diff --git a/src/executorlib/standalone/command_pysqa.py b/src/executorlib/standalone/command_pysqa.py index 77525a54..c910d040 100644 --- a/src/executorlib/standalone/command_pysqa.py +++ b/src/executorlib/standalone/command_pysqa.py @@ -29,6 +29,31 @@ def pysqa_terminate( qa.delete_job(process_id=queue_id) +def pysqa_get_status_of_job( + queue_id: int, + config_directory: Optional[str] = None, + backend: Optional[str] = None, +) -> Optional[str]: + """ + Query the status of a job from the queuing system. + + Args: + queue_id (int): Queuing system ID of the job to check. + config_directory (str, optional): path to the config directory. + backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"]. + + Returns: + str: status of the job as reported by the queuing system, None if the queuing system no + longer knows about the job (e.g. it timed out, was killed or already finished). + """ + qa = QueueAdapter( + directory=config_directory, + queue_type=backend, + execute_command=pysqa_execute_command, + ) + return qa.get_status_of_job(process_id=queue_id) + + def pysqa_execute_command( commands: str, working_directory: Optional[str] = None, diff --git a/src/executorlib/task_scheduler/file/shared.py b/src/executorlib/task_scheduler/file/shared.py index 8d346b71..eb4a3e5c 100644 --- a/src/executorlib/task_scheduler/file/shared.py +++ b/src/executorlib/task_scheduler/file/shared.py @@ -2,7 +2,7 @@ import os import queue from concurrent.futures import Future -from time import sleep +from time import monotonic, sleep from typing import Any, Callable, Optional from executorlib.standalone.command import get_cache_execute_command @@ -10,6 +10,12 @@ from executorlib.standalone.serialize import serialize_funct from executorlib.task_scheduler.file.spawner_subprocess import subprocess_terminate +# Minimum time between two queries of the queuing system for the status of a task whose output +# file has not appeared yet. Detecting a dead job (timeout, OOM, node failure, scancel, ...) relies +# on this status query, but it must not be issued on every poll of the (much faster) refresh_rate +# loop, as that would flood the queuing system commands (e.g. squeue/sacct) with requests. +_JOB_STATUS_CHECK_INTERVAL = 30.0 + class FutureItem: def __init__(self, file_name: str, selector: Optional[int | str] = None): @@ -92,6 +98,7 @@ def execute_tasks_h5( cache_dir_dict: dict = {} file_name_dict: dict = {} duplicate_dict: dict = {} + status_check_dict: dict = {} while True: task_dict = None with contextlib.suppress(queue.Empty): @@ -104,6 +111,7 @@ def execute_tasks_h5( process_dict=process_dict, duplicate_dict=duplicate_dict, cache_dir_dict=cache_dir_dict, + status_check_dict=status_check_dict, terminate_function=terminate_function, pysqa_config_directory=pysqa_config_directory, backend=backend, @@ -188,6 +196,7 @@ def execute_tasks_h5( cache_dir_dict=cache_dir_dict, process_dict=process_dict, duplicate_dict=duplicate_dict, + status_check_dict=status_check_dict, terminate_function=terminate_function, pysqa_config_directory=pysqa_config_directory, backend=backend, @@ -199,15 +208,29 @@ def _check_task_output( task_key: str, future_obj: Future, cache_directory: str, + queue_id: Optional[int] = None, + pysqa_config_directory: Optional[str] = None, + backend: Optional[str] = None, + status_check_dict: Optional[dict] = None, duplicate_dict: Optional[dict] = None, ) -> Future: """ Check the output of a task and set the result of the future object if available. + If the output file is missing and the task is running on a queuing system backend, this also + detects jobs which died without producing output (e.g. walltime TIMEOUT, OOM, NODE_FAIL or an + external scancel) by periodically querying the job status via pysqa and fails the future + instead of leaving it pending forever. + Args: task_key (str): The key of the task. future_obj (Future): The future object associated with the task. cache_directory (str): The directory where the HDF5 files are stored. + queue_id (int, optional): The queuing system ID of the task, if submitted via pysqa. + pysqa_config_directory (str, optional): path to the pysqa config directory. + backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"]. + status_check_dict (dict): Dictionary tracking when each task's job status was last queried, + used to throttle calls to the queuing system. duplicate_dict (dict): The dictionary mapping task keys to their associated duplicate future objects. Returns: Future: The updated future object. @@ -215,8 +238,27 @@ def _check_task_output( """ file_name = os.path.join(cache_directory, task_key + "_o.h5") if not os.path.exists(file_name): - return future_obj - exec_flag, no_error_flag, result = get_output(file_name=file_name) + if not _job_died_without_output( + task_key=task_key, + file_name=file_name, + queue_id=queue_id, + pysqa_config_directory=pysqa_config_directory, + backend=backend, + status_check_dict=status_check_dict, + ): + return future_obj + exec_flag, no_error_flag, result = ( + True, + False, + RuntimeError( + f"executorlib: queue job {queue_id} for task {task_key} terminated without " + "producing output (timeout, out-of-memory, node failure or cancellation)." + ), + ) + else: + exec_flag, no_error_flag, result = get_output(file_name=file_name) + if status_check_dict is not None: + status_check_dict.pop(task_key, None) _update_future( future_obj=future_obj, exec_flag=exec_flag, @@ -235,6 +277,56 @@ def _check_task_output( return future_obj +def _job_died_without_output( + task_key: str, + file_name: str, + queue_id: Optional[int], + pysqa_config_directory: Optional[str], + backend: Optional[str], + status_check_dict: Optional[dict], +) -> bool: + """ + Check whether the queuing system job backing a task has died without ever writing its output + file. Only applies to queuing system backends (pysqa) and is throttled to at most once every + ``_JOB_STATUS_CHECK_INTERVAL`` seconds per task, to avoid flooding the queuing system with + status queries on every poll of the (much faster) refresh_rate loop. + + Args: + task_key (str): The key of the task. + file_name (str): Path of the expected output HDF5 file. + queue_id (int, optional): The queuing system ID of the task. + pysqa_config_directory (str, optional): path to the pysqa config directory. + backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"]. + status_check_dict (dict): Dictionary tracking when each task's job status was last queried. + + Returns: + bool: True if the job is no longer known to the queuing system and still has no output. + """ + if backend is None or queue_id is None: + return False + try: + # Imported lazily so subprocess-only (non-pysqa) task submissions - including every + # cache_serial.py backend subprocess spawned for local execution - never pay the cost of + # importing pysqa. + from executorlib.standalone.command_pysqa import pysqa_get_status_of_job + except ImportError: + return False + now = monotonic() + last_checked = ( + status_check_dict.get(task_key, 0.0) if status_check_dict is not None else 0.0 + ) + if now - last_checked < _JOB_STATUS_CHECK_INTERVAL: + return False + if status_check_dict is not None: + status_check_dict[task_key] = now + status = pysqa_get_status_of_job( + queue_id=queue_id, + config_directory=pysqa_config_directory, + backend=backend, + ) + return status is None and not os.path.exists(file_name) + + def _update_future( future_obj: Future, exec_flag: bool, no_error_flag: bool, result: Any ) -> None: @@ -321,6 +413,7 @@ def _refresh_memory_dict( cache_dir_dict: dict, process_dict: dict, duplicate_dict: Optional[dict] = None, + status_check_dict: Optional[dict] = None, terminate_function: Optional[Callable] = None, pysqa_config_directory: Optional[str] = None, backend: Optional[str] = None, @@ -334,6 +427,8 @@ def _refresh_memory_dict( cache_dir_dict (dict): dictionary with task keys and cache directories process_dict (dict): dictionary with task keys and process reference. duplicate_dict (dict): dictionary with task keys and duplicate future objects. + status_check_dict (dict): dictionary with task keys and the last time their queuing system + job status was queried, used to throttle detection of jobs that died without output. terminate_function (callable): The function to terminate the tasks. pysqa_config_directory (str): path to the pysqa config directory (only for pysqa based backend). backend (str): name of the backend used to spawn tasks. @@ -351,11 +446,18 @@ def _refresh_memory_dict( pysqa_config_directory=pysqa_config_directory, backend=backend, ) + if status_check_dict is not None: + for key in cancelled_lst: + status_check_dict.pop(key, None) memory_updated_dict = { key: _check_task_output( task_key=key, future_obj=value, cache_directory=cache_dir_dict[key], + queue_id=process_dict.get(key), + pysqa_config_directory=pysqa_config_directory, + backend=backend, + status_check_dict=status_check_dict, duplicate_dict=duplicate_dict, ) for key, value in memory_dict.items() @@ -443,6 +545,7 @@ def _shutdown_executor( process_dict: dict, cache_dir_dict: dict, duplicate_dict: Optional[dict] = None, + status_check_dict: Optional[dict] = None, terminate_function: Optional[Callable] = None, pysqa_config_directory: Optional[str] = None, backend: Optional[str] = None, @@ -466,6 +569,8 @@ def _shutdown_executor( process_dict (dict): Mapping of task keys to process handles or queue IDs. duplicate_dict (dict): Mapping of task keys to lists of duplicate Future objects. cache_dir_dict (dict): Mapping of task keys to the cache directory for each task. + status_check_dict (dict): Mapping of task keys to the last time their queuing system job + status was queried, used to throttle detection of jobs that died without output. terminate_function (Callable, optional): Function used to terminate running processes. pysqa_config_directory (str, optional): Path to the pysqa config directory. backend (str, optional): Name of the backend ("slurm", "flux", or None for subprocess). @@ -478,6 +583,7 @@ def _shutdown_executor( cache_dir_dict=cache_dir_dict, process_dict=process_dict, duplicate_dict=duplicate_dict, + status_check_dict=status_check_dict, terminate_function=terminate_function, pysqa_config_directory=pysqa_config_directory, backend=backend, @@ -493,6 +599,7 @@ def _shutdown_executor( cache_dir_dict=cache_dir_dict, process_dict=process_dict, duplicate_dict=duplicate_dict, + status_check_dict=status_check_dict, terminate_function=terminate_function, pysqa_config_directory=pysqa_config_directory, backend=backend, @@ -512,6 +619,7 @@ def _shutdown_executor( cache_dir_dict=cache_dir_dict, process_dict=process_dict, duplicate_dict=duplicate_dict, + status_check_dict=status_check_dict, terminate_function=terminate_function, pysqa_config_directory=pysqa_config_directory, backend=backend, diff --git a/tests/unit/task_scheduler/file/test_backend.py b/tests/unit/task_scheduler/file/test_backend.py index bf189f7e..ff3ba090 100644 --- a/tests/unit/task_scheduler/file/test_backend.py +++ b/tests/unit/task_scheduler/file/test_backend.py @@ -1,7 +1,9 @@ from concurrent.futures import Future import os import shutil +import sys import unittest +from unittest.mock import patch from executorlib.standalone.select import FutureSelector @@ -16,6 +18,13 @@ except ImportError: skip_h5io_test = True +try: + import pysqa # noqa: F401 + + skip_pysqa_test = False +except ImportError: + skip_pysqa_test = True + def my_funct(a, b): return a + b @@ -219,5 +228,91 @@ def test_execute_function_error(self): with self.assertRaises(ValueError): future_file_obj.result() + @unittest.skipIf(sys.platform == "win32" or skip_pysqa_test, "pysqa module patching not supported on Windows or when pysqa is not installed") + def test_check_task_output_dead_job_without_output(self): + # Reproduces https://github.com/pyiron/executorlib/issues/1037 : a queuing system job + # which dies without ever writing its output file (e.g. walltime TIMEOUT, OOM, NODE_FAIL + # or an external scancel) must fail the future instead of leaving it pending forever. + cache_directory = os.path.abspath("executorlib_cache") + os.makedirs(cache_directory, exist_ok=True) + task_key, data_dict = serialize_funct(fn=my_funct, fn_args=[1], fn_kwargs={"b": 2}) + future_obj = Future() + with patch( + "executorlib.standalone.command_pysqa.pysqa_get_status_of_job", + return_value=None, + ) as status_mock: + _check_task_output( + task_key=task_key, + future_obj=future_obj, + cache_directory=cache_directory, + queue_id=123, + backend="slurm", + ) + status_mock.assert_called_once() + self.assertTrue(future_obj.done()) + with self.assertRaises(RuntimeError): + future_obj.result() + + @unittest.skipIf(sys.platform == "win32" or skip_pysqa_test, "pysqa module patching not supported on Windows or when pysqa is not installed") + def test_check_task_output_job_still_running(self): + cache_directory = os.path.abspath("executorlib_cache") + os.makedirs(cache_directory, exist_ok=True) + task_key, data_dict = serialize_funct(fn=my_funct, fn_args=[1], fn_kwargs={"b": 2}) + future_obj = Future() + with patch( + "executorlib.standalone.command_pysqa.pysqa_get_status_of_job", + return_value="running", + ) as status_mock: + _check_task_output( + task_key=task_key, + future_obj=future_obj, + cache_directory=cache_directory, + queue_id=123, + backend="slurm", + ) + status_mock.assert_called_once() + self.assertFalse(future_obj.done()) + + @unittest.skipIf(sys.platform == "win32" or skip_pysqa_test, "pysqa module patching not supported on Windows or when pysqa is not installed") + def test_check_task_output_status_check_is_throttled(self): + cache_directory = os.path.abspath("executorlib_cache") + os.makedirs(cache_directory, exist_ok=True) + task_key, data_dict = serialize_funct(fn=my_funct, fn_args=[1], fn_kwargs={"b": 2}) + status_check_dict = {} + with patch( + "executorlib.standalone.command_pysqa.pysqa_get_status_of_job", + return_value="running", + ) as status_mock: + for _ in range(3): + _check_task_output( + task_key=task_key, + future_obj=Future(), + cache_directory=cache_directory, + queue_id=123, + backend="slurm", + status_check_dict=status_check_dict, + ) + status_mock.assert_called_once() + + @unittest.skipIf(sys.platform == "win32" or skip_pysqa_test, "pysqa module patching not supported on Windows or when pysqa is not installed") + def test_check_task_output_no_backend_never_queries_status(self): + # subprocess-backed tasks (backend=None) must never trigger a queuing system status check. + cache_directory = os.path.abspath("executorlib_cache") + os.makedirs(cache_directory, exist_ok=True) + task_key, data_dict = serialize_funct(fn=my_funct, fn_args=[1], fn_kwargs={"b": 2}) + future_obj = Future() + with patch( + "executorlib.standalone.command_pysqa.pysqa_get_status_of_job", + ) as status_mock: + _check_task_output( + task_key=task_key, + future_obj=future_obj, + cache_directory=cache_directory, + queue_id=123, + backend=None, + ) + status_mock.assert_not_called() + self.assertFalse(future_obj.done()) + def tearDown(self): shutil.rmtree("executorlib_cache", ignore_errors=True)