fractal-server 2.13.1__py3-none-any.whl → 2.14.0a0__py3-none-any.whl

fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -1,1281 +0,0 @@
-import json
-import math
-import shlex
-import subprocess  # nosec
-import sys
-import threading
-import time
-import uuid
-from concurrent.futures import Executor
-from concurrent.futures import Future
-from concurrent.futures import InvalidStateError
-from copy import copy
-from pathlib import Path
-from subprocess import CompletedProcess  # nosec
-from typing import Any
-from typing import Callable
-from typing import Optional
-from typing import Sequence
-
-import cloudpickle
-
-from ......config import get_settings
-from ......logger import set_logger
-from ......syringe import Inject
-from ....exceptions import JobExecutionError
-from ....exceptions import TaskExecutionError
-from ....filenames import SHUTDOWN_FILENAME
-from ....task_files import get_task_file_paths
-from ....task_files import TaskFiles
-from ...slurm._slurm_config import SlurmConfig
-from .._batching import heuristics
-from ..utils_executors import get_pickle_file_path
-from ..utils_executors import get_slurm_file_path
-from ..utils_executors import get_slurm_script_file_path
-from ._executor_wait_thread import FractalSlurmSudoWaitThread
-from ._subprocess_run_as_user import _glob_as_user
-from ._subprocess_run_as_user import _glob_as_user_strict
-from ._subprocess_run_as_user import _path_exists_as_user
-from ._subprocess_run_as_user import _run_command_as_user
-from fractal_server import __VERSION__
-from fractal_server.app.runner.components import _COMPONENT_KEY_
-from fractal_server.string_tools import validate_cmd
-
-
-logger = set_logger(__name__)
-
-
-def _subprocess_run_or_raise(full_command: str) -> Optional[CompletedProcess]:
-    """
-    Wrap `subprocess.run` and raise  appropriate `JobExecutionError` if needed.
-
-    Args:
-        full_command: Full string of the command to execute.
-
-    Raises:
-        JobExecutionError: If `subprocess.run` raises a `CalledProcessError`.
-
-    Returns:
-        The actual `CompletedProcess` output of `subprocess.run`.
-    """
-    validate_cmd(full_command)
-    try:
-        output = subprocess.run(  # nosec
-            shlex.split(full_command),
-            capture_output=True,
-            check=True,
-            encoding="utf-8",
-        )
-        return output
-    except subprocess.CalledProcessError as e:
-        error_msg = (
-            f"Submit command `{full_command}` failed. "
-            f"Original error:\n{str(e)}\n"
-            f"Original stdout:\n{e.stdout}\n"
-            f"Original stderr:\n{e.stderr}\n"
-        )
-        logger.error(error_msg)
-        raise JobExecutionError(info=error_msg)
-
-
-class SlurmJob:
-    """
-    Collect information related to a FractalSlurmExecutor job
-
-    This includes three groups of attributes:
-
-    1. Attributes related to the (possibly multi-task) SLURM job, e.g.
-       submission-file path.
-    2. Attributes related to single tasks, e.g. the paths of their input/output
-       pickle files.
-    3. SLURM configuration options, encoded in a SlurmConfig object.
-
-    Note: A SlurmJob object is generally defined as a multi-task job. Jobs
-    coming from the `map` method must have `single_task_submission=False` (even
-    if `num_tasks_tot=1`), while jobs coming from `submit` must have it set to
-    `True`.
-
-    Attributes:
-        num_tasks_tot:
-            Total number of tasks to be executed as part of this SLURM job.
-        single_task_submission:
-            This must be `True` for jobs submitted as part of the `submit`
-            method, and `False` for jobs coming from the `map` method.
-        slurm_file_prefix:
-            Prefix for SLURM-job related files (submission script and SLURM
-            stdout/stderr); this is also needed in the
-            `_copy_files_from_remote_to_local` method.
-        wftask_file_prefixes:
-            Prefix for files that are created as part of the functions
-            submitted for execution on the `FractalSlurmExecutor`; this is
-            needed in the `_copy_files_from_remote_to_local` method, and also
-            to construct the names of per-task input/output pickle files.
-        wftask_subfolder_name:
-            Name of the per-task subfolder (e.g. `7_task_name`).
-        slurm_script:
-            Path of SLURM submission script.
-        slurm_stdout:
-            Path of SLURM stdout file; if this includes `"%j"`, then this
-            string will be replaced by the SLURM job ID upon `sbatch`
-            submission.
-        slurm_stderr:
-            Path of SLURM stderr file; see `slurm_stdout` concerning `"%j"`.
-        workerids:
-            IDs that enter in the per-task input/output pickle files (one per
-            task).
-        input_pickle_files:
-            Input pickle files (one per task).
-        output_pickle_files:
-            Output pickle files (one per task).
-        slurm_config:
-            `SlurmConfig` object.
-    """
-
-    # Job-related attributes
-    num_tasks_tot: int
-    single_task_submission: bool
-    slurm_file_prefix: str
-    slurm_script: Path
-    slurm_stdout: Path
-    slurm_stderr: Path
-    # Per-task attributes
-    workerids: tuple[str, ...]
-    wftask_file_prefixes: tuple[str, ...]
-    wftask_subfolder_name: str
-    input_pickle_files: tuple[Path, ...]
-    output_pickle_files: tuple[Path, ...]
-    # Slurm configuration
-    slurm_config: SlurmConfig
-
-    def __init__(
-        self,
-        num_tasks_tot: int,
-        slurm_config: SlurmConfig,
-        slurm_file_prefix: Optional[str] = None,
-        wftask_file_prefixes: Optional[tuple[str, ...]] = None,
-        single_task_submission: bool = False,
-    ):
-        if single_task_submission and num_tasks_tot > 1:
-            raise ValueError(
-                "Trying to initialize SlurmJob with"
-                f"{single_task_submission=} and {num_tasks_tot=}."
-            )
-        self.num_tasks_tot = num_tasks_tot
-        self.single_task_submission = single_task_submission
-        self.slurm_file_prefix = slurm_file_prefix or "default_slurm_prefix"
-        if wftask_file_prefixes is None:
-            self.wftask_file_prefixes = tuple(
-                "default_wftask_prefix" for i in range(self.num_tasks_tot)
-            )
-        else:
-            self.wftask_file_prefixes = wftask_file_prefixes
-        self.workerids = tuple(uuid.uuid4() for i in range(self.num_tasks_tot))
-        self.slurm_config = slurm_config
-
-    def get_clean_output_pickle_files(self) -> tuple[str, ...]:
-        """
-        Transform all pathlib.Path objects in self.output_pickle_files to
-        strings
-        """
-        return tuple(str(f.as_posix()) for f in self.output_pickle_files)
-
-
-class FractalSlurmSudoExecutor(Executor):
-    """
-    Executor to submit SLURM jobs as a different user, via `sudo -u`
-
-    This class is a custom re-implementation of the SLURM executor from
-
-    > clusterfutures <https://github.com/sampsyo/clusterfutures>
-    > Original Copyright
-    > Copyright 2021 Adrian Sampson <asampson@cs.washington.edu>
-    > License: MIT
-
-
-    Attributes:
-        slurm_user:
-            Shell username that runs the `sbatch` command.
-        common_script_lines:
-            Arbitrary script lines that will always be included in the
-            sbatch script
-        workflow_dir_local:
-            Directory for both the cfut/SLURM and fractal-server files and logs
-        workflow_dir_remote:
-            Directory for both the cfut/SLURM and fractal-server files and logs
-        map_jobid_to_slurm_files:
-            Dictionary with paths of slurm-related files for active jobs
-    """
-
-    wait_thread_cls = FractalSlurmSudoWaitThread
-    slurm_user: str
-    shutdown_file: str
-    common_script_lines: list[str]
-    user_cache_dir: str
-    workflow_dir_local: Path
-    workflow_dir_remote: Path
-    map_jobid_to_slurm_files: dict[str, tuple[str, str, str]]
-    slurm_account: Optional[str] = None
-    jobs: dict[str, tuple[Future, SlurmJob]]
-
-    def __init__(
-        self,
-        slurm_user: str,
-        workflow_dir_local: Path,
-        workflow_dir_remote: Path,
-        shutdown_file: Optional[str] = None,
-        user_cache_dir: Optional[str] = None,
-        common_script_lines: Optional[list[str]] = None,
-        slurm_poll_interval: Optional[int] = None,
-        slurm_account: Optional[str] = None,
-        *args,
-        **kwargs,
-    ):
-        """
-        Init method for FractalSlurmExecutor
-        """
-
-        if not slurm_user:
-            raise RuntimeError(
-                "Missing attribute FractalSlurmExecutor.slurm_user"
-            )
-
-        self.jobs = {}
-        self.job_outfiles = {}
-        self.jobs_lock = threading.Lock()
-        self.jobs_empty_cond = threading.Condition(self.jobs_lock)
-
-        self.wait_thread = self.wait_thread_cls(self._completion)
-        self.wait_thread.start()
-
-        # Assign `wait_thread.shutdown_callback` early, since it may be called
-        # from within `_stop_and_join_wait_thread` (e.g. if an exception is
-        # raised within `__init__`).
-        self.wait_thread.shutdown_callback = self.shutdown
-
-        self.slurm_user = slurm_user
-        self.slurm_account = slurm_account
-
-        self.common_script_lines = common_script_lines or []
-        settings = Inject(get_settings)
-
-        if settings.FRACTAL_SLURM_WORKER_PYTHON is not None:
-            try:
-                self.check_remote_python_interpreter()
-            except Exception as e:
-                self._stop_and_join_wait_thread()
-                raise RuntimeError(f"Original error {str(e)}")
-
-        # Check that SLURM account is not set here
-        try:
-            invalid_line = next(
-                line
-                for line in self.common_script_lines
-                if line.startswith("#SBATCH --account=")
-            )
-            self._stop_and_join_wait_thread()
-            raise RuntimeError(
-                "Invalid line in `FractalSlurmExecutor.common_script_lines`: "
-                f"'{invalid_line}'.\n"
-                "SLURM account must be set via the request body of the "
-                "apply-workflow endpoint, or by modifying the user properties."
-            )
-        except StopIteration:
-            pass
-
-        self.workflow_dir_local = workflow_dir_local
-        if not _path_exists_as_user(
-            path=str(workflow_dir_remote), user=self.slurm_user
-        ):
-            logger.info(f"Missing folder {workflow_dir_remote=}")
-        self.user_cache_dir = user_cache_dir
-
-        self.workflow_dir_remote = workflow_dir_remote
-        self.map_jobid_to_slurm_files = {}
-
-        # Set the attribute slurm_poll_interval for self.wait_thread (see
-        # cfut.SlurmWaitThread)
-        if not slurm_poll_interval:
-            slurm_poll_interval = settings.FRACTAL_SLURM_POLL_INTERVAL
-        self.wait_thread.slurm_poll_interval = slurm_poll_interval
-        self.wait_thread.slurm_user = self.slurm_user
-
-        self.wait_thread.shutdown_file = (
-            shutdown_file
-            or (self.workflow_dir_local / SHUTDOWN_FILENAME).as_posix()
-        )
-
-    def _cleanup(self, jobid: str) -> None:
-        """
-        Given a job ID as returned by _start, perform any necessary
-        cleanup after the job has finished.
-        """
-        with self.jobs_lock:
-            self.map_jobid_to_slurm_files.pop(jobid)
-
-    def submit(
-        self,
-        fun: Callable[..., Any],
-        *fun_args: Sequence[Any],
-        slurm_config: SlurmConfig,
-        task_files: TaskFiles,
-        **fun_kwargs: dict,
-    ) -> Future:
-        """
-        Submit a function for execution on `FractalSlurmExecutor`
-
-        Arguments:
-            fun: The function to be executed
-            fun_args: Function positional arguments
-            fun_kwargs: Function keyword arguments
-            slurm_config:
-                A `SlurmConfig` object.
-            task_files:
-                A `TaskFiles` object.
-
-        Returns:
-            Future representing the execution of the current SLURM job.
-        """
-
-        # Do not continue if auxiliary thread was shut down
-        if self.wait_thread.shutdown:
-            error_msg = "Cannot call `submit` method after executor shutdown"
-            logger.warning(error_msg)
-            raise JobExecutionError(info=error_msg)
-
-        # Set slurm_file_prefix
-        slurm_file_prefix = task_files.file_prefix
-
-        # Include common_script_lines in extra_lines
-        logger.debug(
-            f"Adding {self.common_script_lines=} to "
-            f"{slurm_config.extra_lines=}, from submit method."
-        )
-        current_extra_lines = slurm_config.extra_lines or []
-        slurm_config.extra_lines = (
-            current_extra_lines + self.common_script_lines
-        )
-
-        # Adapt slurm_config to the fact that this is a single-task SlurmJob
-        # instance
-        slurm_config.tasks_per_job = 1
-        slurm_config.parallel_tasks_per_job = 1
-
-        fut = self._submit_job(
-            fun,
-            slurm_config=slurm_config,
-            slurm_file_prefix=slurm_file_prefix,
-            task_files=task_files,
-            single_task_submission=True,
-            args=fun_args,
-            kwargs=fun_kwargs,
-        )
-        return fut
-
-    def map(
-        self,
-        fn: Callable[..., Any],
-        iterable: list[Sequence[Any]],
-        *,
-        slurm_config: SlurmConfig,
-        task_files: TaskFiles,
-    ):
-        """
-        Return an iterator with the results of several execution of a function
-
-        This function is based on `concurrent.futures.Executor.map` from Python
-        Standard Library 3.11.
-        Original Copyright 2009 Brian Quinlan. All Rights Reserved. Licensed to
-        PSF under a Contributor Agreement.
-
-        Main modifications from the PSF function:
-
-        1. Only `fn` and `iterable` can be assigned as positional arguments;
-        2. `*iterables` argument replaced with a single `iterable`;
-        3. `timeout` and `chunksize` arguments are not supported.
-
-        Arguments:
-            fn:
-                The function to be executed
-            iterable:
-                An iterable such that each element is the list of arguments to
-                be passed to `fn`, as in `fn(*args)`.
-            slurm_config:
-                A `SlurmConfig` object.
-            task_files:
-                A `TaskFiles` object.
-
-        """
-
-        # Do not continue if auxiliary thread was shut down
-        if self.wait_thread.shutdown:
-            error_msg = "Cannot call `map` method after executor shutdown"
-            logger.warning(error_msg)
-            raise JobExecutionError(info=error_msg)
-
-        def _result_or_cancel(fut):
-            """
-            This function is based on the Python Standard Library 3.11.
-            Original Copyright 2009 Brian Quinlan. All Rights Reserved.
-            Licensed to PSF under a Contributor Agreement.
-            """
-            try:
-                try:
-                    return fut.result()
-                finally:
-                    fut.cancel()
-            finally:
-                # Break a reference cycle with the exception in
-                # self._exception
-                del fut
-
-        # Include common_script_lines in extra_lines
-        logger.debug(
-            f"Adding {self.common_script_lines=} to "
-            f"{slurm_config.extra_lines=}, from map method."
-        )
-        current_extra_lines = slurm_config.extra_lines or []
-        slurm_config.extra_lines = (
-            current_extra_lines + self.common_script_lines
-        )
-
-        # Set file prefixes
-        general_slurm_file_prefix = str(task_files.task_order)
-
-        # Transform iterable into a list and count its elements
-        list_args = list(iterable)
-        tot_tasks = len(list_args)
-
-        # Set/validate parameters for task batching
-        tasks_per_job, parallel_tasks_per_job = heuristics(
-            # Number of parallel components (always known)
-            tot_tasks=len(list_args),
-            # Optional WorkflowTask attributes:
-            tasks_per_job=slurm_config.tasks_per_job,
-            parallel_tasks_per_job=slurm_config.parallel_tasks_per_job,  # noqa
-            # Task requirements (multiple possible sources):
-            cpus_per_task=slurm_config.cpus_per_task,
-            mem_per_task=slurm_config.mem_per_task_MB,
-            # Fractal configuration variables (soft/hard limits):
-            target_cpus_per_job=slurm_config.target_cpus_per_job,
-            target_mem_per_job=slurm_config.target_mem_per_job,
-            target_num_jobs=slurm_config.target_num_jobs,
-            max_cpus_per_job=slurm_config.max_cpus_per_job,
-            max_mem_per_job=slurm_config.max_mem_per_job,
-            max_num_jobs=slurm_config.max_num_jobs,
-        )
-        slurm_config.parallel_tasks_per_job = parallel_tasks_per_job
-        slurm_config.tasks_per_job = tasks_per_job
-
-        # Divide arguments in batches of `n_tasks_per_script` tasks each
-        args_batches = []
-        batch_size = tasks_per_job
-        for ind_chunk in range(0, tot_tasks, batch_size):
-            args_batches.append(
-                list_args[ind_chunk : ind_chunk + batch_size]  # noqa
-            )
-        if len(args_batches) != math.ceil(tot_tasks / tasks_per_job):
-            raise RuntimeError("Something wrong here while batching tasks")
-
-        # Fetch configuration variable
-        settings = Inject(get_settings)
-        FRACTAL_SLURM_SBATCH_SLEEP = settings.FRACTAL_SLURM_SBATCH_SLEEP
-
-        # Construct list of futures (one per SLURM job, i.e. one per batch)
-        fs = []
-        current_component_index = 0
-        for ind_batch, batch in enumerate(args_batches):
-            batch_size = len(batch)
-            this_slurm_file_prefix = (
-                f"{general_slurm_file_prefix}_batch_{ind_batch:06d}"
-            )
-            fs.append(
-                self._submit_job(
-                    fn,
-                    slurm_config=slurm_config,
-                    slurm_file_prefix=this_slurm_file_prefix,
-                    task_files=task_files,
-                    single_task_submission=False,
-                    components=batch,
-                )
-            )
-            current_component_index += batch_size
-            time.sleep(FRACTAL_SLURM_SBATCH_SLEEP)
-
-        # Yield must be hidden in closure so that the futures are submitted
-        # before the first iterator value is required.
-        # NOTE: In this custom map() method, _result_or_cancel(fs.pop()) is an
-        # iterable of results (if successful), and we should yield its elements
-        # rather than the whole iterable.
-        def result_iterator():
-            """
-            This function is based on the Python Standard Library 3.11.
-            Original Copyright 2009 Brian Quinlan. All Rights Reserved.
-            Licensed to PSF under a Contributor Agreement.
-            """
-            try:
-                # reverse to keep finishing order
-                fs.reverse()
-                while fs:
-                    # Careful not to keep a reference to the popped future
-                    results = _result_or_cancel(fs.pop())
-                    for res in results:
-                        yield res
-            finally:
-                for future in fs:
-                    future.cancel()
-
-        return result_iterator()
-
-    def _submit_job(
-        self,
-        fun: Callable[..., Any],
-        slurm_file_prefix: str,
-        task_files: TaskFiles,
-        slurm_config: SlurmConfig,
-        single_task_submission: bool = False,
-        args: Optional[Sequence[Any]] = None,
-        kwargs: Optional[dict] = None,
-        components: Optional[list[Any]] = None,
-    ) -> Future:
-        """
-        Submit a multi-task job to the pool, where each task is handled via the
-        pickle/remote logic
-
-        NOTE: this method has different behaviors when it is called from the
-        `self.submit` or `self.map` methods (which is also encoded in
-        `single_task_submission`):
-
-        * When called from `self.submit`, it supports general `args` and
-          `kwargs` arguments;
-        * When called from `self.map`, there cannot be any `args` or `kwargs`
-          argument, but there must be a `components` argument.
-
-        Arguments:
-            fun:
-            slurm_file_prefix:
-            task_files:
-            slurm_config:
-            single_task_submission:
-            args:
-            kwargs:
-            components:
-
-        Returns:
-            Future representing the execution of the current SLURM job.
-        """
-
-        # Prevent calling sbatch if auxiliary thread was shut down
-        if self.wait_thread.shutdown:
-            error_msg = (
-                "Cannot call `_submit_job` method after executor shutdown"
-            )
-            logger.warning(error_msg)
-            raise JobExecutionError(info=error_msg)
-
-        fut: Future = Future()
-
-        # Inject SLURM account (if set) into slurm_config
-        if self.slurm_account:
-            slurm_config.account = self.slurm_account
-
-        # Define slurm-job-related files
-        if single_task_submission:
-            if components is not None:
-                raise ValueError(
-                    f"{single_task_submission=} but components is not None"
-                )
-            job = SlurmJob(
-                slurm_file_prefix=slurm_file_prefix,
-                num_tasks_tot=1,
-                slurm_config=slurm_config,
-            )
-            if job.num_tasks_tot > 1:
-                raise ValueError(
-                    "{single_task_submission=} but {job.num_tasks_tot=}"
-                )
-            job.single_task_submission = True
-            job.wftask_file_prefixes = (task_files.file_prefix,)
-            job.wftask_subfolder_name = task_files.subfolder_name
-
-        else:
-            if not components or len(components) < 1:
-                raise ValueError(
-                    "In FractalSlurmExecutor._submit_job, given "
-                    f"{components=}."
-                )
-            num_tasks_tot = len(components)
-            job = SlurmJob(
-                slurm_file_prefix=slurm_file_prefix,
-                num_tasks_tot=num_tasks_tot,
-                slurm_config=slurm_config,
-            )
-
-            _prefixes = []
-            _subfolder_names = []
-            for component in components:
-                # In Fractal, `component` is a `dict` by construction (e.g.
-                # `component = {"zarr_url": "/something", "param": 1}``). The
-                # try/except covers the case of e.g. `executor.map([1, 2])`,
-                # which is useful for testing.
-                try:
-                    actual_component = component.get(_COMPONENT_KEY_, None)
-                except AttributeError:
-                    actual_component = str(component)
-                _task_file_paths = get_task_file_paths(
-                    workflow_dir_local=task_files.workflow_dir_local,
-                    workflow_dir_remote=task_files.workflow_dir_remote,
-                    task_name=task_files.task_name,
-                    task_order=task_files.task_order,
-                    component=actual_component,
-                )
-                _prefixes.append(_task_file_paths.file_prefix)
-                _subfolder_names.append(_task_file_paths.subfolder_name)
-            job.wftask_file_prefixes = tuple(_prefixes)
-
-            num_subfolders = len(set(_subfolder_names))
-            if num_subfolders != 1:
-                error_msg_short = (
-                    f"[_submit_job] Subfolder list has {num_subfolders} "
-                    "different values, but it must have only one (since "
-                    "workflow tasks are executed one by one)."
-                )
-                error_msg_detail = (
-                    "[_submit_job] Current unique subfolder names: "
-                    f"{set(_subfolder_names)}"
-                )
-                logger.error(error_msg_short)
-                logger.error(error_msg_detail)
-                raise ValueError(error_msg_short)
-            job.wftask_subfolder_name = _subfolder_names[0]
-
-        # Check that server-side subfolder exists
-        subfolder_path = self.workflow_dir_local / job.wftask_subfolder_name
-        if not subfolder_path.exists():
-            raise FileNotFoundError(
-                f"Missing folder {subfolder_path.as_posix()}."
-            )
-
-        job.input_pickle_files = tuple(
-            get_pickle_file_path(
-                arg=job.workerids[ind],
-                workflow_dir=self.workflow_dir_local,
-                subfolder_name=job.wftask_subfolder_name,
-                in_or_out="in",
-                prefix=job.wftask_file_prefixes[ind],
-            )
-            for ind in range(job.num_tasks_tot)
-        )
-        job.output_pickle_files = tuple(
-            get_pickle_file_path(
-                arg=job.workerids[ind],
-                workflow_dir=self.workflow_dir_remote,
-                subfolder_name=job.wftask_subfolder_name,
-                in_or_out="out",
-                prefix=job.wftask_file_prefixes[ind],
-            )
-            for ind in range(job.num_tasks_tot)
-        )
-        # Define SLURM-job file names/paths
-        job.slurm_script = get_slurm_script_file_path(
-            workflow_dir=self.workflow_dir_local,
-            subfolder_name=job.wftask_subfolder_name,
-            prefix=job.slurm_file_prefix,
-        )
-        job.slurm_stdout = get_slurm_file_path(
-            workflow_dir=self.workflow_dir_remote,
-            subfolder_name=job.wftask_subfolder_name,
-            out_or_err="out",
-            prefix=job.slurm_file_prefix,
-        )
-        job.slurm_stderr = get_slurm_file_path(
-            workflow_dir=self.workflow_dir_remote,
-            subfolder_name=job.wftask_subfolder_name,
-            out_or_err="err",
-            prefix=job.slurm_file_prefix,
-        )
-
-        # Dump serialized versions+function+args+kwargs to pickle
-        versions = dict(
-            python=sys.version_info[:3],
-            cloudpickle=cloudpickle.__version__,
-            fractal_server=__VERSION__,
-        )
-        if job.single_task_submission:
-            _args = args or []
-            _kwargs = kwargs or {}
-            funcser = cloudpickle.dumps((versions, fun, _args, _kwargs))
-            with open(job.input_pickle_files[0], "wb") as f:
-                f.write(funcser)
-        else:
-            for ind_component, component in enumerate(components):
-                _args = [component]
-                _kwargs = {}
-                funcser = cloudpickle.dumps((versions, fun, _args, _kwargs))
-                with open(job.input_pickle_files[ind_component], "wb") as f:
-                    f.write(funcser)
-
-        # Submit job to SLURM, and get jobid
-        jobid, job = self._start(job)
-
-        # Add the SLURM script/out/err paths to map_jobid_to_slurm_files (this
-        # must be after self._start(job), so that "%j" has already been
-        # replaced with the job ID)
-        with self.jobs_lock:
-            self.map_jobid_to_slurm_files[jobid] = (
-                job.slurm_script.as_posix(),
-                job.slurm_stdout.as_posix(),
-                job.slurm_stderr.as_posix(),
-            )
-
-        # Thread will wait for it to finish.
-        self.wait_thread.wait(
-            filenames=job.get_clean_output_pickle_files(),
-            jobid=jobid,
-        )
-
-        with self.jobs_lock:
-            self.jobs[jobid] = (fut, job)
-        return fut
-
-    def _prepare_JobExecutionError(
-        self, jobid: str, info: str
-    ) -> JobExecutionError:
-        """
-        Prepare the `JobExecutionError` for a given job
-
-        This method creates a `JobExecutionError` object and sets its attribute
-        to the appropriate SLURM-related file names. Note that the method
-        should always be called after values in `self.map_jobid_to_slurm_files`
-        have been updated, so that they point to `self.workflow_dir_local`
-        files which are readable from `fractal-server`.
-
-        Arguments:
-            jobid:
-                ID of the SLURM job.
-            info:
-        """
-        # Extract SLURM file paths
-        with self.jobs_lock:
-            (
-                slurm_script_file,
-                slurm_stdout_file,
-                slurm_stderr_file,
-            ) = self.map_jobid_to_slurm_files[jobid]
-        # Construct JobExecutionError exception
-        job_exc = JobExecutionError(
-            cmd_file=slurm_script_file,
-            stdout_file=slurm_stdout_file,
-            stderr_file=slurm_stderr_file,
-            info=info,
-        )
-        return job_exc
-
-    def _completion(self, jobid: str) -> None:
-        """
-        Callback function to be executed whenever a job finishes.
-
-        This function is executed by self.wait_thread (triggered by either
-        finding an existing output pickle file `out_path` or finding that the
-        SLURM job is over). Since this takes place on a different thread,
-        failures may not be captured by the main thread; we use a broad
-        try/except block, so that those exceptions are reported to the main
-        thread via `fut.set_exception(...)`.
-
-        Arguments:
-            jobid: ID of the SLURM job
-        """
-        # Handle all uncaught exceptions in this broad try/except block
-        try:
-            # Retrieve job
-            with self.jobs_lock:
-                try:
-                    fut, job = self.jobs.pop(jobid)
-                except KeyError:
-                    return
-                if not self.jobs:
-                    self.jobs_empty_cond.notify_all()
-
-            # Copy all relevant files from self.workflow_dir_remote to
-            # self.workflow_dir_local
-
-            self._copy_files_from_remote_to_local(job)
-
-            # Update the paths to use the files in self.workflow_dir_local
-            # (rather than the user's ones in self.workflow_dir_remote)
-            with self.jobs_lock:
-                self.map_jobid_to_slurm_files[jobid]
-                (
-                    slurm_script_file,
-                    slurm_stdout_file,
-                    slurm_stderr_file,
-                ) = self.map_jobid_to_slurm_files[jobid]
-            new_slurm_stdout_file = str(
-                self.workflow_dir_local
-                / job.wftask_subfolder_name
-                / Path(slurm_stdout_file).name
-            )
-            new_slurm_stderr_file = str(
-                self.workflow_dir_local
-                / job.wftask_subfolder_name
-                / Path(slurm_stderr_file).name
-            )
-            with self.jobs_lock:
-                self.map_jobid_to_slurm_files[jobid] = (
-                    slurm_script_file,
-                    new_slurm_stdout_file,
-                    new_slurm_stderr_file,
-                )
-
-            in_paths = job.input_pickle_files
-            out_paths = tuple(
-                (self.workflow_dir_local / job.wftask_subfolder_name / f.name)
-                for f in job.output_pickle_files
-            )
-
-            outputs = []
-            for ind_out_path, out_path in enumerate(out_paths):
-                in_path = in_paths[ind_out_path]
-
-                # The output pickle file may be missing because of some slow
-                # filesystem operation; wait some time before considering it as
-                # missing
-                if not out_path.exists():
-                    settings = Inject(get_settings)
-                    time.sleep(settings.FRACTAL_SLURM_ERROR_HANDLING_INTERVAL)
-                if not out_path.exists():
-                    # Output pickle file is missing
-                    info = (
-                        "Output pickle file of the FractalSlurmExecutor job "
-                        "not found.\n"
-                        f"Expected file path: {str(out_path)}.\n"
-                        "Here are some possible reasons:\n"
-                        "1. The SLURM job was scancel-ed, either by the user "
-                        "or due to an error (e.g. an out-of-memory or timeout "
-                        "error). Note that if the scancel took place before "
-                        "the job started running, the SLURM out/err files "
-                        "will be empty.\n"
-                        "2. Some error occurred upon writing the file to disk "
-                        "(e.g. because there is not enough space on disk, or "
-                        "due to an overloaded NFS filesystem). "
-                        "Note that the server configuration has "
-                        "FRACTAL_SLURM_ERROR_HANDLING_INTERVAL="
-                        f"{settings.FRACTAL_SLURM_ERROR_HANDLING_INTERVAL} "
-                        "seconds.\n"
-                    )
-                    job_exc = self._prepare_JobExecutionError(jobid, info=info)
-                    try:
-                        fut.set_exception(job_exc)
-                        return
-                    except InvalidStateError:
-                        logger.warning(
-                            f"Future {fut} (SLURM job ID: {jobid}) was already"
-                            " cancelled, exit from"
-                            " FractalSlurmExecutor._completion."
-                        )
-                        in_path.unlink()
-                        self._cleanup(jobid)
-                        return
-
-                # Read the task output (note: we now know that out_path exists)
-                with out_path.open("rb") as f:
-                    outdata = f.read()
-                # Note: output can be either the task result (typically a
-                # dictionary) or an ExceptionProxy object; in the latter
-                # case, the ExceptionProxy definition is also part of the
-                # pickle file (thanks to cloudpickle.dumps).
-                success, output = cloudpickle.loads(outdata)
-                try:
-                    if success:
-                        outputs.append(output)
-                    else:
-                        proxy = output
-                        if proxy.exc_type_name == "JobExecutionError":
-                            job_exc = self._prepare_JobExecutionError(
-                                jobid, info=proxy.kwargs.get("info", None)
-                            )
-                            fut.set_exception(job_exc)
-                            return
-                        else:
-                            # This branch catches both TaskExecutionError's
-                            # (coming from the typical fractal-server
-                            # execution of tasks, and with additional
-                            # fractal-specific kwargs) or arbitrary
-                            # exceptions (coming from a direct use of
-                            # FractalSlurmExecutor, possibly outside
-                            # fractal-server)
-                            kwargs = {}
-                            for key in [
-                                "workflow_task_id",
-                                "workflow_task_order",
-                                "task_name",
-                            ]:
-                                if key in proxy.kwargs.keys():
-                                    kwargs[key] = proxy.kwargs[key]
-                            exc = TaskExecutionError(proxy.tb, **kwargs)
-                            fut.set_exception(exc)
-                            return
-                    out_path.unlink()
-                except InvalidStateError:
-                    logger.warning(
-                        f"Future {fut} (SLURM job ID: {jobid}) was already"
-                        " cancelled, exit from"
-                        " FractalSlurmExecutor._completion."
-                    )
-                    out_path.unlink()
-                    in_path.unlink()
-                    self._cleanup(jobid)
-                    return
-
-                # Clean up input pickle file
-                in_path.unlink()
-            self._cleanup(jobid)
-            if job.single_task_submission:
-                fut.set_result(outputs[0])
-            else:
-                fut.set_result(outputs)
-            return
-
-        except Exception as e:
-            try:
-                fut.set_exception(e)
-                return
-            except InvalidStateError:
-                logger.warning(
-                    f"Future {fut} (SLURM job ID: {jobid}) was already"
-                    " cancelled, exit from"
-                    " FractalSlurmExecutor._completion."
-                )
-
-    def _copy_files_from_remote_to_local(
-        self,
-        job: SlurmJob,
-    ):
-        """
-        Impersonate the user and copy task-related files
-
-        For all files in `self.workflow_dir_remote` that start with
-        `job.file_prefix`, read them (with `sudo -u` impersonation) and write
-        them to `self.workflow_dir_local`.
-
-        Files to copy:
-        * Job-related files (SLURM stderr/stdout files); with prefix
-          `job.slurm_file_prefix`;
-        * Task-related files (stderr/stdout, args.json, metadiff.json, output
-          pickle), with prefixes `job.wftask_file_prefixes`.
-
-        Arguments:
-            job:
-                `SlurmJob` object (needed for its prefixes-related attributes).
-
-        Raises:
-            JobExecutionError: If a `cat` command fails.
-        """
-        logger.debug("[_copy_files_from_remote_to_local] Start")
-
-        if self.workflow_dir_remote == self.workflow_dir_local:
-            logger.debug(
-                "[_copy_files_from_remote_to_local] "
-                "workflow_dir_local corresponds to workflow_dir_remote, "
-                "return."
-            )
-            return
-
-        subfolder_name = job.wftask_subfolder_name
-        prefixes = set(
-            [job.slurm_file_prefix] + list(job.wftask_file_prefixes)
-        )
-
-        logger.debug(
-            "[_copy_files_from_remote_to_local] "
-            f"WorkflowTask subfolder_name: {subfolder_name}"
-        )
-        logger.debug(f"[_copy_files_from_remote_to_local] {prefixes=}")
-        logger.debug(
-            "[_copy_files_from_remote_to_local] "
-            f"{str(self.workflow_dir_remote)=}"
-        )
-
-        for prefix in prefixes:
-            if prefix == job.slurm_file_prefix:
-                files_to_copy = _glob_as_user(
-                    folder=str(self.workflow_dir_remote / subfolder_name),
-                    user=self.slurm_user,
-                    startswith=prefix,
-                )
-            else:
-                files_to_copy = _glob_as_user_strict(
-                    folder=str(self.workflow_dir_remote / subfolder_name),
-                    user=self.slurm_user,
-                    startswith=prefix,
-                )
-
-            logger.debug(
-                "[_copy_files_from_remote_to_local] "
-                f"{prefix=}, {len(files_to_copy)=}"
-            )
-
-            for source_file_name in files_to_copy:
-                if " " in source_file_name:
-                    raise ValueError(
-                        f'source_file_name="{source_file_name}" '
-                        "contains whitespaces"
-                    )
-                source_file_path = str(
-                    self.workflow_dir_remote
-                    / subfolder_name
-                    / source_file_name
-                )
-
-                # Read source_file_path (requires sudo)
-                # NOTE: By setting encoding=None, we read/write bytes instead
-                # of strings; this is needed to also handle pickle files.
-                cmd = f"cat {source_file_path}"
-                res = _run_command_as_user(
-                    cmd=cmd, user=self.slurm_user, encoding=None
-                )
-                if res.returncode != 0:
-                    info = (
-                        f'Running cmd="{cmd}" as {self.slurm_user=} failed\n\n'
-                        f"{res.returncode=}\n\n"
-                        f"{res.stdout=}\n\n{res.stderr=}\n"
-                    )
-                    logger.error(info)
-                    raise JobExecutionError(info)
-                # Write to dest_file_path (including empty files)
-                dest_file_path = str(
-                    self.workflow_dir_local / subfolder_name / source_file_name
-                )
-                with open(dest_file_path, "wb") as f:
-                    f.write(res.stdout)
-        logger.debug("[_copy_files_from_remote_to_local] End")
-
-    def _start(
-        self,
-        job: SlurmJob,
-    ) -> tuple[str, SlurmJob]:
-        """
-        Submit function for execution on a SLURM cluster
-        """
-
-        # Prepare commands to be included in SLURM submission script
-        settings = Inject(get_settings)
-        python_worker_interpreter = (
-            settings.FRACTAL_SLURM_WORKER_PYTHON or sys.executable
-        )
-
-        cmdlines = []
-        for ind_task in range(job.num_tasks_tot):
-            input_pickle_file = job.input_pickle_files[ind_task]
-            output_pickle_file = job.output_pickle_files[ind_task]
-            cmdlines.append(
-                (
-                    f"{python_worker_interpreter}"
-                    " -m fractal_server.app.runner.executors.slurm.remote "
-                    f"--input-file {input_pickle_file} "
-                    f"--output-file {output_pickle_file}"
-                )
-            )
-
-        # ...
-        sbatch_script = self._prepare_sbatch_script(
-            slurm_config=job.slurm_config,
-            list_commands=cmdlines,
-            slurm_out_path=str(job.slurm_stdout),
-            slurm_err_path=str(job.slurm_stderr),
-        )
-
-        # Print warning for ignored parameter
-        if len(job.slurm_config.pre_submission_commands) > 0:
-            logger.warning(
-                f"Ignoring {job.slurm_config.pre_submission_commands=}."
-            )
-
-        # Submit job via sbatch, and retrieve jobid
-
-        # Write script content to a job.slurm_script
-        with job.slurm_script.open("w") as f:
-            f.write(sbatch_script)
-
-        # Prepare submission command
-        pre_command = f"sudo --set-home --non-interactive -u {self.slurm_user}"
-        submit_command = f"sbatch --parsable {job.slurm_script}"
-        full_command = f"{pre_command} {submit_command}"
-
-        # Submit SLURM job and retrieve job ID
-        output = _subprocess_run_or_raise(full_command)
-        try:
-            jobid = int(output.stdout)
-        except ValueError as e:
-            error_msg = (
-                f"Submit command `{full_command}` returned "
-                f"`{output.stdout=}` which cannot be cast to an integer "
-                f"SLURM-job ID. Original error:\n{str(e)}"
-            )
-            logger.error(error_msg)
-            raise JobExecutionError(info=error_msg)
-        jobid_str = str(jobid)
-
-        # Plug SLURM job id in stdout/stderr file paths
-        job.slurm_stdout = Path(
-            job.slurm_stdout.as_posix().replace("%j", jobid_str)
-        )
-        job.slurm_stderr = Path(
-            job.slurm_stderr.as_posix().replace("%j", jobid_str)
-        )
-
-        return jobid_str, job
-
-    def _prepare_sbatch_script(
-        self,
-        *,
-        list_commands: list[str],
-        slurm_out_path: str,
-        slurm_err_path: str,
-        slurm_config: SlurmConfig,
-    ):
-        num_tasks_max_running = slurm_config.parallel_tasks_per_job
-        mem_per_task_MB = slurm_config.mem_per_task_MB
-
-        # Set ntasks
-        ntasks = min(len(list_commands), num_tasks_max_running)
-        if len(list_commands) < num_tasks_max_running:
-            ntasks = len(list_commands)
-            slurm_config.parallel_tasks_per_job = ntasks
-            logger.debug(
-                f"{len(list_commands)=} is smaller than "
-                f"{num_tasks_max_running=}. Setting {ntasks=}."
-            )
-
-        # Prepare SLURM preamble based on SlurmConfig object
-        script_lines = slurm_config.to_sbatch_preamble(
-            remote_export_dir=self.user_cache_dir
-        )
-
-        # Extend SLURM preamble with variable which are not in SlurmConfig, and
-        # fix their order
-        script_lines.extend(
-            [
-                f"#SBATCH --err={slurm_err_path}",
-                f"#SBATCH --out={slurm_out_path}",
-                f"#SBATCH -D {self.workflow_dir_remote}",
-            ]
-        )
-        script_lines = slurm_config.sort_script_lines(script_lines)
-        logger.debug(script_lines)
-
-        # Always print output of `uname -n` and `pwd`
-        script_lines.append(
-            '"Hostname: `uname -n`; current directory: `pwd`"\n'
-        )
-
-        # Complete script preamble
-        script_lines.append("\n")
-
-        # Include command lines
-        tmp_list_commands = copy(list_commands)
-        while tmp_list_commands:
-            if tmp_list_commands:
-                cmd = tmp_list_commands.pop(0)  # take first element
-                script_lines.append(
-                    "srun --ntasks=1 --cpus-per-task=$SLURM_CPUS_PER_TASK "
-                    f"--mem={mem_per_task_MB}MB "
-                    f"{cmd} &"
-                )
-        script_lines.append("wait\n")
-
-        script = "\n".join(script_lines)
-        return script
-
-    def shutdown(self, wait=True, *, cancel_futures=False):
-        """
-        Clean up all executor variables. Note that this function is executed on
-        the self.wait_thread thread, see _completion.
-        """
-
-        logger.debug("Executor shutdown: start")
-
-        # Handle all job futures
-        slurm_jobs_to_scancel = []
-        with self.jobs_lock:
-            while self.jobs:
-                jobid, fut_and_job = self.jobs.popitem()
-                slurm_jobs_to_scancel.append(jobid)
-                fut = fut_and_job[0]
-                self.map_jobid_to_slurm_files.pop(jobid)
-                if not fut.cancelled():
-                    fut.set_exception(
-                        JobExecutionError(
-                            "Job cancelled due to executor shutdown."
-                        )
-                    )
-                    fut.cancel()
-
-        # Cancel SLURM jobs
-        if slurm_jobs_to_scancel:
-            scancel_string = " ".join(slurm_jobs_to_scancel)
-            logger.warning(f"Now scancel-ing SLURM jobs {scancel_string}")
-            pre_command = f"sudo --non-interactive -u {self.slurm_user}"
-            submit_command = f"scancel {scancel_string}"
-            full_command = f"{pre_command} {submit_command}"
-            validate_cmd(full_command)
-            logger.debug(f"Now execute `{full_command}`")
-            try:
-                subprocess.run(  # nosec
-                    shlex.split(full_command),
-                    capture_output=True,
-                    check=True,
-                    encoding="utf-8",
-                )
-            except subprocess.CalledProcessError as e:
-                error_msg = (
-                    f"Cancel command `{full_command}` failed. "
-                    f"Original error:\n{str(e)}"
-                )
-                logger.error(error_msg)
-                raise JobExecutionError(info=error_msg)
-
-        # Redudantly set thread shutdown attribute to True
-        self.wait_thread.shutdown = True
-
-        logger.debug("Executor shutdown: end")
-
-    def _stop_and_join_wait_thread(self):
-        self.wait_thread.shutdown = True
-        self.wait_thread.join()
-
-    def __exit__(self, *args, **kwargs):
-        """
-        See
-        https://github.com/fractal-analytics-platform/fractal-server/issues/1508
-        """
-        logger.debug(
-            "[FractalSlurmExecutor.__exit__] Stop and join `wait_thread`"
-        )
-        self._stop_and_join_wait_thread()
-        logger.debug("[FractalSlurmExecutor.__exit__] End")
-
-    def check_remote_python_interpreter(self):
-        """
-        Check fractal-server version on the _remote_ Python interpreter.
-        """
-        settings = Inject(get_settings)
-        output = _subprocess_run_or_raise(
-            (
-                f"{settings.FRACTAL_SLURM_WORKER_PYTHON} "
-                "-m fractal_server.app.runner.versions"
-            )
-        )
-        runner_version = json.loads(output.stdout.strip("\n"))[
-            "fractal_server"
-        ]
-
-        if runner_version != __VERSION__:
-            error_msg = (
-                "Fractal-server version mismatch.\n"
-                "Local interpreter: "
-                f"({sys.executable}): {__VERSION__}.\n"
-                "Remote interpreter: "
-                f"({settings.FRACTAL_SLURM_WORKER_PYTHON}): {runner_version}."
-            )
-            logger.error(error_msg)
-            raise ValueError(error_msg)