Prev TBD version = {dt[0].tiledbsoma_version} Curr TBD version = {dt[1].tiledbsoma_version}"
+    )

profiler/profiler.py

@@ -10,11 +10,10 @@
 from typing import Any, Dict, Optional
 
 import somacore
+from context_generator import host_context
 
 import tiledbsoma
-
-from .context_generator import host_context
-from .data import FileBasedProfileDB, ProfileData, ProfileDB
+from data import FileBasedProfileDB, ProfileData, ProfileDB
 
 GNU_TIME_FORMAT = (
     'Command being timed: "%C"\n'
@@ -149,6 +148,7 @@ def main():
         required=False,
         help="The flamegraph output produced by prof2",
     )
+
     args = parser.parse_args(sys.argv[1:])
 
     print(f"Command to be run: {args.command}", file=stderr)
@@ -159,7 +159,6 @@ def main():
         stderr=PIPE,
     )
 
-    print(f"Running command to be profiled, PID = {p.pid}", file=stderr)
     # Running additional profilers to extract flame graphs for the run
     p1 = None
     p2 = None
@@ -206,3 +205,7 @@ def main():
         f"{data.command_key=}, {data.command=}, {data.exit_status=}, {db_record_file=}",
         file=stderr,
     )
+
+
+if __name__ == "__main__":
+    main()

profiler/setup.py

@@ -4,5 +4,5 @@
     name="soma-profiler",
     version="1.0",
     packages=find_packages(),
-    requires=["gitpython", "psutil"],
+    requires=["gitpython", "psutil", "tiledbsoma", "cellxgene_census"],
 )