-
Notifications
You must be signed in to change notification settings - Fork 22
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* Add profiler to run_workflow script * Wrap CI workflow run in memory profiler * Enable workflow script to run just one step (ecm_prep or run) * Add flag in run workflow script to turn on/off profiler * Trigger CI when a pull request is created * Enable integration test runs on PR event triggers
- Loading branch information
Showing
3 changed files
with
123 additions
and
17 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,24 +1,111 @@ | ||
| from __future__ import annotations | ||
| from pathlib import Path | ||
| from argparse import ArgumentParser | ||
| import io | ||
| import sys | ||
| import logging | ||
| import cProfile | ||
| import pstats | ||
|
|
||
| sys.path.append(str(Path(__file__).parent.parent.parent.parent)) | ||
| sys.path.append(str(Path(__file__).parent.parent.parent)) | ||
| from scout import ecm_prep # noqa: E402 | ||
| from scout.ecm_prep_args import ecm_args # noqa: E402 | ||
| from scout import run # noqa: E402 | ||
|
|
||
| logger = logging.getLogger(__name__) | ||
| logging.basicConfig( | ||
| level=logging.INFO, | ||
| format="%(asctime)s - %(levelname)s: %(message)s", | ||
| datefmt="%d-%b-%y %H:%M:%S", | ||
| ) | ||
|
|
||
|
|
||
| def run_workflow(run_step: str = None, with_profiler: bool = False) -> None: | ||
| """Runs Scout workflow steps with optional profiling | ||
| Args: | ||
| run_step (str, optional): Specify which step to run {ecm_prep, run}, if None | ||
| then both run. Defaults to None. | ||
| with_profiler (Bool, optional): Run workfow step(s) with profiler to track | ||
| compute time and peak memory. Defaults to False. | ||
| """ | ||
|
|
||
| results_dir = Path(__file__).parent / "results" | ||
|
|
||
| def run_workflow(): | ||
| # Run ecm_prep.py | ||
| opts = ecm_args( | ||
| ["--add_typ_eff", "--rp_persist", "--alt_regions_option", "EMM"] | ||
| ) | ||
| ecm_prep.main(opts) | ||
| if run_step == "ecm_prep" or run_step is None: | ||
| opts = ecm_args(["--add_typ_eff", "--rp_persist", "--alt_regions_option", "EMM"]) | ||
| if with_profiler: | ||
| run_with_profiler(ecm_prep.main, opts, results_dir / "profile_ecm_prep.csv") | ||
| else: | ||
| ecm_prep.main(opts) | ||
|
|
||
| # Run run.py | ||
| opts = run.parse_args([]) | ||
| run.main(opts) | ||
| if run_step == "run" or run_step is None: | ||
| opts = run.parse_args([]) | ||
| if with_profiler: | ||
| run_with_profiler(run.main, opts, results_dir / "profile_run.csv") | ||
| else: | ||
| run.main(opts) | ||
|
|
||
|
|
||
| def run_with_profiler( | ||
| func: Callable[[argparse.Namespace], None], # noqa: F821 | ||
| args: argparse.Namespace, # noqa: F821 | ||
| output_file: pathlib.Path, # noqa: F821 | ||
| ) -> None: | ||
| """Runs a function wrapped in a profiler using the cProfile library, writes profile stats | ||
| Args: | ||
| func (Callable[[argparse.Namespace], None]): A function that takes argsparse.Namespace args | ||
| args (argparse.Namespace): The arguments to the function | ||
| output_file (pathlib.Path): .csv filepath to write profiling stats | ||
| """ | ||
|
|
||
| pr = cProfile.Profile() | ||
| pr.enable() | ||
| func(args) | ||
| pr.disable() | ||
| write_profile_stats(pr, output_file) | ||
|
|
||
|
|
||
| def write_profile_stats(pr: cProfile.Profile, filepath: pathlib.Path) -> None: # noqa: F821 | ||
| """Writes profile stats and stores a .csv file | ||
| Args: | ||
| pr (cProfile.Profile): Profile instance that has previously been enabled (pr.enable()) | ||
| filepath (pathlib.Path): .csv filepath to write profiling stats | ||
| """ | ||
|
|
||
| # Capture io stream | ||
| result = io.StringIO() | ||
| pstats.Stats(pr, stream=result).sort_stats("cumulative").print_stats() | ||
| result = result.getvalue() | ||
|
|
||
| # Parse stats and write to csv | ||
| top_data, result = result.split("ncalls") | ||
| top_data = "\n".join([line.strip() for line in top_data.split("\n")]) | ||
| result = "ncalls" + result | ||
| result = "\n".join([",".join(line.rstrip().split(None, 5)) for line in result.split("\n")]) | ||
| result_out = top_data + result | ||
|
|
||
| f = open(filepath, "w") | ||
| f.write(result_out) | ||
| f.close() | ||
| logger.info(f"Wrote profiler stats to {filepath}") | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| run_workflow() | ||
| parser = ArgumentParser() | ||
| parser.add_argument( | ||
| "--run_step", choices=["ecm_prep", "run"], required=False, help="Specify which step to run" | ||
| ) | ||
| parser.add_argument( | ||
| "--with_profiler", | ||
| action="store_true", | ||
| required=False, | ||
| help="Run workflow step(s) with profiler", | ||
| ) | ||
| opts = parser.parse_args() | ||
| run_workflow(run_step=opts.run_step, with_profiler=opts.with_profiler) |